https://wiki.plantontology.org/api.php?action=feedcontributions&user=Preecej&feedformat=atomPlant Ontology Wiki - User contributions [en]2024-03-29T08:17:05ZUser contributionsMediaWiki 1.35.0https://wiki.plantontology.org/index.php?title=POC_Conf._Call_6-18-13&diff=23048POC Conf. Call 6-18-132013-06-18T17:19:39Z<p>Preecej: /* Update on Image analysis: AISO */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday June 18th, 2013 10am PST/1pm EST<br />
<br />
In attendance:<br />
Absent:<br />
<br />
=Update on Image analysis: AISO and the Image Annotation DB=<br />
<br />
* Laura Moore has segmented and annotated two dozen images provided by DWS. We will be using these as a test set for linking to and displaying from term detail pages on the PO site.<br />
* Nikhil finished a basic version of an annotated image data import script. We now have versions of DWS' images, annotated w/ whole-image keywords, inserted in our new Annotated Image DB. FYI: Nikhil has left the lab for a summer internship and a subsequent full-time software job in San Francisco. Thanks for your efforts, Nikhil!<br />
* I have begun expanding AISO to allow access to multiple ontologies, and to make ontology data available offline, when desired.<br />
* Pankaj and I are collaborating w/ iPlant to integrate AISO features and data structures into iPlant Bisque. We held a conf call on this subject w/ iPlant personnel 2-3 wks ago. Next step: work w/ Kris @ iPlant to run a test insertion of existing plant images and accompanying metadata.<br />
NOTE: All of this work will be dormant for roughly the next four weeks while I attend to another project deadline.<br />
<br />
=Image-Net Site=<br />
<br />
This is part of the WordNet family of computerized lexica. Image-Net<br />
is a computerized lexicon with images.<br />
<br />
http://www.image-net.org/synset?wnid=n00017222<br />
<br />
<br />
=Collaboration with New Phytologist=<br />
<br />
We were contacted by Sarah Lennon from New Phytologist:<br />
<br />
"We are undertaking a content enrichment project, which I believe is the first of its kind for a plant science journal. The New Phytologist content enrichment project will involve the creation of a fixed vocabulary to link New Phytologist content to other resources and to provide an enhanced experience for the reader. "<br />
<br />
"WE are interested in using PO terms as part of our controlled vocabulary/knowledge model. We aim to build a collection of taxonomies/ontologies/lists which accurately classifies our content and which we will then use to this to make our content even more valuable to readers. The exact delivery method for this is yet to be determined, but we are working with our publisher, Wiley Blackwell, to find the best way that will benefit plant scientists."<br />
<br />
<br />
-Her colleagues at Wiley Blackwell and requested a copy of the ontology data. I think they just need the data of the ontology itself, and if it could be made available in SKOS format that would be the most helpful, but any other xml/csv type of structure would also be great.<br />
<br />
Sent to them: "The latest development version will always be available from this link:<br />
http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OWL_format/plant_ontology.owl<br />
<br />
<br />
-"Dr Helen Ougham is a colleague on the project and we have some great ideas for the future. In collaboration with Wiley Blackwell we have been using Plant Ontology terms in some custom software to classify New Phytologist content and the results so far are interesting. Helen is a New Phytologist Co-Editor and has great expertise in both bioinformatics and plant science. Helen is currently assessing the output of the custom software.<br />
<br />
We would very much like to discuss the results of Helen's assessment with you and revisit the idea of potential collaboration. Ideally it would be great to meet in person, but a virtual meeting would also be good."<br />
<br />
- Should we set up a webex meeting with them? Dennis said he may be able to meet when in London, he knows Matt Pacey.<br />
<br />
==Flower development stage (PO:0021004) and subclasses==<br />
<br />
'''* Flower development stage (PO:0021004):''' A reproductive shoot system development stage (PO:0025530) that has as primary participant a flower (PO:0009046). [source: POC:curators]<br />
<br />
comment: Defined by characteristic morphological, structural, histological or other visible features. <br />
<br />
* 1 flower meristem visible stage (PO:0007601)<br />
* 2 flower meristem notched stage (PO:0007602) <br />
* 3 flower organ development stage (PO:0007600)<br />
* 4 anthesis stage (PO:0007616) <br />
* 5 post anthesis stage (PO:0007617): <br />
<br />
Current definitions:<br />
* '''1 flower meristem visible stage (PO:0007601):''' Stage of flower development marked by the emergence of the floral meristem on the flank of the inflorescence meristem.<br />
<br />
Revised def'n: A Flower development stage (PO:0021004)....<br />
<br />
-Needs to refer to apical meristem, not inflorescence meristem (same for the rest of them).<br />
<br />
* '''2 flower meristem notched stage (PO:0007602):'''Stage of floral development that begins when the floral meristem becomes demarcated from the inflorescence meristem by a slight indentation. [source: POC:curators] <br />
<br />
* '''flower organ development stage (PO:0007600):'''Stages of development of floral organs defined by characteristic morphological, structural, histological or other visible features. [source: POC:curators] <br />
<br />
- Should be an inferred class (like floral organ), and the subclasses should move to their proper parent. <br />
<br />
For example, gynoecium development stage and corolla development stage should be collective plant organ structure development stages and palea development stage should be a phyllome development stage. These classes should be part_of flower development stage, not is_a.<br />
<br />
* PO:0007605 : androecium development stage [0] <br />
* PO:0007603 : calyx development stage [0] <br />
* PO:0007604 : corolla development stage [0] <br />
* PO:0007606 : gynoecium development stage [0] <br />
* PO:0001047 : lemma development stage [0] <br />
* PO:0001049 : lodicule development stage [0] <br />
* PO:0001048 : palea development stage [0]<br />
<br />
<br />
'''* 4 anthesis stage (PO:0007616):''' The phase of a flower when pollen is presented and/or the stigma is receptive. [source: APweb:Glossary] <br />
<br />
<br />
'''* 5 post anthesis stage (PO:0007617):''' The phase of a flower after the pollen is presented and/or the stigma is receptive. [source: POC:curators]<br />
<br />
<br />
=Upcoming meetings and Presentations 2013:=<br />
<br />
==MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013==<br />
[http://www.regonline.com/builder/site/Default.aspx?EventID=1060172 MONOCOTS V]: <br />
<br />
5th International Conference on Comparative Biology of Monocotyledons<br />
Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)<br />
<br />
The New York Botanical Garden & Fordham University<br />
<br />
==ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013==<br />
4th International Conference on Biomedical Ontologies 2013 ([http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO 2013]), Concordia University, Montreal, Quebec, July 7th - 9th 2013 <br />
<br />
The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.<br />
<br />
The event is part of the [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/ Semantic Trilogy 2013] featuring:<br />
<br />
* International Conference on Biomedical Ontologies ([http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO 2013])<br />
* Canadian Semantic Web Symposium ([http://www.unbsj.ca/sase/csas/data/ws/csws2013/accepted.html CSWS 2013])<br />
* Data Integration in the Life Sciences ([http://www.unbsj.ca/sase/csas/data/ws/dils2013/accepted.html DILS 2013])<br />
<br />
Workshop on [https://sites.google.com/site/semsysbio/ Semantic Systems Biology 2013 (SSB2013)] will be held as part of the International Conference on Biomedical Ontologies (ICBO2013) at Concordia University, Montreal, Quebec, on July 7th, 2013. The event is part of the Semantic Trilogy 2013 (above)<br />
<br />
Topics of interest include, but are not limited to:<br />
* ontologies & terminologies for modeling computational biology<br />
* ontologies & terminologies for simulation (and result data) in computational biology/medicine/neuroscience<br />
* semantic web technologies for description, integration, query and discovery of models, simulations and result data<br />
* semantic web technologies for biological data and analysis<br />
* semantic annotations of bio-models<br />
* applications of ontologies in computational systems biology/medicine/neuroscience<br />
* semantic platforms for undertaking and visualizing simulation results<br />
<br />
==Botanical Society Meeting July 27-31st New Orleans==<br />
<br />
[http://www.2013.botanyconference.org/ BSA 2013]<br />
<br />
- MAG will present the work she has been doing with the images and slides [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=104 CUPAC- The Cornell University Plant Anatomy Collection: a web-based tool for the Plant Sciences teachers and researchers]<br />
<br />
- BA will present a poster on his work: [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=449 New evidence for the radiation of basal Cupressaceae]<br />
<br />
=Next meeting scheduled for Tuesday, June 25th, 2013 at 10am Pacific/1pm Eastern=</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2012&diff=22815Plant Ontology Web Site Update: 20122013-06-04T17:16:29Z<p>Preecej: moved Plant Ontology Web Site Update: 2012 to Plant Ontology Web Site Update: 2013:&#32;carry-over for this year</p>
<hr />
<div>#REDIRECT [[Plant Ontology Web Site Update: 2013]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=22814Plant Ontology Web Site Update: 20132013-06-04T17:16:29Z<p>Preecej: moved Plant Ontology Web Site Update: 2012 to Plant Ontology Web Site Update: 2013:&#32;carry-over for this year</p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under <br />
"/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link<br />
to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not<br />
their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking<br />
you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email<br />
notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Current PO Site Map===<br />
<br />
Screenshots of site content (''circa'' Spring 2012) have been collected, mapped to URLs, and tagged with summary descriptions. You can download the site map '''[[media:PO Site Map Spring 2012.pdf|here]]'''. This is a clickable PDF: the screenshots are linked to the actual site.<br />
<br />
Or, if you would rather just look at the pretty picture...<br />
<br />
[[image:PO Site Map Spring 2012.png|400px|PO Site Map - Spring 2012]]<br />
<br />
This document is intended to capture the state of affairs on the site ''as they are'', not necessarily as we wish them to be. The grouping and categorization of pages is arbitrary and meant to be a discussion starter about how you would like the site content to be organized going forward. If corrections are needed, just let us know.<br />
<br />
For the moment, please feel free to leave your comments and suggestions about site content organization here. If that discussion becomes substantial, we can move it to its own page.<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
* GARNet has a clean, fresh look- I like it: [http://www.garnetcommunity.org.uk/ GARNet] LC<br />
<br />
* MosDB: http://mips.helmholtz-muenchen.de/plant/rice/index.jsp<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our Palea web server (''currently in progress'').<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
See also the items listed on the [[POC_Technical_Issues_Page]]- some of which are AmiGO specific<br />
<br />
==High priority fixes==<br />
<br />
RW has marked these as high priority to fix before the Botany meeting (by mid-June).<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to log in to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
RW (4/2012): Maybe this has been fixed? Seems to work. I have created a wiki page for [[How_to_use_the_SourceForge_tracker]].<br />
<br />
This could be made into a web page, as part of the browser, rather than leaving it on the wiki. <br />
<br />
''(7/3/12) The "Request term" tab now links to the wiki help page, instead of directly to Source Forge. The wiki help page should be converted to a web page. Need to check PO web site for other places that link to SourceForge, and see if they should stay as direct links or go to the help page first.''<br />
<br />
===Plant Ontology Browser Users Guide===<br />
http://plantontology.org/amigo_user_guide/index.html#intro ''fixed''<br />
<br />
- No images show up. Text not displaying correctly (missing spaces).<br />
<br />
-This page would be very useful for the PO workshop.<br />
<br />
JE (6/5/12) -- Fixed missing images in svn revision 247. Spacing fixed in revision 248.<br />
<br />
RW (6/6/12) -- Thanks Justin! A few of the images reference "gametophyte", which is now obsolete. I will try to update those before July.<br />
<br />
RW (6/28/12) -- Updated this file and added new images as needed. Committed to SVN in revision 249.<br />
<br />
===Web pages that are out of date - high priority===<br />
* [http://www.plantontology.org/docs/references/pub.html publications] Needs updated<br />
<br />
* [http://www.plantontology.org/mailarchs/mail_list.html links to mailing lists and archives] Needs updated<br />
<br />
*http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date. This page is labeled, and starts out as, an overview of the PO, but the second part of this page cover only plant anatomical entities. I (RW) will keep this page as an overview of the PO, since that seems to be its main content, and create a separate page for anatomical entities, to correspond to the growth and development pages.<br />
*http://plantontology.org/docs/growth/growth_stages.html - Out of date. This page should be changed to reflect whole plant development stages.<br />
*http://plantontology.org/docs/faq/growth_faq.html - Out of date. ''fixed with commit #251''<br />
*http://plantontology.org/docs/development/developmental_stages.html - Out of date. This page should be changed to reflect plant structure development stages, other than whole plant stages.<br />
<br />
*http://plantontology.org/docs/otherdocs/ontology_doc.html Developers' guide. Content is not too bad, but this should be only on the wiki, and not on the web page since it is only for developers -- most users never need to see this.<br />
<br />
''Changes:''<br />
*''Updated growth_faq.html (6/28/12), principles_rationales.html (6/29/12), developmental_stages.htm (6/29/12), growth_stages.html (6/29/12), docs.html (6/20/12)''<br />
*''Created a new doc for anatomical entities, but have not updated the content or committed the file yet. This page could be updated to parallel the development stage pages.''<br />
<br />
===Tutorials and Demos out-of-date===<br />
Presentations/tutorials that need to be updated:<br />
<br />
*[http://plantontology.org/docs/presentations/demo/poc-demo-1.html Introduction to the project] - Slide show. There are links to this from both the web page and the wiki. Much of it is still valid, so it could be updated, rater than replaced. [http://palea.cgrb.oregonstate.edu/viewsvn/plantontology/html/docs/presentations/demo/ link to svn folder]<br />
<br />
''(7/3/12) Fixed and loaded onto beta and dev browsers.''<br />
<br />
<br />
'''Tutorials:'''<br />
<br />
http://wiki.plantontology.org/index.php/Plant_Ontology_Tutorials is the wiki equivalent of http://plantontology.org/docs/otherdocs/tutorials.html<br />
<br />
*Introduction to ontologies: http://plantontology.org/docs/presentations/tutorials/poc_intro.mov, http://plantontology.org/docs/presentations/tutorials/poc_intro.ppt Powerpoint slides<br />
*Development of ontologies: http://plantontology.org/docs/presentations/tutorials/ontology.mov, http://plantontology.org/docs/presentations/tutorials/ontology.ppt<br />
*Annotations: http://plantontology.org/docs/presentations/tutorials/annotation.mov, http://plantontology.org/docs/presentations/tutorials/annotation.ppt<br />
*Plant ontology browser and POC web site: http://plantontology.org/docs/presentations/tutorials/website.mov, http://plantontology.org/docs/presentations/tutorials/website.ppt<br />
<br />
===Out of date wiki pages===<br />
Principles, Rationales and Key Organizing Rules of the PO (These correspond to the out of date web pages):<br />
* [[Plant_Structure_Principles_Rules|Plant Structure Ontology]] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure. <br />
* [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked questions]]<br />
* [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]]<br />
<br />
RW: Rather than maintain duplicate pages, this links form the wiki should go to the corresponding web pages, once they are updated.<br />
<br />
<br />
*Wiki home page: under Formats of the Ontology Files, needs info on OWL (provide link).<br />
<br />
''RW: Added comment about OWL and link to Protege home page. (7/1/12)''<br />
<br />
===Developers guide -Download SVN Page===<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
http://www.plantontology.org/download/svn_doc.html Developers guide<br />
<br />
RW: Thanks for adding instructions for Mac users!<br />
<br />
''RW: Fixed grammer and punctuation issues, removed section on DAG Edit and replaced with sections on OBO-Edit and Protege. Fixed with commit #250 on 6/28/12.''<br />
<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an images for all these relations.''<br />
<br />
''RW: Minor point, but perhaps the list of icons could be have is_a first (as it is now) and then list the rest of them in alphabetical order.''<br />
<br />
==Medium priority fixes==<br />
These fixes are important, but can wait until after June.<br />
<br />
===Web pages that are out of date - medium priority===<br />
*http://plantontology.org/docs/otherdocs/poc_project.html - Was updated in the past year, but needs new updates. Still refers to "Plant Growth and Developmental Stages". Could use more detail on the project.<br />
*http://plantontology.org/docs/otherdocs/charter.html POC charter is out of date.<br />
*http://plantontology.org/docs/otherdocs/resources.html out of date<br />
*http://plantontology.org/docs/references/pub.html out of date<br />
<br />
==Feature requests==<br />
===Link to PO curators page===<br />
We have this page: http://wiki.plantontology.org/index.php/Plant_Ontology_curators <br />
<br />
Barry has requested that we put this material on the main PO page.<br />
<br />
Also requested that we add a prominent link from the main PO page to the wiki.<br />
<br />
''(7/3/12) A link to this page has been added from the "Documentation" page of the PO website.''<br />
<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
RW: Yes! This would be really great.</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_4-23-13&diff=22304POC Conf. Call 4-23-132013-04-23T17:52:53Z<p>Preecej: /* Image annotations */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday April 23rd, 2013 10am PST/1pm EST<br />
<br />
In attendance:<br />
<br />
Absent: <br />
<br />
<br />
<br />
<br />
<br />
=Other Items=<br />
Chelsea Specht (http://spechtlab.berkeley.edu/) will be visiting OSU to give the Templeton Lecture. Her talk is entitled: "Petaloidy, polarity, and pollination: the evolution and diversification of floral form in the Zingiberales." <br />
<br />
She will be on campus all day Thursday(4/25) and Friday morning (4/26). Should we plan to meet with her?<br />
<br />
=Image annotations=<br />
''The image annotation "dual-track" plan'':<br />
:1) Import keyword-annotated whole images (from DWS) into our image annotation database.<br />
:2) Segment and annotate DWS-contributed images with AISO; then import those newer, annotated versions into the image annotation database as an update for <br />
<br />
''Annotation progress''<br />
*DWS has provided over a dozen images (in both unlabeled and labeled versions) and has filled out the [https://docs.google.com/spreadsheet/ccc?key=0Ah7juewi_ZCOdDBPUXYybmc0ZmxrTVZhZk5mb3hydEE#gid=0 image data submission data template]. Thanks, Dennis!<br />
*Lol and Laura have received basic training on using AISO and have begun annotating images<br />
*Let's prioritize which terms need images: PJ: Physco terms, grass florets, root anatomy, SAM (fern and flowering plant), different kinds of veins in leaves, part of ATOL project (NOTE: DWS has images of thorns and prickles, septum, locule, pericarp)<br />
<br />
''Database development''<br />
*We have designed and built a database for holding annotated image data, with ontology terms and/or keywords<br />
*Nikhil is currently developing a data import script to bring Dennis' images and annotations into this db (whole image annotations first, segmented annotations next)<br />
<br />
''AISO Software Updates''<br />
*Current public version for download: http://files.cgrb.oregonstate.edu/Jaiswal_Lab/AISO/v0.2.1/<br />
*We have an updated version (0.3) currently in testing; it will be made available for public download in a few days.<br />
<br />
=New Requests:=<br />
<br />
<br />
=Request from DWS for terms to describe [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3610599&group_id=76834 root protoxylem development]=<br />
<br />
[http://dev.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0000272&session_id=4132b1366735007 protoxylem (PO:0000272)]: A portion of primary xylem (PO:0005849) tissue that has as parts tracheary elements (PO:0000290) with only annular or helical secondary wall thickening that are the first formed tracheary elements at a particular location. [source: ISBN:047125208] <br />
<br />
Comment: Develops while the vascular tissue (PO:0009015) is still elongating. Tracheary elements in protoxylem are smaller than in metaxylem (PO:0000372). Tracheary elements have lignified cell walls with secondary thickening and are dead at maturity. <br />
<br />
These are patterns of xylem development see: http://en.wikipedia.org/wiki/Xylem<br />
<br />
From Esau:<br />
* centarch protoxylem<br />
** shoot axis centarch protoxylem <br />
** root axis centarch protoxylem <br />
* mesarch<br />
* exarch protoxylem- A portion of protoxylem (PO:0000272) tissue in which the maturation of cells progresses centripedally, the oldest elements (protoxylem) are farthest from the center of the axis.<br />
* endarch- maturation of cells progresses centrifugally, the oldest elements (protoxylem) are towards the center of the axis. typical of seed plants <br />
<br />
* root protoxylem<br />
<br />
* root diarch protoxylem- A portion of protoxylem (PO:0000272) tissue in which the primary xylem of the root has two protoxylem strands or two protoxylem poles<br />
* triarch- A portion of protoxylem (PO:0000272) tissue in which the primary xylem of the root has three protoxylem strands or three protoxylem poles<br />
* tertrach- primary xylem of the root has 4 protoxylem strands or 4 protoxylem poles<br />
* pentarch- primary xylem of the root has 5 protoxylem strands or 5 protoxylem poles<br />
* polyarch- primary xylem of the root has many protoxylem strands or many protoxylem poles<br />
<br />
<br />
These are patterns of xylem development see: http://en.wikipedia.org/wiki/Xylem<br />
<br />
=[https://sourceforge.net/tracker/?func=detail&aid=3609161&group_id=76834&atid=835555 accessary paraclade] etc=<br />
Request from JL for the Plant Phenotype project for the term 'accessory branch' or accessory paraclade:<br />
<br />
Suggested term and def'n: accessory branch (new PO:ID): A shoot axis (PO:00025029) that develops from a shoot node (PO:0005004) that has produced at least one axillary branch (PO:0006343) <br />
<br />
Literature citation: The term 'accessory branch' is used in the description of the different types of phytomers (pg. 2724, top of left column):<br />
<br />
"...In both of these phytomer types, a second branch (accessory branch) may later develop '''between the axillary branch and its subtending leaf''' (Fig. 1A)." [http://dev.biologists.org/content/121/9/2723.long Talbert et al, 1995]<br />
<br />
This figure is actually referring to an accessory paraclade, not simply an accessory branch.<br />
<br />
We had an extensive discussion last week, so to help clarify things I took the figure from last week and labelled it with the new terms<br />
<br />
Annotated figure:<br />
<br />
[[File:Talbert-paraclade terms.jpg]]<br />
<br />
==Changes that were made to the [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3150504&group_id=76834 inflorescence branch] terms==<br />
<br />
[[File:Inflorescence branches.jpg]]<br />
<br />
'''* primary inflorescence branch (PO:0006321):''' An inflorescence branch (PO:0009081) arising from a first order inflorescence axis (PO:0025104).<br />
was 'second order inflorescence axis' - swapped name and exact synonym and removed the related synonym: second order inflorescence branch as it was inconsistent.<br />
<br />
'''* second order inflorescence branch (PO:0006322)'''- An inflorescence branch (PO:0009081) arising from a primary inflorescence branch (PO:0006321). (was third order inflorescence axis). <br />
Added exact synonyms: second order paraclade, secondary inflorescence branch, third order inflorescence axis, Removed the related synonym: second order inflorescence branch as it was inconsistent.<br />
<br />
'''* third order inflorescence branch (PO:0025105):''' An inflorescence branch (PO:0009081) arising from a secondary inflorescence branch (PO:0006322). (was fourth order third order inflorescence axis (PO:0025105).<br />
<br />
Added exact synonyms: third order paraclade, third order inflorescence branch, fourth order inflorescence axis, tertiary inflorescence branch<br />
<br />
Please see https://sourceforge.net/tracker/index.php?func=detail&aid=3609161&group_id=76834&atid=835555<br />
for details about the paraclade terms<br />
<br />
<br />
<br />
<br />
see this paper for additional information http://aob.oxfordjournals.org/content/early/2011/03/01/aob.mcr039.full<br />
<br />
=[https://sourceforge.net/tracker/?func=detail&aid=3610120&group_id=76834&atid=835555 trichome tip and apex]=<br />
Based on the discussion on POC call 4-16-13, make new terms and extensively revised the trichome branch of the ontology: <br />
<br />
Added unicellular trichome, rather than having it a synonym of trichome cell. <br />
<br />
Added new terms and revised the rest: <br />
<br />
'''* multicellular trichome (PO:0025162):''' A portion of plant tissue that forms a non-sclerified outgrowth from the epidermis. [source: POC:curators] <br />
<br />
'''* unicellular trichome (PO:0025537):'''- A trichome (PO:0000282) that is a single plant cell (PO:0009002). is_a trichome, is_a plant cell. comment: This should not be confused with a trichome cell, which is a plant cell (PO:0009002) that is part of a multicellular trichome (PO:0000282).<br />
<br />
'''* trichome apex (new PO:0025550):''' A plant structure (PO:0009011) that is the apical most portion of a trichome (PO:0000282). comment: An apex of a unicellular trichome is a GO sub-cellular component GO:xxxxxxx. is_a plant structure, part_of trichome<br />
'''** multicellular trichome apex (new PO:0025551):''' A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162). is_a trichome apex, part_of multicellular trichome (PO:0025551)<br />
<br />
'''* trichome tip (new PO:0025549):''' A plant structure (PO:0009011) that is the apical most portion of trichome apex (PO:0025550). is_a plant structure, part of trichome apex<br />
'''** multicellular trichome tip (PO:0025535):''' comment:<br />
<br />
<br />
Have requested the [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3611615&group_id=36855 parts of the unicellular trichome from GO]<br />
<br />
<br />
[[File:trichome terms.jpg]]<br />
<br />
<br />
[http://understorey.tumblr.com/post/48509863848/currrentbiology-cucumber-skin-barbs-under-800x Tichome image from AOB]<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3609180&group_id=76834&atid=835555 petal nanoridges]==<br />
<br />
Suggested Definition: Microscopic, often parallel, ridges composed of cutin occurring on the surface of petals.<br />
Parent/relationship: part_of petal epidermis (PO:0006041)<br />
<br />
Reference: PMID 19959665<br />
<br />
Added new term: '''plant cuticle ridge (PO:0025536):''' A portion of plant cuticle (PO:000022) that forms a ridge, may be overlayed with epicuticluar wax (PO:0025388).<br />
<br />
epicuticular wax (PO:0025388): A portion of cuticular wax that forms crystalloids or a smooth film on the exterior of a cuticle. [source: PMID:12467640, PO_Ref:00010] <br />
<br />
Comment: Epicuticular waxes may take a variety of forms, such as plates, ribbons, tubes, and rods.<br />
<br />
=Other Items for discussion=<br />
- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting<br />
<br />
=Upcoming meetings and Presentations 2013:=<br />
<br />
==[http://www.bioontology.org/wiki/index.php/NCBO_Hackathon_2013 NCBO Hackathon] April 29-30, 2013==<br />
<br />
The NCBO Hackathon will take place at Stanford University on April 29-30, 2013. This event will focus on projects in biomedical or clinical informatics that can benefit from use of ontology-based technology. <br />
<br />
The entire NCBO Team will be available to brainstorm application ideas and to answer development questions. We will also have separate sessions to provide training on the NCBO Web services, the BioPortal SPARQL endpoint, and other topics of interest requested by participants. <br />
<br />
If you are thinking of incorporating semantics into your software application, the Hackathon will provide a great opportunity to get a head start on your project.<br />
<br />
==Phenotype RCN Plant Group Meeting- Ames, Iowa April 30th-May 3rd==<br />
<br />
We will be meeting to work on the Plant Phenotype Pilot Project, LC is going<br />
<br />
==PR-PO-GO meeting, May 15-16th 2013==<br />
Please see this page for more information: [[PRO-PO-GO_Meeting]]<br />
<br />
Location: Buffalo, NY <br />
<br />
Dates: May 15-16th, 2013. <br />
<br />
*1. To inform members of the Protein, Plant, Gene Ontology communities of developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies. Specifically: <br />
**a. To enhance the PO treatment of plant-related proteins <br />
**b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages<br />
*2. To contribute to the [http://wiki.plantontology.org/index.php/The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative cROP] (Common Reference Ontologies for Plants) initiative<br />
*3. To contribute to the ontological understanding of phenotype and disease in all model organisms.<br />
*4. To identify potentially fruitful applications which enhanced ontology coordination might bring.<br />
<br />
==1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013==<br />
[http://semantic-biodiversity.mpl.ird.fr/ S4BIODIV]<br />
<br />
[http://2013.eswc-conferences.org/join-participant-0/participant-eswc2013 Registration Information ESWC 2013] <br />
<br />
Early Registration deadline March 17th<br />
<br />
Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.<br />
<br />
Held in parallel with the 10th [http://2013.eswc-conferences.org/ Extended Semantic Web Conference (ESWC 2013)]<br />
<br />
Workshop date: May 27, 2013<br />
<br />
==MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013==<br />
<br />
[http://www.regonline.com/builder/site/Default.aspx?EventID=1060172 MONOCOTS V]: <br />
<br />
5th International Conference on Comparative Biology of Monocotyledons<br />
Friday, July 05, 2013 7:00 AM -<br />
Sunday, July 14, 2013 12:00 PM (Eastern Time)<br />
<br />
The New York Botanical Garden & Fordham University<br />
<br />
<br />
==ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013==<br />
4th International Conference on Biomedical Ontologies 2013 (ICBO2013)<br />
<br />
Concordia University, Montreal, Quebec, July 7th - 9th 2013 [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/cfp.html call for papers]<br />
<br />
The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.<br />
<br />
The event is part of the [http://www.unbsj.ca/sase/csas/data/semantic-trilogy-2013/ Semantic Trilogy 2013] featuring:<br />
<br />
* International Conference on Biomedical Ontologies (ICBO 2013)<br />
* Canadian Semantic Web Symposium (CSWS 2013)<br />
* Data Integration in the Life Sciences (DILS 2013)<br />
<br />
Workshop on [https://sites.google.com/site/semsysbio/ Semantic Systems Biology 2013 (SSB2013)] will be held as part of the International Conference on Biomedical Ontologies (ICBO2013) at Concordia University, Montreal, Quebec, on July 7th, 2013. The event is part of the Semantic Trilogy 2013 (above)<br />
<br />
Topics of interest include, but are not limited to:<br />
*ontologies & terminologies for modeling computational biology<br />
*ontologies & terminologies for simulation (and result data) in computational biology/medicine/neuroscience<br />
*semantic web technologies for description, integration, query and discovery of models, simulations and result data<br />
*semantic web technologies for biological data and analysis<br />
*semantic annotations of bio-models<br />
*applications of ontologies in computational systems biology/medicine/neuroscience<br />
*semantic platforms for undertaking and visualizing simulation results<br />
<br />
We welcome four types of submissions:<br />
* short papers, up to 4 pages.<br />
* long papers, up to 7 pages.<br />
* position papers, up to 1 page.<br />
* late breaking reports, up to 1 page.<br />
<br />
See the ICBO website for further information on the submission types.<br />
<br />
All submission are due on Monday, April 15 2013.<br />
Notification of acceptance: May 6th, 2013<br />
<br />
==Botanical Society Meeting July 27-31st New Orleans==<br />
<br />
[http://www.2013.botanyconference.org/ BSA 2013]<br />
<br />
- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_12-11-12&diff=20883POC Conf. Call 12-11-122012-12-11T18:08:02Z<p>Preecej: /* PAG 2013, San Diego, CA; January 12th - 16th, 2013 */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Dec 11th, 2012 10am PST/1pm EST<br />
<br />
In attendance:<br />
<br />
<br />
=Plans for Upcoming Release #19=<br />
<br />
Timeline for Release: Goal is mid December 2012 [[Release_19]]<br />
<br />
Priorities for inclusion in the Release:<br />
<br />
- Revisions to PSDS: including Fruit development stages<br />
<br />
- Cleaning up some of the open trackers for the PAE branch<br />
<br />
- New datasets: grape, cotton, rice<br />
<br />
- LC has been working with YY and JE to update the Japanese translations- in the next release, we anticipate these will be displayed on the live site.<br />
<br />
Updated Goal: is to complete the edits and annotation sets by end of the day Wed Dec 12th, then load the database onto beta. That will give us the following week to troubleshoot issues and hopefully have it completed by Dec 18th.<br />
<br />
=Open trackers: To be fixed:=<br />
<br />
<br />
==[https://sourceforge.net/tracker/?func=detail&aid=3525242&group_id=76834&atid=835555 generative cell (PO:0020097)] and related terms==<br />
<br />
<br />
We need to fix this definition, as it currently only includes angiosperms:<br />
<br />
Current name and def'n:<br />
<br />
generative cell (PO:0020097): A cell of the male gametophyte of angiosperms that divides to produce two male gametes or sperm cells. [source: APweb:Glossary]<br />
<br />
Definitions from Raven 5th ed: <br />
'''generative cell:'''<br />
1. In gymnosperms, the cell of the male gametophyte that divides to form the sterile and spermatogenous cells<br />
<br />
2. In angiosperms, the cell of the male gametophyte that divides to form two sperm<br />
<br />
'''spermatogenous cell:''' the cell of the male gametophyte or pollen grain of gymnosperms, which divides to form 2 sperm cells<br />
<br />
<br />
'''Originally we proposed changing generative cell (PO:0020097) to a spermatogenous cell and make generative cell a synonym of it, but a different solution is below:''' <br />
<br />
Propose new parent term spermatogenous cell, which would encompass the spermatogenous cells in the lower plants and would have child terms: 'generative cell' (PO:0020097) for angiosperms, and 'body cell' (new PO:0025526) for the gymnosperms.<br />
<br />
'''spermatogenous cell (new; PO:0025525):''' A plant cell (PO:0009002) that gives rise to one or more plant sperm cells (PO:0000084).<br />
<br />
'''generative cell (PO:0020097):''' A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280)in angiosperms, that divides to produce two pollen sperm cells (PO:0025121) in angiosperms.<br />
<br />
'''body cell (new; PO:0025525):''' A spermatogenous cell (PO:0025525) of the microgametophyte (PO:0025280) in gymnosperms, that divides to produce the sterile and pollen sperm cells (PO:0025121).<br />
<br />
add broad synonym: generative cell <br />
<br />
Question: Can we define the pollen sperm cell (PO:0025121) as: A plant sperm cell (PO:0000084) that develops from a generative cell (PO:0020097) or the body cell (PO:0025526) and is part of the pollen (PO:0025281).<br />
<br />
<br />
[[File:Spermatogenous_cells.jpg ]]<br />
<br />
Add reference: to Singh 1978- Gymnosperm embryology, Raven 5th edition<br />
<br />
* should be: part_of the microgametophyte (PO:0025280)<br />
<br />
Notes from previous discussions: <br />
* spermatogenous cells also occur in non-seed plants- (check with Eames)... in ferns as well, so we cannot refer to seed plants alone. <br />
<br />
<br />
* May need to add new term for pollen sperm cell in angiosperms, which develops from generative cell and pollen sperm cell in gymnos, which develops from pollen spermatogenous cell (or body cell)<br />
<br />
* Do we need to differentiate the gymno pollen from the angiosperm pollen?<br />
<br />
<br />
<br />
Other new terms that we should probably add with definitions derived from Singh and Raven: <br />
<br />
* prothallial cell- part of the gymnosperm pollen grain<br />
<br />
Definition from Raven 5th ed: The sterile cell or cells found in the male gametophytes, or microgametophytes of vascular plants other than angiosperms; believed to be the remnants of the vegetative tissue of the male gametophyte.<br />
<br />
Singh: The sterile cell cut off by the microspore and the central cell. Formed by the <br />
<br />
<br />
<br />
* central cell- ''could be called microspore central cell, to avoid confusion''<br />
<br />
* stalk cell (of sterile cell)<br />
* antheridial inital<br />
* antheridial cell <br />
* tube cell<br />
<br />
* male gametes<br />
<br />
Existing terms:<br />
<br />
* plant sperm cell (PO:0000084)<br />
<br />
* microspore (PO:0020048)<br />
<br />
=archegonium and associated parts:=<br />
<br />
==[http://sourceforge.net/tracker/index.php?func=detail&aid=3109542&group_id=76834&atid=835555 archegonium] (PO:0025126)== <br />
<br />
Revised def'n: A multicellular plant gametangium (PO:0025124) that develops from an archegonium initial cell (PO:0025510) and has as parts a venter (PO:0030038) and an archegonium neck (PO:0030039).<br />
<br />
Revised comment: At maturity, the archegonium produces an archegonium egg cell (PO:0025122). In mosses, the archegonium also has part an archegonium stalk (PO:0030036). The archegonium (PO:0025126) occurs in bryophytes and pteridophytes, but never in angiosperms, where the female gamete (plant egg cell; PO:0020094) is produced by the embryo sac (PO:0025074), a specialized (reduced) gametangium.<br />
<br />
[http://books.google.com/books?id=L8DHHSO2RFsC&dq=ventral+canal+cell&source=gbs_navlinks_s Plants:Diversity and Evolution- Ingrouille and Eddie(2006)] [http://openisbn.com/isbn/9780521794336/ ISBN-10: 0521794331,ISBN-13: 9780521794336]<br />
<br />
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3577440&group_id=76834&atid=835555 archegonium initial cell]==<br />
Existing (new): <br />
<br />
archegonium initial cell (PO:0025510): An initial cell (PO:0004011) that is part of the archegonium megagametophyte (PO:0025282), and which divides asymmetrically to form an archegonium central cell (PO:0025509) and a smaller archegonium neck canal cell (PO:0030035).<br />
<br />
relations: <br />
* archegonium initial cell (PO:0025510) part_of archegonium megagametophyte (PO:0025282)<br />
* archegonium central cell (PO:0025509) develops_from archegonium initial cell (PO:0025510)<br />
* archegonium neck canal cell (PO:0030035) develops_from archegonium initial cell (PO:0025510)<br />
<br />
<br />
from Rudall, 2006: "In gymnosperms such as Ephedera, each archegonial initial undergoes an asymmetric mitosis to form a large central cell and a smaller neck cell." <br />
<br />
''Question: Does the archegonium always exist as part of the archegonium megagametophyte, and does the archegonium megagametophyte always have as part an archegomnium? What about in bryophytes and pteridophytes?''<br />
<br />
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3080937&group_id=76834&atid=835555 archegonium central cell]== <br />
archegonium central cell (PO:0025509): A plant cell (PO:0009002) that is the larger, distal cell arising from the first division of an archegonium initial cell (PO:0025510).<br />
<br />
Comment: The archegonium central cell divides asymmetrically to form a smaller ventral canal cell (PO:0025524) and a larger archegonium egg cell (PO:0025122). It is larger than the archegonium neck canal cell (PO:0030065), which also develops from the archegonium initial cell (PO:0025510). The archegonium central cell only occurs in gymnosperms.<br />
<br />
Reference rudall paper: PMID_17041880<br />
<br />
''Is this true: The archegonium central cell only occurs in gymnosperms. Note from Skype discussion: MG: In ferns they do not use the term 'central cell'- use ventral canal cell.''<br />
<br />
<br />
===[https://sourceforge.net/tracker/index.php?func=detail&aid=3080937&group_id=76834&atid=835555 embryo sac central cell]=== <br />
embryo sac central cell (PO:0020090): The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.<br />
<br />
only in angiosperms<br />
<br />
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3234981&group_id=76834&atid=835555 venter] (PO:0030038)==<br />
venter (PO:0030038): <br />
<br />
Revised def'n: A cardinal organ part (PO:0025001) that is the enlarged basal part of an archegonium (PO:0025126) and has an archegonium egg cell (PO:0025122) located in it.<br />
<br />
''moved the relation "archegonium egg cell located_in venter" rather than "archegonium egg cell located_in archegonium". Is this true for all?''<br />
<br />
New comment: <br />
<br />
<br />
http://en.wikipedia.org/wiki/Calyptra<br />
<br />
In bryophytes, the calyptra (plural calyptrae) is an enlarged archegonial venter that protects the capsule containing the embryonic sporophyte.[1] The calyptra is usually lost before the spores are released from the capsule. The shape of the calyptra can be used for identification purposes.[2]<br />
<br />
# Ralf Reski (1998): Development, genetics and molecular biology of mosses. In: Botanica Acta. 111, 1-15.<br />
# Malcolm; Malcolm, Bill; Nancy (2006), Mosses and other Bryophytes, an Illustrated Glossary, Micro-Optics Press, p. 65, ISBN 0-9582224-7-9<br />
<br />
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3234985&group_id=76834&atid=835555 archegonium neck] (PO:0030039)==<br />
<br />
Added PO IDs:<br />
<br />
archegonium neck (PO:0030039): A cardinal organ part (PO:0025001) that is the elongated, apical part of an archegonium (PO:0025126).<br />
<br />
Comment: At maturity, the neck canal cells (PO:0030065) and the ventral canal cell (PO:0025524) disintegrate, creating a archegonium neck canal (PO:0030066) for the plant sperm cells (PO:0000084) to enter the archegonium (PO:0025126).<br />
<br />
*''' archegonium neck canal (PO:0030066)''': <br />
<br />
A canal (PO:0025132) in the center of an archegonium neck (PO:0030039). <br />
<br />
Comment: During archegonium development, the archegonium neck canal cells (PO:0030065) and the ventral canal cell (PO:0025524) disintegrate, creating a archegonium neck canal for the plant sperm cells (PO:0000084) to enter the archegonium (PO:0025126).<br />
<br />
* '''archegonium neck canal cell (PO:0030065)''':<br />
A plant cell (PO:0009002) that is one of the axial row of cells in an immature archegonium neck (PO:0030039).<br />
<br />
== New term: [https://sourceforge.net/tracker/?func=detail&aid=3594092&group_id=76834&atid=835555 ventral canal cell]: ==<br />
<br />
proposed def'n: ventral canal cell (PO:0025524): A plant cell (PO:0009002) that develops from the archegonium central cell (PO:0025509) and lies at the base of the archegonium neck (PO:0030039), above the archegonium egg cell (PO:0025122) in the venter (PO:0030038).<br />
<br />
proposed comment: The ventral canal cell is smaller than the archegonium egg cell (PO:0025122), which also develops from the asymmetric division of the archegonium central cell (PO:0025509). It lack a plant-type cell wall (GO:0009505) (ref?). When the archegonium (PO:0025126) is mature, the ventral canal cell (along with the archegonium neck canal cells; PO:0030065), contributes to the formation of the archegonium neck canal (PO:0030066) by distintegrating and becoming mucilaginous. The canal cells and may produce chemicals to attract the male gametes.<br />
<br />
Relations: <br />
* ventral canal cell (PO:0025524) part_of the venter (PO:0030038)<br />
* ventral canal cell (PO:0025524) develops_from archegonium central cell (PO:0025509)<br />
<br />
References: <br />
*Ingrouille M, Eddie B (2006) Plants: Diversity and Evolution. Cambridge University Press<br />
*Rudall PJ (2006) How many nuclei make an embryo sac in flowering plants? BioEssays 28: 1067–1071<br />
<br />
==archegonium stalk (PO:0030036)==<br />
Revised def'n: A stalk (PO:0025066) that the most basal part of an archegonium (PO:0025126). <br />
<br />
Comment: Raises the venter (PO:0030038) above the rest of the gametophyte.<br />
<br />
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3030032&group_id=76834&atid=835555 archegonium egg cell]==<br />
<br />
Revised def'n: A plant egg cell (PO:0020094) that develops from the archegonium central cell (PO:0025509) and is located in the archegonium (PO:0025126).<br />
<br />
Comment: The archegonium central cell divides asymmetrically to form a smaller archegonium neck canal cell (PO:0030065) and a larger archegonium egg cell (PO:0025122) in gymnosperms.<br />
<br />
''Notes: The archegonium egg cell develops_from the archegonium central cell, it has a common origin with the neck canal cell, in ferns they do not use the term 'central cell'- ventral canal cell.''<br />
<br />
==[http://sourceforge.net/tracker/index.php?func=detail&aid=3109542&group_id=76834&atid=835555 antheridium] and associated parts:==<br />
<br />
Current def'n: <br />
antheridium (PO:0025125): A plant gametangium that produces antheridium sperm cells that are located in it. [source: POC:curators] <br />
<br />
Comment: An antheridium has a sterile jacket layer that does not produce sperm cells.<br />
<br />
Revised def'n: A multicellular plant gametangium (PO:0025124) that produces antheridium sperm cells (PO:0025120)and has as parts an antheridium jacket layer (PO:0030053) and an antheridium stalk (PO:0030035). <br />
<br />
Revised comment: An antheridium has a sterile jacket layer (PO:0030052). In both gymnosperms and angiosperms, the antheridium (PO:0025125) is replaced by pollen (PO:0025281).<br />
<br />
<br />
<br />
<br />
===Structures associated with the antheridium:===<br />
Added PO IDs<br />
<br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=3293931&group_id=76834&atid=835555 antheridium jacket layer] (PO:0030053): A portion of plant tissue (PO:0009007) that is a single layer of cells on the outside of an antheridium (PO:0025125).<br />
<br />
''Revised comment: Cells in the antheridium jacket layer surround the inner spermatogenous cells (new PO ID) and do not give rise to antheridium sperm cells (PO:0025120).''<br />
<br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=3293290&group_id=76834&atid=835555 antheridium jacket layer cell] (PO:0030052): A plant cell (PO:0009002) that is part of an antheridium jacket layer (PO:0030053).<br />
<br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=3109542&group_id=76834&atid=835555 antheridium stalk] (PO:0030035): A stalk (PO:0025066) that is the basal part of an antheridium (PO:0025125).<br />
<br />
''Revised comment: The antheridium stalk raises the antheridium (PO:0025125) from the antheridium head (PO:0030075).''<br />
<br />
<br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=3030033&group_id=76834&atid=835555 antheridium sperm cell] (PO:0025120): A plant sperm cell that is produced by and located in an antheridium.<br />
<br />
''revised def'n: A plant sperm cell (PO:0000084) that develops from a spermatogenous cell (new PO ID) and is located in an antheridium (PO:0025125).''<br />
<br />
existing Comment: Antheridial sperm cells are motile and lack a plasma membrane.<br />
<br />
Revised comment: Antheridium sperm cells are motile. <br />
<br />
remove the relation part_of antheridium, replace with located_in<br />
<br />
<br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=3272612&group_id=76834&atid=835555 antheridium head](PO:0030075): A disk-shaped cardinal organ part (PO:0025001) that is the apical portion of an antheridiophore (PO:0030033) and bears antheridia (PO:0025125).<br />
<br />
''revised comment: Found in mosses and other bryophytes such as the liverwort Marchantiales.''<br />
<br />
<br />
[https://sourceforge.net/tracker/index.php?func=detail&aid=3272612&group_id=76834&atid=835555 antheridiophore] (PO:0030033): A plant axis (PO:0025004) that bears two or more antheridia (PO:0025125) on an antheridium head (PO:0030075).<br />
''revised comment: Found in mosses and other bryophytes such as the liverwort Marchantiales.''<br />
<br />
=Upcoming meetings and Presentations 2012-2013:=<br />
<br />
==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12th - 16th, 2013==<br />
We will be running a workshop focusing on:<br />
<br />
[https://pag.confex.com/pag/xxi/webprogram/Session1596.html Applications of Ontologies for Plant and Animal Genomics]<br />
<br />
* Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6<br />
<br />
Speakers: Eva Huala, Reinhard Simon, Elizabeth Arnaud, Chris Mungall, and Pankal will present the cROP Vision <br />
<br />
<br />
JP will be presenting an [https://pag.confex.com/pag/xxi/webprogram/Paper7520.html AISO Computer Demo]: <br />
<br />
Date and Time: Sunday, January 13, 2013; 5:20 PM, California room<br />
<br />
==Biocuration 2013 conference, Cambridge, 7-10th April 2013==<br />
<br />
submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.<br />
<br />
possible venue for cROP white paper?<br />
<br />
website and registration are now open: [http://www.ebi.ac.uk/biocuration2013/ Biocuration 2013]<br />
<br />
==PRO-PO-GO meeting, May 15-16th 2013==<br />
Please see this page for more information: [[PRO-PO-GO_Meeting]]<br />
<br />
Location: Buffalo, NY <br />
<br />
Dates: May 15-16th, 2013. <br />
<br />
Goals:<br />
# To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination<br />
# To identify potentially fruitful applications which such enhanced coordination might bring <br />
# To enhance the Protein Ontology treatment of plant-related proteins <br />
# To address coordination issues between the GO and PO, for example as concerns treatment of development stages<br />
# To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP] <br />
<br />
<br />
Tentative participant list: <br />
<br />
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others? <br />
<br />
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?<br />
<br />
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)<br />
<br />
''BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO''<br />
<br />
<br />
==10th Extended Semantic Web Conference (ESWC) Montpellier, 26-30 May 2013==<br />
<br />
[http://2013.eswc-conferences.org/ Extended Semantic Web Conference] Montpellier<br />
<br />
Location: Montpellier, 26-30 May 2013.<br />
<br />
Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.<br />
<br />
Paraphrased from email exchange with EA (Bioversity):<br />
<br />
[https://docs.google.com/document/d/1XlWuku3VRXvavxml8Bl7fQzfP_xxXHhjR_NRIWpK0DI/edit workshop proposal]<br />
<br />
"We are finalizing a workshop proposal to be submitted in the 23rd to the conference organizing committee. In parallel, we are developing a proposal for raising some support funds.<br />
<br />
Ontologies will be part of the workshop discussion. The latest development sent by Justin on AISO also raised interest of the organizing committee. So, we would you like that the Plant Ontology team be represented in the scientific committee of our workshop. <br />
<br />
This is a very first draft of course but will provide you with the context, scientific objectives, and expected outputs. Would you accept in principle (if the workshop is accepted and funds raised) to join our committee and submit a a paper for a presentation and/or poster? Deadline will be March and April.<br />
<br />
==MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013==<br />
<br />
[http://www.regonline.com/builder/site/Default.aspx?EventID=1060172 MONOCOTS V]: <br />
<br />
5th International Conference on Comparative Biology of Monocotyledons<br />
Friday, July 05, 2013 7:00 AM -<br />
Sunday, July 14, 2013 12:00 PM (Eastern Time)<br />
<br />
The New York Botanical Garden & Fordham University<br />
<br />
=Next meeting scheduled for Tuesday, Dec 18th, 2012 at 10am Pacific/1pm Eastern=</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_10-9-12&diff=19989POC Conf. Call 10-9-122012-10-11T01:18:07Z<p>Preecej: /* SIA v0.2.1 Released */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Oct 9th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-2-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=68952927&rKey=8ea2a20393db7805<br />
<br />
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=68952927&rKey=f7ca49a945781e72<br />
<br />
<br />
=SIA v0.2.1 Released=<br />
<br />
'''Note the update to v0.2.1 already. I solved a nagging issue and enhanced the data storage structure today. If you downloaded v0.2 yesterday, please upgrade to v0.2.1 before continuing to try out SIA.''' Thanks! - JP<br />
<br />
Justin Preece has packaged and uploaded a new version of SIA for Mac and Linux (Windows still in progress). This version is fit for public consumption, although it is still very much beta software with lots of opportunity for improvement. Several technical issues have been fixed and a few small enhancements have been made.<br />
<br />
*Our lab site post: http://jaiswallab.cgrb.oregonstate.edu/software#SIA<br />
*Downloads: http://files.cgrb.oregonstate.edu/Jaiswal_Lab/sia/v0.2.1/<br />
<br />
It would be great if folks on today's call with access to Linux and Mac machines could give the installation instructions a test drive. Feel free to let me know if anything seems amiss. If you want to report any bugs or request new features, just send an email to <sia-support@palea.cgrb.oregonstate.edu><br />
<br />
JP will coordinate the appropriate PO emails and web site announcements with Lol. Thanks!<br />
<br />
=Update from Cornell=<br />
Ale has been in communication with Bob Turgeon and got comments from him on phloem terms. fill in details...<br />
<br />
=Manuscripts in prep=<br />
<br />
=Change to [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 gametophyte development stage]=<br />
This change is urgent, because we need to address this in the manuscript in prep.<br />
<br />
gametophyte development stage (PO:0028003) is currently defined as "A whole plant development stage that has as primary participant a whole plant during the interval between meiosis or apospory and its death ''or fertilization''."<br />
<br />
I think the last part about fertilization is misleading, because it suggests that the gametophyte stage could end in ''any'' plant with fertilization. Many gametophytic plants continue to live (and nourish the sporophyte) long after fertilization. In seed plants, the gametophyte does not exactly die after fertilization, but is transformed. I suggest we add something to the comment to help explain this, but keep the definition simpler.<br />
<br />
'''New proposed definition:''' A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between meiosis or apospory and its death.<br />
<br />
'''New addition to comment (rest stays the same):''' In seed plants, the gametophyte may be transformed by fertilization but not strictly die, such as when pollen (PO:0025281) germinates or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperms.<br />
<br />
=Fruit development stages for whole plants=<br />
==[https://sourceforge.net/tracker/?func=detail&aid=3574905&group_id=76834&atid=835555 whole plant fruit development stage (PO:0025500)]==<br />
New term<br />
<br />
'''proposed defintion:''' A sporophyte reproductive stage that begins when a fruit (PO:0009001) enters its fruit initiation stage (PO:0025503) on a whole plant (PO:0000003) ''that does not have any other fruits as part'', and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.<br />
<br />
Comment: Includes whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage.<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3565057&group_id=76834&atid=835555 whole plant fruit formation stage (PO:0007042)]==<br />
''postponed to future meeting''<br />
<br />
'''New proposed def.:''' A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends with the onset of a whole plant fruit ripening stage (PO:0007010).<br />
<br />
Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An iteroparous plant will only have one fruit formation stage in its life, while a semelparous plant may have multiple whole plant fruit development stages during its life. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun. Although the use of synonyms like 07-milk stage in rice properly refer to the development of an individual fruits, they are used as here to extrapolate to a whole plant.<br />
<br />
<br />
Is it better to use whole plant fruit formation stage has_part fruit formation stage (new term, see below) or fruit formation stage part_of whole plant fruit formation stage?? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3565059&group_id=76834&atid=835555 whole plant fruit ripening stage (PO:0007010)]==<br />
''postponed to future meeting''<br />
<br />
'''New proposed def.:''' A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.<br />
<br />
<br />
comment: Succeeds a whole plant fruit formation stage. This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing ripening (which is a type of senescence) during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, followed by a sporophyte senescent stage (PO:0007017), as in case (1). A semelparous species may have one fruit ripening stage for each whole plant fruit developments stage (PO:0025500), followed by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species, a plant may have multiple fruit development stages and in the sporophyte reproductive stage (PO:0007130) after all fruit has ripened, without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of stages like dough stage properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.<br />
<br />
<br />
Is it better to add whole plant fruit ripening stage has_part fruit ripening stage or fruit ripening stage has_part whole plant fruit ripening stage? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.<br />
<br />
=New fruit development stages=<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3573602&group_id=76834&atid=835555 fruit development stage (PO:0001002)]==<br />
def.: A plant structure development stage (PO:0009012) that has as primary participant a single fruit (PO:0009001).<br />
<br />
comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.<br />
<br />
==New proposed subclasses==<br />
''still need to create SF tracker items and add xref to terms''<br />
===fruit formation stage (PO:0025501)===<br />
Proposed def.: A fruit development stage (PO:0001002) that being with the formation of the plant zygote (PO:0000423) ''that is contained in that fruit'' and ends when ''its'' fruit ripening stage (PO:0025502) begins.<br />
<br />
comment: ''A fruit formation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions.'' This stage applies to an individual fruit (PO:0009001). For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage (PO:0007042).<br />
<br />
====new subclasses of fruit formation stage====<br />
These are the stages that were developed for whole plants, but groups like SGN really need to apply them to individual fruits. I also added a new stage for fruit initiation.<br />
<br />
<br />
'''fruit initiation stage (PO:0025503)''': A fruit formation stage (PO:0025501) that begins with the formation of the plant zygote (PO:0000423) ''that is contained in that fruit (PO:0009001)'' and ends when the plant cells (PO:0009002) in the fruit begin to divide or expand (add GO terms)''.<br />
<br />
Comment: The fruit initiation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage ends as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).<br />
<br />
''Apply similar changes as for PO:0025501. Copy comment to PO:0025501.''<br />
<br />
<br />
'''fruit size up to 10% stage (PO:0025504):''' A fruit formation stage (PO:0025501) that begins after a fruit initiation stage (PO:0025503), and ends when the fruit (PO:0009001) has reached 10% of its final size.<br />
<br />
Comment: Begins as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. Succeeds a fruit initiation stage (PO:0025503) and proceeds a fruit size 10 to 30% stage (PO:0025505). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).<br />
<br />
<br />
'''fruit size 10 to 30% stage (PO:0025505):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 10% to 30% of its final size.<br />
<br />
Comment: Succeeds a fruit size up to 10% stage (PO:0025504) and proceeds a fruit size 30 to 50% stage (PO:0025506). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 10 to 30% (PO:0007009).<br />
<br />
<br />
'''fruit size 30 to 50% stage (PO:0025506):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 30 to 50% of its final size.<br />
<br />
Comment: Succeeds a fruit size 10 to 30% stage (PO:0025505) and proceeds a fruit size 50 to 70% stage (PO:0025507). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 30 to 50% (PO:0007029).<br />
<br />
<br />
'''fruit size 50 to 70% stage (PO:0025507):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 50 to 70% of its final size.<br />
<br />
Comment: Succeeds a fruit size 30 to 50% stage (PO:0025505) and proceeds a fruit size 70% to final size stage (PO:0025508). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 50 to 70% (PO:0007007).<br />
<br />
<br />
'''fruit size 70% to final size stage (PO:0025508):''' A fruit formation stage (PO:0025501) that spans begins when a fruit (PO:0009001) has reached 70% of its final size and ends when a fruit has reached its final size and a fruit ripening stage (PO:0025502) begins.<br />
<br />
Comment: Succeeds a fruit size 50 to 70% stage (PO:0025507) and proceeds a fruit ripening stage. This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 70% to final size (PO:0007027).<br />
<br />
===fruit ripening stage===<br />
Proposed def.: A fruit development stage (PO:0001002) during which a fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).<br />
<br />
Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).<br />
<br />
=Subclasses of whole plant fruit formation stage (PO:0007042)=<br />
See SF tracker for [https://sourceforge.net/tracker/index.php?func=detail&aid=3374186&group_id=76834&atid=835555 FF.00 fruit size 10% and sibling terms]<br />
<br />
''postponed to future meeting''<br />
<br />
At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.<br />
<br />
''What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of there existing annotations and move them to fruit development stage and its new subtypes as necessary.''<br />
<br />
====FF.00 fruit size up to 10% stage (PO:0007032)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage up to 10%:''' A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% of final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504). <br />
<br />
====FF.01 fruit size 10 to 30% stage (PO:0007009)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 10 to 30%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505). <br />
<br />
====FF.02 fruit size 30 to 50% stage (PO:0007029)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 30 to 50%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 30 to 50% stage (PO:0025506). <br />
<br />
====FF.03 fruit size 50 to 70% stage (PO:0007007)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 50 to 70%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 50 to 70% stage (PO:0025507).<br />
<br />
====FF.04 fruit size 70% to final size stage (PO:0007027)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 70% to final size:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.<br />
<br />
comment: Succeeded by a whole plant fruit ripening stage (PO:0007010). This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 70% to final size stage (PO:0025508).<br />
<br />
related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79<br />
<br />
==Add new synonyms for grapes==<br />
<br />
''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch''<br />
<br />
''Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)''<br />
<br />
''Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)''<br />
<br />
''Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)''<br />
<br />
=Subclasses of whole plant fruit ripening stage (PO:0007010)=<br />
''postponed to future meeting''<br />
<br />
The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.<br />
<br />
==FR.00 beginning of fruit ripening stage (PO:0007036)==<br />
current def.: The stage at which fruit maturation begins.<br />
<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant beginning of fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
<br />
''Add related synonym: BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour<br />
<br />
''Add related synonym: grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison ''<br />
<br />
==FR.01 early stage of fruit ripening (PO:0007001)==<br />
current def.: The early stage in fruit ripening<br />
<br />
related synonym: BBCH principal growth stage 83<br />
<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant early fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
''Add related synonym: middle of veraison''<br />
<br />
==FR.02 mid stage of fruit ripening (PO:0007031)==<br />
current def.: The stage when fruit ripening is midway.<br />
<br />
'''whole plant mid fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
==FR.03 late stage of fruit ripening (PO:0007050)==<br />
current def.: The late stage of fruit ripening.<br />
<br />
'''whole plant late fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
==FR.04 fruit ripening complete stage (PO:0007038)==<br />
current def.: The stage at which fruit ripening is complete.<br />
<br />
'''whole plant fruit ripening complete stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
related synonym: BBCH principal growth stage 89<br />
<br />
''Add related synonym: grape E-L stage: 38; Berries ripe for harvest''<br />
<br />
<br />
References for grape terms: <br />
<br />
Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00086.x/abstract link]<br />
<br />
Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00085.x/abstract link]<br />
<br />
[http://en.wikipedia.org/wiki/BBCH-scale_%28grape%29 BBCH grapes]<br />
<br />
=Upcoming meetings and Presentations 2012-2013:=<br />
<br />
==[http://phenotypercn.org/ Phenotype RCN meeting], Oct 26-29th 2012==<br />
<br />
Asilomar, CA<br />
<br />
LC is going and has been working with LM to compile EQ statments to describe ~100 rice mutants. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.<br />
<br />
The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are orthologs.<br />
<br />
==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12th - 16th, 2013==<br />
* Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6<br />
<br />
We will be running a workshop focusing on:<br />
<br />
[https://pag.confex.com/pag/xxi/webprogram/Session1596.html Applications of Ontologies for Plant and Animal Genomics]<br />
<br />
Three speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud. <br />
<br />
* PJ present the Ref Plant Ontology Vision? <br />
<br />
* Would like to invite someone from Textpresso and AgriGO as these are applications that would attract a number of people.<br />
<br />
from 9/4- ''PJ: Suggestions- someone from GO in Berkeley, e.g. Nigam Shaw'' <br />
<br />
* Can we offer something to entice the speakers, in addition to the $100 discount on registration offered by the conference?<br />
<br />
* Need to submit list of speakers by November 1, 2012. <br />
<br />
<br />
Deadline for computer demo- Nov 1st<br />
<br />
''I would imagine a SIA demo would be appropriate. - JP''<br />
<br />
==Biocuration 2013 conference, Cambridge, 7-10th April 2013==<br />
<br />
submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.<br />
<br />
possible venue for CROP white paper?<br />
<br />
==PRO-PO-GO meeting, May 2013==<br />
<br />
Location: Buffalo, NY <br />
<br />
Tentative Dates: May 8-9th or May 15-16th, 2013. <br />
<br />
Goals:<br />
# To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination<br />
# To identify potentially fruitful applications which such enhanced coordination might bring <br />
# To enhance the Protein Ontology treatment of plant-related proteins <br />
# To address coordination issues between the GO and PO, for example as concerns treatment of development stages<br />
# To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP] <br />
<br />
<br />
Tentative participant list: <br />
<br />
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others? <br />
<br />
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?<br />
<br />
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)<br />
<br />
<br />
<br />
<br />
=Next meeting scheduled for Tuesday, Oct 16th, 2012 at 10am PDT/1pm EDT=</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_10-9-12&diff=19940POC Conf. Call 10-9-122012-10-09T17:40:23Z<p>Preecej: /* SIA v0.2 Released */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Oct 9th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-2-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
=SIA v0.2 Released=<br />
<br />
Justin Preece has packaged and uploaded a new version of SIA for Mac and Linux (Windows still in progress). This version is fit for public consumption, although it is still very much beta software with lots of opportunity for improvement. Several technical issues have been fixed and a few small enhancements have been made.<br />
<br />
*Our lab site post: http://jaiswallab.cgrb.oregonstate.edu/software#SIA<br />
*Downloads: http://files.cgrb.oregonstate.edu/Jaiswal_Lab/sia/v0.2/<br />
<br />
It would be great if folks on today's call with access to Linux and Mac machines could give the installation instructions a test drive. Feel free to let me know if anything seems amiss. If you want to report any bugs or request new features, just send an email to <sia-support@palea.cgrb.oregonstate.edu><br />
<br />
JP will coordinate the appropriate PO emails and web site announcements with Lol. Thanks!<br />
<br />
=Update from Cornell=<br />
Ale has been in communication with Bob Turgeon and got comments from him on phloem terms. fill in details...<br />
<br />
=Manuscripts in prep=<br />
<br />
=Change to [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 gametophyte development stage]=<br />
This change is urgent, because we need to address this in the manuscript in prep.<br />
<br />
gametophyte development stage (PO:0028003) is currently defined as "A whole plant development stage that has as primary participant a whole plant during the interval between meiosis or apospory and its death ''or fertilization''."<br />
<br />
I think the last part about fertilization is misleading, because it suggests that the gametophyte stage could end in ''any'' plant with fertilization. Many gametophytic plants continue to live (and nourish the sporophyte) long after fertilization. In seed plants, the gametophyte does not exactly die after fertilization, but is transformed. I suggest we add something to the comment to help explain this, but keep the definition simpler.<br />
<br />
'''New proposed definition:''' A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between meiosis or apospory and its death.<br />
<br />
'''New addition to comment (rest stays the same):''' In seed plants, the gametophyte may be transformed by fertilization but not strictly die, such as when pollen (PO:0025281) germinates or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperms.<br />
<br />
=Fruit development stages for whole plants=<br />
==[https://sourceforge.net/tracker/?func=detail&aid=3574905&group_id=76834&atid=835555 whole plant fruit development stage (PO:0025500)]==<br />
New term<br />
<br />
'''proposed defintion:''' A sporophyte reproductive stage that begins when a fruit (PO:0009001) enters a fruit initiation stage (PO:0025503) on a whole plant (PO:0000003) that does not yet have any other fruits as part enters and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.<br />
<br />
Comment: Includes whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage.<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3565057&group_id=76834&atid=835555 whole plant fruit formation stage (PO:0007042)]==<br />
<br />
'''New proposed def.:''' A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends with the onset of a whole plant fruit ripening stage (PO:0007010).<br />
<br />
Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An iteroparous plant will only have one fruit formation stage in its life, while a semelparous plant may have multiple whole plant fruit development stages during its life. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun. Although the use of synonyms like 07-milk stage in rice properly refer to the development of an individual fruits, they are used as here to extrapolate to a whole plant.<br />
<br />
<br />
Is it better to use whole plant fruit formation stage has_part fruit formation stage (new term, see below) or fruit formation stage part_of whole plant fruit formation stage?? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3565059&group_id=76834&atid=835555 whole plant fruit ripening stage (PO:0007010)]==<br />
<br />
'''New proposed def.:''' A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.<br />
<br />
<br />
comment: Succeeds a whole plant fruit formation stage. This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing ripening (which is a type of senescence) during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, followed by a sporophyte senescent stage (PO:0007017), as in case (1). A semelparous species may have one fruit ripening stage for each whole plant fruit developments stage (PO:0025500), followed by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species, a plant may have multiple fruit development stages and in the sporophyte reproductive stage (PO:0007130) after all fruit has ripened, without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of stages like dough stage properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.<br />
<br />
<br />
Is it better to add whole plant fruit ripening stage has_part fruit ripening stage or fruit ripening stage has_part whole plant fruit ripening stage? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.<br />
<br />
=New fruit development stages=<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3573602&group_id=76834&atid=835555 fruit development stage (PO:0001002)]==<br />
def.: A plant structure development stage (PO:0009012) that has as primary participant a single fruit (PO:0009001).<br />
<br />
comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.<br />
<br />
==New proposed subclasses==<br />
''still need to create SF tracker items and add xref to terms''<br />
===fruit formation stage (PO:0025501)===<br />
Proposed def.: A fruit development stage (PO:0001002) that being with the formation of a plant zygote (PO:0000423) and ends when a fruit ripening stage (PO:0025502) begins.<br />
<br />
comment: This stage applies to an individual fruit (PO:0009001). For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage (PO:0007042).<br />
<br />
====new subclasses of fruit formation stage====<br />
These are the stages that were developed for whole plants, but groups like SGN really need to apply them to individual fruits. I also added a new stage for fruit initiation.<br />
<br />
<br />
'''fruit initiation stage (PO:0025503)''': A fruit formation stage (PO:0025501) that begins with the formation of a plant zygote (PO:0000423) and ends as soon as the fruit (PO:0009001) starts to grow.<br />
<br />
Comment: The fruit initiation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage ends as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).<br />
<br />
<br />
'''fruit size up to 10% stage (PO:0025504):''' A fruit formation stage (PO:0025501) that begins after a fruit initiation stage (PO:0025503), and ends when the fruit (PO:0009001) has reached 10% of its final size.<br />
<br />
Comment: Begins as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. Succeeds a fruit initiation stage (PO:0025503) and proceeds a fruit size 10 to 30% stage (PO:0025505). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).<br />
<br />
<br />
'''fruit size 10 to 30% stage (PO:0025505):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 10% to 30% of its final size.<br />
<br />
Comment: Succeeds a fruit size up to 10% stage (PO:0025504) and proceeds a fruit size 30 to 50% stage (PO:0025506). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 10 to 30% (PO:0007009).<br />
<br />
<br />
'''fruit size 30 to 50% stage (PO:0025506):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 30 to 50% of its final size.<br />
<br />
Comment: Succeeds a fruit size 10 to 30% stage (PO:0025505) and proceeds a fruit size 50 to 70% stage (PO:0025507). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 30 to 50% (PO:0007029).<br />
<br />
<br />
'''fruit size 50 to 70% stage (PO:0025507):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 50 to 70% of its final size.<br />
<br />
Comment: Succeeds a fruit size 30 to 50% stage (PO:0025505) and proceeds a fruit size 70% to final size stage (PO:0025508). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 50 to 70% (PO:0007007).<br />
<br />
<br />
'''fruit size 70% to final size stage (PO:0025508):''' A fruit formation stage (PO:0025501) that spans begins when a fruit (PO:0009001) has reached 70% of its final size and ends when a fruit has reached its final size and a fruit ripening stage (PO:0025502) begins.<br />
<br />
Comment: Succeeds a fruit size 50 to 70% stage (PO:0025507) and proceeds a fruit ripening stage. This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 70% to final size (PO:0007027).<br />
<br />
===fruit ripening stage===<br />
Proposed def.: A fruit development stage (PO:0001002) during which a fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).<br />
<br />
Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).<br />
<br />
=Subclasses of whole plant fruit formation stage (PO:0007042)=<br />
See SF tracker for [https://sourceforge.net/tracker/index.php?func=detail&aid=3374186&group_id=76834&atid=835555 FF.00 fruit size 10% and sibling terms]<br />
<br />
<br />
At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.<br />
<br />
''What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of there existing annotations and move them to fruit development stage and its new subtypes as necessary.''<br />
<br />
====FF.00 fruit size up to 10% stage (PO:0007032)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage up to 10%:''' A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% of final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504). <br />
<br />
====FF.01 fruit size 10 to 30% stage (PO:0007009)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 10 to 30%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505). <br />
<br />
====FF.02 fruit size 30 to 50% stage (PO:0007029)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 30 to 50%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 30 to 50% stage (PO:0025506). <br />
<br />
====FF.03 fruit size 50 to 70% stage (PO:0007007)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 50 to 70%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 50 to 70% stage (PO:0025507).<br />
<br />
====FF.04 fruit size 70% to final size stage (PO:0007027)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 70% to final size:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.<br />
<br />
comment: Succeeded by a whole plant fruit ripening stage (PO:0007010). This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 70% to final size stage (PO:0025508).<br />
<br />
related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79<br />
<br />
==Add new synonyms for grapes==<br />
<br />
''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch''<br />
<br />
''Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)''<br />
<br />
''Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)''<br />
<br />
''Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)''<br />
<br />
=Subclasses of whole plant fruit ripening stage (PO:0007010)=<br />
<br />
The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.<br />
<br />
==FR.00 beginning of fruit ripening stage (PO:0007036)==<br />
current def.: The stage at which fruit maturation begins.<br />
<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant beginning of fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
<br />
''Add related synonym: BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour<br />
<br />
''Add related synonym: grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison ''<br />
<br />
==FR.01 early stage of fruit ripening (PO:0007001)==<br />
current def.: The early stage in fruit ripening<br />
<br />
related synonym: BBCH principal growth stage 83<br />
<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant early fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
''Add related synonym: middle of veraison''<br />
<br />
==FR.02 mid stage of fruit ripening (PO:0007031)==<br />
current def.: The stage when fruit ripening is midway.<br />
<br />
'''whole plant mid fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
==FR.03 late stage of fruit ripening (PO:0007050)==<br />
current def.: The late stage of fruit ripening.<br />
<br />
'''whole plant late fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
==FR.04 fruit ripening complete stage (PO:0007038)==<br />
current def.: The stage at which fruit ripening is complete.<br />
<br />
'''whole plant fruit ripening complete stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
related synonym: BBCH principal growth stage 89<br />
<br />
''Add related synonym: grape E-L stage: 38; Berries ripe for harvest''<br />
<br />
<br />
References for grape terms: <br />
<br />
Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00086.x/abstract link]<br />
<br />
Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00085.x/abstract link]<br />
<br />
[http://en.wikipedia.org/wiki/BBCH-scale_%28grape%29 BBCH grapes]<br />
<br />
=Upcoming meetings and Presentations 2012-2013:=<br />
<br />
==[http://phenotypercn.org/ Phenotype RCN meeting], Oct 26-29th 2012==<br />
<br />
Asilomar, CA<br />
<br />
LC is going and has been working with LM to compile EQ statments to describe ~100 rice mutants. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.<br />
<br />
The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are orthologs.<br />
<br />
==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12th - 16th, 2013==<br />
* Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6<br />
<br />
We will be running a workshop focusing on:<br />
<br />
[https://pag.confex.com/pag/xxi/webprogram/Session1596.html Applications of Ontologies for Plant and Animal Genomics]<br />
<br />
Three speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud. <br />
<br />
* PJ present the Ref Plant Ontology Vision? <br />
<br />
* Would like to invite someone from Textpresso and AgriGO as these are applications that would attract a number of people.<br />
<br />
from 9/4- ''PJ: Suggestions- someone from GO in Berkeley, e.g. Nigam Shaw'' <br />
<br />
* Can we offer something to entice the speakers, in addition to the $100 discount on registration offered by the conference?<br />
<br />
* Need to submit list of speakers by November 1, 2012. <br />
<br />
<br />
Deadline for computer demo- Nov 1st<br />
<br />
''I would imagine a SIA demo would be appropriate. - JP''<br />
<br />
==Biocuration 2013 conference, Cambridge, 7-10th April 2013==<br />
<br />
submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.<br />
<br />
possible venue for CROP white paper?<br />
<br />
==PRO-PO-GO meeting, May 2013==<br />
<br />
Location: Buffalo, NY <br />
<br />
Tentative Dates: May 8-9th or May 15-16th, 2013. <br />
<br />
Goals:<br />
# To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination<br />
# To identify potentially fruitful applications which such enhanced coordination might bring <br />
# To enhance the Protein Ontology treatment of plant-related proteins <br />
# To address coordination issues between the GO and PO, for example as concerns treatment of development stages<br />
# To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP] <br />
<br />
<br />
Tentative participant list: <br />
<br />
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others? <br />
<br />
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?<br />
<br />
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)<br />
<br />
<br />
<br />
<br />
=Next meeting scheduled for Tuesday, Oct 16th, 2012 at 10am PDT/1pm EDT=</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_10-9-12&diff=19936POC Conf. Call 10-9-122012-10-09T17:37:43Z<p>Preecej: </p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Oct 9th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_10-2-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
=SIA v0.2 Released=<br />
<br />
Justin Preece has packaged and uploaded a new version of SIA for Mac and Linux (Windows still in progress). This version is fit for public consumption, although it is still very much beta software with lots of opportunity for improvement. Several technical issues have been fixed and a few small enhancements have been made.<br />
<br />
*:Our lab site post: http://jaiswallab.cgrb.oregonstate.edu/software#SIA<br />
*:Downloads: http://files.cgrb.oregonstate.edu/Jaiswal_Lab/sia/v0.2/<br />
<br />
It would be great if folks on today's call with access to Linux and Mac machines could give the installation instructions a test drive. Feel free to let me know if anything seems amiss. If you want to report any bugs or request new features, just send an email to <sia-support@palea.cgrb.oregonstate.edu><br />
<br />
JP will coordinate the appropriate PO emails and web site announcements with Lol. Thanks!<br />
<br />
=Update from Cornell=<br />
Ale has been in communication with Bob Turgeon and got comments from him on phloem terms. fill in details...<br />
<br />
=Manuscripts in prep=<br />
<br />
=Change to [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 gametophyte development stage]=<br />
This change is urgent, because we need to address this in the manuscript in prep.<br />
<br />
gametophyte development stage (PO:0028003) is currently defined as "A whole plant development stage that has as primary participant a whole plant during the interval between meiosis or apospory and its death ''or fertilization''."<br />
<br />
I think the last part about fertilization is misleading, because it suggests that the gametophyte stage could end in ''any'' plant with fertilization. Many gametophytic plants continue to live (and nourish the sporophyte) long after fertilization. In seed plants, the gametophyte does not exactly die after fertilization, but is transformed. I suggest we add something to the comment to help explain this, but keep the definition simpler.<br />
<br />
'''New proposed definition:''' A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between meiosis or apospory and its death.<br />
<br />
'''New addition to comment (rest stays the same):''' In seed plants, the gametophyte may be transformed by fertilization but not strictly die, such as when pollen (PO:0025281) germinates or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperms.<br />
<br />
=Fruit development stages for whole plants=<br />
==[https://sourceforge.net/tracker/?func=detail&aid=3574905&group_id=76834&atid=835555 whole plant fruit development stage (PO:0025500)]==<br />
New term<br />
<br />
'''proposed defintion:''' A sporophyte reproductive stage that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.<br />
<br />
Comment: Includes whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage.<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3565057&group_id=76834&atid=835555 whole plant fruit formation stage (PO:0007042)]==<br />
<br />
'''New proposed def.:''' A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends with the onset of a whole plant fruit ripening stage (PO:0007010).<br />
<br />
Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An iteroparous plant will only have one fruit formation stage in its life, while a semelparous plant may have multiple whole plant fruit development stages during its life. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun. Although the use of synonyms like 07-milk stage in rice properly refer to the development of an individual fruits, they are used as here to extrapolate to a whole plant.<br />
<br />
<br />
Is it better to use whole plant fruit formation stage has_part fruit formation stage (new term, see below) or fruit formation stage part_of whole plant fruit formation stage?? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3565059&group_id=76834&atid=835555 whole plant fruit ripening stage (PO:0007010)]==<br />
<br />
'''New proposed def.:''' A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.<br />
<br />
<br />
comment: Succeeds a whole plant fruit formation stage. This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing ripening (which is a type of senescence) during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, followed by a sporophyte senescent stage (PO:0007017), as in case (1). A semelparous species may have one fruit ripening stage for each whole plant fruit developments stage (PO:0025500), followed by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species, a plant may have multiple fruit development stages and in the sporophyte reproductive stage (PO:0007130) after all fruit has ripened, without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of stages like dough stage properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.<br />
<br />
<br />
Is it better to add whole plant fruit ripening stage has_part fruit ripening stage or fruit ripening stage has_part whole plant fruit ripening stage? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.<br />
<br />
=New fruit development stages=<br />
<br />
==[http://sourceforge.net/tracker/?func=detail&aid=3573602&group_id=76834&atid=835555 fruit development stage (PO:0001002)]==<br />
def.: A plant structure development stage (PO:0009012) that has as primary participant a single fruit (PO:0009001).<br />
<br />
comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.<br />
<br />
==New proposed subclasses==<br />
''still need to create SF tracker items and add xref to terms''<br />
===fruit formation stage (PO:0025501)===<br />
Proposed def.: A fruit development stage (PO:0001002) that being with the formation of a plant zygote (PO:0000423) and ends when a fruit ripening stage (PO:0025502) begins.<br />
<br />
comment: This stage applies to an individual fruit (PO:0009001). For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage (PO:0007042).<br />
<br />
====new subclasses of fruit formation stage====<br />
These are the stages that were developed for whole plants, but groups like SGN really need to apply them to individual fruits. I also added a new stage for fruit initiation.<br />
<br />
<br />
'''fruit initiation stage (PO:0025503)''': A fruit formation stage (PO:0025501) that begins with the formation of a plant zygote (PO:0000423) and ends as soon as the fruit (PO:0009001) starts to grow.<br />
<br />
Comment: The fruit initiation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage ends as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).<br />
<br />
<br />
'''fruit size up to 10% stage (PO:0025504):''' A fruit formation stage (PO:0025501) that begins after a fruit initiation stage (PO:0025503), and ends when the fruit (PO:0009001) has reached 10% of its final size.<br />
<br />
Comment: Begins as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. Succeeds a fruit initiation stage (PO:0025503) and proceeds a fruit size 10 to 30% stage (PO:0025505). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).<br />
<br />
<br />
'''fruit size 10 to 30% stage (PO:0025505):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 10% to 30% of its final size.<br />
<br />
Comment: Succeeds a fruit size up to 10% stage (PO:0025504) and proceeds a fruit size 30 to 50% stage (PO:0025506). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 10 to 30% (PO:0007009).<br />
<br />
<br />
'''fruit size 30 to 50% stage (PO:0025506):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 30 to 50% of its final size.<br />
<br />
Comment: Succeeds a fruit size 10 to 30% stage (PO:0025505) and proceeds a fruit size 50 to 70% stage (PO:0025507). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 30 to 50% (PO:0007029).<br />
<br />
<br />
'''fruit size 50 to 70% stage (PO:0025507):''' A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 50 to 70% of its final size.<br />
<br />
Comment: Succeeds a fruit size 30 to 50% stage (PO:0025505) and proceeds a fruit size 70% to final size stage (PO:0025508). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 50 to 70% (PO:0007007).<br />
<br />
<br />
'''fruit size 70% to final size stage (PO:0025508):''' A fruit formation stage (PO:0025501) that spans begins when a fruit (PO:0009001) has reached 70% of its final size and ends when a fruit has reached its final size and a fruit ripening stage (PO:0025502) begins.<br />
<br />
Comment: Succeeds a fruit size 50 to 70% stage (PO:0025507) and proceeds a fruit ripening stage. This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 70% to final size (PO:0007027).<br />
<br />
===fruit ripening stage===<br />
Proposed def.: A fruit development stage (PO:0001002) during which a fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).<br />
<br />
Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).<br />
<br />
=Subclasses of whole plant fruit formation stage (PO:0007042)=<br />
See SF tracker for [https://sourceforge.net/tracker/index.php?func=detail&aid=3374186&group_id=76834&atid=835555 FF.00 fruit size 10% and sibling terms]<br />
<br />
<br />
At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.<br />
<br />
''What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of there existing annotations and move them to fruit development stage and its new subtypes as necessary.''<br />
<br />
====FF.00 fruit size up to 10% stage (PO:0007032)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage up to 10%:''' A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% of final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504). <br />
<br />
====FF.01 fruit size 10 to 30% stage (PO:0007009)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 10 to 30%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505). <br />
<br />
====FF.02 fruit size 30 to 50% stage (PO:0007029)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 30 to 50%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 30 to 50% stage (PO:0025506). <br />
<br />
====FF.03 fruit size 50 to 70% stage (PO:0007007)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 50 to 70%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 50 to 70% stage (PO:0025507).<br />
<br />
====FF.04 fruit size 70% to final size stage (PO:0007027)====<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant fruit formation stage 70% to final size:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.<br />
<br />
comment: Succeeded by a whole plant fruit ripening stage (PO:0007010). This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 70% to final size stage (PO:0025508).<br />
<br />
related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79<br />
<br />
==Add new synonyms for grapes==<br />
<br />
''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch''<br />
<br />
''Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)''<br />
<br />
''Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)''<br />
<br />
''Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)''<br />
<br />
=Subclasses of whole plant fruit ripening stage (PO:0007010)=<br />
<br />
The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.<br />
<br />
==FR.00 beginning of fruit ripening stage (PO:0007036)==<br />
current def.: The stage at which fruit maturation begins.<br />
<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant beginning of fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
<br />
''Add related synonym: BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour<br />
<br />
''Add related synonym: grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison ''<br />
<br />
==FR.01 early stage of fruit ripening (PO:0007001)==<br />
current def.: The early stage in fruit ripening<br />
<br />
related synonym: BBCH principal growth stage 83<br />
<br />
'''proposed new name and definition:''' <br />
<br />
'''whole plant early fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
''Add related synonym: middle of veraison''<br />
<br />
==FR.02 mid stage of fruit ripening (PO:0007031)==<br />
current def.: The stage when fruit ripening is midway.<br />
<br />
'''whole plant mid fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
==FR.03 late stage of fruit ripening (PO:0007050)==<br />
current def.: The late stage of fruit ripening.<br />
<br />
'''whole plant late fruit ripening stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
==FR.04 fruit ripening complete stage (PO:0007038)==<br />
current def.: The stage at which fruit ripening is complete.<br />
<br />
'''whole plant fruit ripening complete stage:''' A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.<br />
<br />
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.<br />
<br />
related synonym: BBCH principal growth stage 89<br />
<br />
''Add related synonym: grape E-L stage: 38; Berries ripe for harvest''<br />
<br />
<br />
References for grape terms: <br />
<br />
Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00086.x/abstract link]<br />
<br />
Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00085.x/abstract link]<br />
<br />
[http://en.wikipedia.org/wiki/BBCH-scale_%28grape%29 BBCH grapes]<br />
<br />
=Upcoming meetings and Presentations 2012-2013:=<br />
<br />
==[http://phenotypercn.org/ Phenotype RCN meeting], Oct 26-29th 2012==<br />
<br />
Asilomar, CA<br />
<br />
LC is going and has been working with LM to compile EQ statments to describe ~100 rice mutants. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.<br />
<br />
The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are orthologs.<br />
<br />
==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12th - 16th, 2013==<br />
* Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6<br />
<br />
We will be running a workshop focusing on:<br />
<br />
[https://pag.confex.com/pag/xxi/webprogram/Session1596.html Applications of Ontologies for Plant and Animal Genomics]<br />
<br />
Three speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud. <br />
<br />
* PJ present the Ref Plant Ontology Vision? <br />
<br />
* Would like to invite someone from Textpresso and AgriGO as these are applications that would attract a number of people.<br />
<br />
from 9/4- ''PJ: Suggestions- someone from GO in Berkeley, e.g. Nigam Shaw'' <br />
<br />
* Can we offer something to entice the speakers, in addition to the $100 discount on registration offered by the conference?<br />
<br />
* Need to submit list of speakers by November 1, 2012. <br />
<br />
<br />
Deadline for computer demo- Nov 1st<br />
<br />
''I would imagine a SIA demo would be appropriate. - JP''<br />
<br />
==Biocuration 2013 conference, Cambridge, 7-10th April 2013==<br />
<br />
submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.<br />
<br />
possible venue for CROP white paper?<br />
<br />
==PRO-PO-GO meeting, May 2013==<br />
<br />
Location: Buffalo, NY <br />
<br />
Tentative Dates: May 8-9th or May 15-16th, 2013. <br />
<br />
Goals:<br />
# To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination<br />
# To identify potentially fruitful applications which such enhanced coordination might bring <br />
# To enhance the Protein Ontology treatment of plant-related proteins <br />
# To address coordination issues between the GO and PO, for example as concerns treatment of development stages<br />
# To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP] <br />
<br />
<br />
Tentative participant list: <br />
<br />
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others? <br />
<br />
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?<br />
<br />
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)<br />
<br />
<br />
<br />
<br />
=Next meeting scheduled for Tuesday, Oct 16th, 2012 at 10am PDT/1pm EDT=</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_9-25-12&diff=19688POC Conf. Call 9-25-122012-09-25T17:29:24Z<p>Preecej: /* PAG 2013, San Diego, CA; January 12-16, 2013 */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Sept 25th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
Collaborators: none<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_9-04-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
=Recent Meeting reports=<br />
<br />
==NSF Plant Genome PIs Meeting==<br />
Arlington, VA, September 6-7, 2012<br />
<br />
PJ presented a 2 pager and poster<br />
<br />
==[https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296 Genome Informatics 2012]==<br />
September 6th-9th <br />
Robinson College, Cambridge, UK<br />
<br />
JP attended and submitted a poster representing the PO<br />
<br />
* made contact with Remco Ursem (bioinformatics @ Rijk Zwaan - Dutch vegetable and seed company); he is interested in PO<br />
* conference was tilted towards biomedical and mammalian research<br />
* lots of buzz about the ENCODE release and its implications for changing research methods in other organisms<br />
*: [http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html ENCODE Summary Paper]<br />
*: "The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions."<br />
* interesting talks:<br />
** Josh Stein (Gramene) - iPlant Discovery Environment (data cloud and analysis applications)<br />
** Dick McCombie - next-gen sequence assembly for plants, emphasis on merging data from multiple sequencing platforms (long-read MiSeq and PacBio, short-read HiSeq) prior to assembly<br />
** Pavel Pezner: new de Bruijn graph assembly model utilizing an extra dimension of network relatedness (represented by color); built for single-cell assembly<br />
** a couple of talks about single-cell sequencing; there seems to be growing interest in that approach<br />
<br />
==PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012==<br />
For more information see the wiki page: [[Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012]]<br />
<br />
Crop Plant Trait Ontology Workshop OSU, Sept. 13-15th, 2012<br />
<br />
The Plant Ontology and the Trait Ontology, along with EBI/TransPlant, GARNet (BBSRC) and the Generation Challenge Program hosted the Crop Plant Trait Ontology Workshop from September 13th-15th 2012 at Oregon State University.<br />
Co-organized with representatives from SGN, SOYbase, maizeGDB and many other groups.<br />
<br />
Plant breeders, biologists and bioinformatics specialists from ten countries, seven US states and representatives from two plant agribusinesses- Syngenta and Monsanto, gathered in Corvallis for a workshop on the latest developments in and broad discussion of the need for a coordinated effort to develop and extend the plant and trait ontologies to describe the anatomy and traits of agronomic importance to major crops cultivated world wide.<br />
<br />
<br />
The goal of this workshop was to widen the awareness and participation of the plant breeding community in the use of ontologies, and to create a semantic framework for meaningful cross-species queries using a common reference ontology for plants. <br />
<br />
* Guest speakers Melissa Haendel; (Ontology Development Group, OHSU Library and Barry Smith (OBO Foundry)<br />
<br />
* Participants engaged in hands-on activities, learning to use the ontology editor OBO-Edit and working in small groups to classify plant trait term requests which had been submitted.<br />
<br />
Outcomes: <br />
<br />
-preparing a short new item for circulation<br />
<br />
-preparing a "vision/white paper" to focus on the ref plant onotlogy concept<br />
<br />
-follow up meeting will occur at PAG 2013, along with Ontology workshop<br />
<br />
-Many new and enhanced collaborations<br />
<br />
=Update from Cornell=<br />
Added 25 more slides and 500 more images to the CUPAC database<br />
<br />
MAG and RW started adding keywords in the last week of August, and came up with a way to add PO's to all the images then link them to the PO pages, but it will probably be a few weeks before Kevin is able to implement the links.<br />
<br />
==Cont. from last meeting:==<br />
===Upper level term: 5 fruit formation stage (PO:0007042)===<br />
current def.: Formation of the seed-bearing structure after flowering.<br />
<br />
'''new name and definition, from last meeting:''' <br />
<br />
'''[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3565057&group_id=76834 whole plant fruit formation stage] (PO:0007042):''' A sporophyte reproductive stage (PO:0007130) that begins with the initiation of the first fruit (PO:0009001) of a growing season and ends with the beginning of a whole plant fruit ripening stage (PO:0007010)..<br />
<br />
Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit formation stage in its life, while a perennial may have one fruit formation stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun.<br />
<br />
''has_part'' fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)<br />
<br />
subset for angiosperms<br />
<br />
Discussion and comments:<br />
<br />
''Maybe refer to initiation of first fruit ripening, instead of fruit ripening stage?''<br />
<br />
''Some discussion of this as a population measure: If you want to apply this to a population, you may choose the point when, e.g., 50% of the plants have initiated fruit. BS suggested that this should be defined for an individual plant, and have population terms defined separately.''<br />
<br />
''Initiation of the first fruit begins with fertilization (formation of zygote). This can be defined more clearly in fruit development stages, then refer to those in these definitions.''<br />
<br />
''For gymnosperms, we could have terms like whole plant strobilus development stage. Seed development stage should apply to gymnos as well as angiosperms.''<br />
<br />
''Do we want a parent for both of these terms: "whole plant fruit development stage"? This would match more closely to fruit development stage (PO:0001002).''<br />
<br />
<br />
===Upper level term: 6 ripening stage (PO:0007010)===<br />
current def.: Maturation of the fruit.<br />
<br />
'''proposed new name and definition from last meeting:''' <br />
<br />
'''[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3565059&group_id=76834 whole plant fruit ripening stage] (PO:0007042):''' A sporophyte reproductive stage (PO:0007130) during which a fruit (PO:0009001) on a whole plant (PO:0000003) is undergoing ripening (GO:0009835).<br />
<br />
comment: This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit ripening stage in its life, which is generally followed by a sporophyte senescent stage (PO:0007017), while a perennial may have one fruit ripening stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant has begun.<br />
<br />
<br />
''has_part'' fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)<br />
<br />
subset for angiosperms<br />
<br />
GO:ripening is defined as a type of senescence. Should the term ripening be used only for fleshy fruits? Fruit drying also probably involves cell death, so perhaps it is type of ripening as well.<br />
<br />
''Add comment that ripening is a type of senescence and a comment to distinguish this stage from senescent stage of whole plant.''<br />
<br />
<br />
''Note: the different fruits on a plant may be in different stages, but the whole plant can only be in one stage.''<br />
<br />
''When does the ripening stage end? For annuals, ripening stage is followed by senescence of whole plant in annuals, but for perennials, maybe different. We need to incorporate this into the definition.''<br />
<br />
''PJ: Some pear varieties do not ripen on the plant. Have to be picked and treated. In that case, the plant never enters the whole plant fruit ripening stage, but the individual fruits to.''<br />
<br />
''We be good to tie this to seed development. Make the connection as part of the fruit development stages, and then link fruit stages to whole plant stages. Seeds may regulate development of fruit. Interaction between progeny and maternal tissue.''<br />
<br />
=Upcoming meetings and Presentations 2012-2013:=<br />
<br />
<br />
==[http://phenotypercn.org/ Phenotype RCN meeting], Oct 26-29th 2012==<br />
<br />
Asilomar, CA<br />
<br />
LC is going and has been working with LM to compile EQ statemnts to describe ~100 rice mutants. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.<br />
<br />
Will be combining the mutants with similar E and Q and looking at the genes and if they are othologs.<br />
<br />
==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12-16, 2013==<br />
* Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6<br />
<br />
We will be running a workshop focusing on:<br />
<br />
[https://pag.confex.com/pag/xxi/webprogram/Session1596.html Applications of Ontologies for Plant and Animal Genomics]<br />
<br />
Three speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud. PJ present the Ref Plant Ontology Vision? <br />
<br />
* Would like to invite someone from Textpresso and AgiGO. <br />
<br />
''PJ: Suggestions- someone from GO in Berkeley, Nigam Shaw'' <br />
<br />
* Can we offer something to entice the speakers, in addition to the $100 discount on registration offered by the conference?<br />
<br />
* Need to submit list of speakers by November 1, 2012. <br />
<br />
''PJ will check with DW about Gramene involvement''<br />
<br />
Deadline for computer demo- Nov 1st<br />
<br />
:''I would imagine a SIA demo would be appropriate. - JP''<br />
<br />
==PRO-PO-GO meeting, ~May 2013==<br />
<br />
Location: Buffalo, NY <br />
<br />
Goals:<br />
<br />
# To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination<br />
# To identify potentially fruitful applications which such enhanced coordination might bring <br />
# To enhance the Protein Ontology treatment of plant-related proteins <br />
# To address coordination issues between the GO and PO, for example as concerns treatment of development stages<br />
# To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP] <br />
<br />
<br />
Tentative participant list: <br />
<br />
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others? <br />
<br />
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?<br />
<br />
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_9-25-12&diff=19687POC Conf. Call 9-25-122012-09-25T17:19:07Z<p>Preecej: /* Genome Informatics 2012 */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Sept 25th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
Collaborators: none<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_9-04-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
=Recent Meeting reports=<br />
<br />
==NSF Plant Genome PIs Meeting==<br />
Arlington, VA, September 6-7, 2012<br />
<br />
PJ presented a 2 pager and poster<br />
<br />
==[https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296 Genome Informatics 2012]==<br />
September 6th-9th <br />
Robinson College, Cambridge, UK<br />
<br />
JP attended and submitted a poster representing the PO<br />
<br />
* made contact with Remco Ursem (bioinformatics @ Rijk Zwaan - Dutch vegetable and seed company); he is interested in PO<br />
* conference was tilted towards biomedical and mammalian research<br />
* lots of buzz about the ENCODE release and its implications for changing research methods in other organisms<br />
*: [http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html ENCODE Summary Paper]<br />
*: "The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions."<br />
* interesting talks:<br />
** Josh Stein (Gramene) - iPlant Discovery Environment (data cloud and analysis applications)<br />
** Dick McCombie - next-gen sequence assembly for plants, emphasis on merging data from multiple sequencing platforms (long-read MiSeq and PacBio, short-read HiSeq) prior to assembly<br />
** Pavel Pezner: new de Bruijn graph assembly model utilizing an extra dimension of network relatedness (represented by color); built for single-cell assembly<br />
** a couple of talks about single-cell sequencing; there seems to be growing interest in that approach<br />
<br />
==PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012==<br />
For more information see the wiki page: [[Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012]]<br />
<br />
Crop Plant Trait Ontology Workshop OSU, Sept. 13-15th, 2012<br />
<br />
The Plant Ontology and the Trait Ontology, along with EBI/TransPlant, GARNet (BBSRC) and the Generation Challenge Program hosted the Crop Plant Trait Ontology Workshop from September 13th-15th 2012 at Oregon State University.<br />
Co-organized with representatives from SGN, SOYbase, maizeGDB and many other groups.<br />
<br />
Plant breeders, biologists and bioinformatics specialists from ten countries, seven US states and representatives from two plant agribusinesses- Syngenta and Monsanto, gathered in Corvallis for a workshop on the latest developments in and broad discussion of the need for a coordinated effort to develop and extend the plant and trait ontologies to describe the anatomy and traits of agronomic importance to major crops cultivated world wide.<br />
<br />
<br />
The goal of this workshop was to widen the awareness and participation of the plant breeding community in the use of ontologies, and to create a semantic framework for meaningful cross-species queries using a common reference ontology for plants. <br />
<br />
* Guest speakers Melissa Haendel; (Ontology Development Group, OHSU Library and Barry Smith (OBO Foundry)<br />
<br />
* Participants engaged in hands-on activities, learning to use the ontology editor OBO-Edit and working in small groups to classify plant trait term requests which had been submitted.<br />
<br />
Outcomes: <br />
<br />
-preparing a short new item for circulation<br />
<br />
-preparing a "vision/white paper" to focus on the ref plant onotlogy concept<br />
<br />
-follow up meeting will occur at PAG 2013, along with Ontology workshop<br />
<br />
-Many new and enhanced collaborations<br />
<br />
=Update from Cornell=<br />
Added 25 more slides and 500 more images to the CUPAC database<br />
<br />
MAG and RW started adding keywords in the last week of August, and came up with a way to add PO's to all the images then link them to the PO pages, but it will probably be a few weeks before Kevin is able to implement the links.<br />
<br />
==Cont. from last meeting:==<br />
===Upper level term: 5 fruit formation stage (PO:0007042)===<br />
current def.: Formation of the seed-bearing structure after flowering.<br />
<br />
'''new name and definition, from last meeting:''' <br />
<br />
'''[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3565057&group_id=76834 whole plant fruit formation stage] (PO:0007042):''' A sporophyte reproductive stage (PO:0007130) that begins with the initiation of the first fruit (PO:0009001) of a growing season and ends with the beginning of a whole plant fruit ripening stage (PO:0007010)..<br />
<br />
Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit formation stage in its life, while a perennial may have one fruit formation stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun.<br />
<br />
''has_part'' fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)<br />
<br />
subset for angiosperms<br />
<br />
Discussion and comments:<br />
<br />
''Maybe refer to initiation of first fruit ripening, instead of fruit ripening stage?''<br />
<br />
''Some discussion of this as a population measure: If you want to apply this to a population, you may choose the point when, e.g., 50% of the plants have initiated fruit. BS suggested that this should be defined for an individual plant, and have population terms defined separately.''<br />
<br />
''Initiation of the first fruit begins with fertilization (formation of zygote). This can be defined more clearly in fruit development stages, then refer to those in these definitions.''<br />
<br />
''For gymnosperms, we could have terms like whole plant strobilus development stage. Seed development stage should apply to gymnos as well as angiosperms.''<br />
<br />
''Do we want a parent for both of these terms: "whole plant fruit development stage"? This would match more closely to fruit development stage (PO:0001002).''<br />
<br />
<br />
===Upper level term: 6 ripening stage (PO:0007010)===<br />
current def.: Maturation of the fruit.<br />
<br />
'''proposed new name and definition from last meeting:''' <br />
<br />
'''[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3565059&group_id=76834 whole plant fruit ripening stage] (PO:0007042):''' A sporophyte reproductive stage (PO:0007130) during which a fruit (PO:0009001) on a whole plant (PO:0000003) is undergoing ripening (GO:0009835).<br />
<br />
comment: This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit ripening stage in its life, which is generally followed by a sporophyte senescent stage (PO:0007017), while a perennial may have one fruit ripening stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant has begun.<br />
<br />
<br />
''has_part'' fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)<br />
<br />
subset for angiosperms<br />
<br />
GO:ripening is defined as a type of senescence. Should the term ripening be used only for fleshy fruits? Fruit drying also probably involves cell death, so perhaps it is type of ripening as well.<br />
<br />
''Add comment that ripening is a type of senescence and a comment to distinguish this stage from senescent stage of whole plant.''<br />
<br />
<br />
''Note: the different fruits on a plant may be in different stages, but the whole plant can only be in one stage.''<br />
<br />
''When does the ripening stage end? For annuals, ripening stage is followed by senescence of whole plant in annuals, but for perennials, maybe different. We need to incorporate this into the definition.''<br />
<br />
''PJ: Some pear varieties do not ripen on the plant. Have to be picked and treated. In that case, the plant never enters the whole plant fruit ripening stage, but the individual fruits to.''<br />
<br />
''We be good to tie this to seed development. Make the connection as part of the fruit development stages, and then link fruit stages to whole plant stages. Seeds may regulate development of fruit. Interaction between progeny and maternal tissue.''<br />
<br />
=Upcoming meetings and Presentations 2012-2013:=<br />
<br />
<br />
==[http://phenotypercn.org/ Phenotype RCN meeting], Oct 26-29th 2012==<br />
<br />
Asilomar, CA<br />
<br />
LC is going and has been working with LM to compile EQ statemnts to describe ~100 rice mutants. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.<br />
<br />
Will be combining the mutants with similar E and Q and looking at the genes and if they are othologs.<br />
<br />
==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12-16, 2013==<br />
* Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6<br />
<br />
We will be running a workshop focusing on:<br />
<br />
[https://pag.confex.com/pag/xxi/webprogram/Session1596.html Applications of Ontologies for Plant and Animal Genomics]<br />
<br />
Three speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud. PJ present the Ref Plant Ontology Vision? <br />
<br />
* Would like to invite someone from Textpresso and AgiGO. <br />
<br />
''PJ: Suggestions- someone from GO in Berkeley, Nigam Shaw'' <br />
<br />
* Can we offer something to entice the speakers, in addition to the $100 discount on registration offered by the conference?<br />
<br />
* Need to submit list of speakers by November 1, 2012. <br />
<br />
''PJ will check with DW about Gramene involvement''<br />
<br />
Deadline for computer demo- Nov 1st<br />
<br />
==PRO-PO-GO meeting, ~May 2013==<br />
<br />
Location: Buffalo, NY <br />
<br />
Goals:<br />
<br />
# To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination<br />
# To identify potentially fruitful applications which such enhanced coordination might bring <br />
# To enhance the Protein Ontology treatment of plant-related proteins <br />
# To address coordination issues between the GO and PO, for example as concerns treatment of development stages<br />
# To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP] <br />
<br />
<br />
Tentative participant list: <br />
<br />
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others? <br />
<br />
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?<br />
<br />
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_9-25-12&diff=19686POC Conf. Call 9-25-122012-09-25T16:52:52Z<p>Preecej: /* Genome Informatics 2012 */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Sept 25th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
Collaborators: none<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_9-04-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
=Recent Meeting reports=<br />
<br />
==NSF Plant Genome PIs Meeting==<br />
Arlington, VA, September 6-7, 2012<br />
<br />
PJ presented a 2 pager and poster<br />
<br />
==[https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296 Genome Informatics 2012]==<br />
September 6th-9th <br />
Robinson College, Cambridge, UK<br />
<br />
JP attended and submitted a poster representing the PO<br />
<br />
* made contact with Remco Ursem (bioinformatics @ Rijk Zwaan - Dutch vegetable and seed company); he is interested in PO<br />
* conference was tilted towards biomedical and mammalian research<br />
* lots of buzz about the ENCODE release and its implications for changing research methods in other organisms<br />
* interesting talks:<br />
** Josh Stein (Gramene) - iPlant Discovery Environment (data cloud and analysis applications)<br />
** Dick McCombie - next-gen sequence assembly for plants, emphasis on merging data from multiple sequencing platforms (long-read MiSeq and PacBio, short-read HiSeq) prior to assembly<br />
** Pavel Pezner: new de Bruijn graph assembly model utilizing an extra dimension of network relatedness (represented by color); built for single-cell assembly<br />
** a couple of talks about single-cell sequencing; there seems to be growing interest in that approach<br />
<br />
==PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012==<br />
For more information see the wiki page: [[Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012]]<br />
<br />
Crop Plant Trait Ontology Workshop OSU, Sept. 13-15th, 2012<br />
<br />
The Plant Ontology and the Trait Ontology, along with EBI/TransPlant, GARNet (BBSRC) and the Generation Challenge Program hosted the Crop Plant Trait Ontology Workshop from September 13th-15th 2012 at Oregon State University.<br />
Co-organized with representatives from SGN, SOYbase, maizeGDB and many other groups.<br />
<br />
Plant breeders, biologists and bioinformatics specialists from ten countries, seven US states and representatives from two plant agribusinesses- Syngenta and Monsanto, gathered in Corvallis for a workshop on the latest developments in and broad discussion of the need for a coordinated effort to develop and extend the plant and trait ontologies to describe the anatomy and traits of agronomic importance to major crops cultivated world wide.<br />
<br />
<br />
The goal of this workshop was to widen the awareness and participation of the plant breeding community in the use of ontologies, and to create a semantic framework for meaningful cross-species queries using a common reference ontology for plants. <br />
<br />
* Guest speakers Melissa Haendel; (Ontology Development Group, OHSU Library and Barry Smith (OBO Foundry)<br />
<br />
* Participants engaged in hands-on activities, learning to use the ontology editor OBO-Edit and working in small groups to classify plant trait term requests which had been submitted.<br />
<br />
Outcomes: <br />
<br />
-preparing a short new item for circulation<br />
<br />
-preparing a "vision/white paper" to focus on the ref plant onotlogy concept<br />
<br />
-follow up meeting will occur at PAG 2013, along with Ontology workshop<br />
<br />
-Many new and enhanced collaborations<br />
<br />
=Update from Cornell=<br />
Added 25 more slides and 500 more images to the CUPAC database<br />
<br />
MAG and RW started adding keywords in the last week of August, and came up with a way to add PO's to all the images then link them to the PO pages, but it will probably be a few weeks before Kevin is able to implement the links.<br />
<br />
==Cont. from last meeting:==<br />
===Upper level term: 5 fruit formation stage (PO:0007042)===<br />
current def.: Formation of the seed-bearing structure after flowering.<br />
<br />
'''new name and definition, from last meeting:''' <br />
<br />
'''[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3565057&group_id=76834 whole plant fruit formation stage] (PO:0007042):''' A sporophyte reproductive stage (PO:0007130) that begins with the initiation of the first fruit (PO:0009001) of a growing season and ends with the beginning of a whole plant fruit ripening stage (PO:0007010)..<br />
<br />
Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit formation stage in its life, while a perennial may have one fruit formation stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun.<br />
<br />
''has_part'' fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)<br />
<br />
subset for angiosperms<br />
<br />
Discussion and comments:<br />
<br />
''Maybe refer to initiation of first fruit ripening, instead of fruit ripening stage?''<br />
<br />
''Some discussion of this as a population measure: If you want to apply this to a population, you may choose the point when, e.g., 50% of the plants have initiated fruit. BS suggested that this should be defined for an individual plant, and have population terms defined separately.''<br />
<br />
''Initiation of the first fruit begins with fertilization (formation of zygote). This can be defined more clearly in fruit development stages, then refer to those in these definitions.''<br />
<br />
''For gymnosperms, we could have terms like whole plant strobilus development stage. Seed development stage should apply to gymnos as well as angiosperms.''<br />
<br />
''Do we want a parent for both of these terms: "whole plant fruit development stage"? This would match more closely to fruit development stage (PO:0001002).''<br />
<br />
<br />
===Upper level term: 6 ripening stage (PO:0007010)===<br />
current def.: Maturation of the fruit.<br />
<br />
'''proposed new name and definition from last meeting:''' <br />
<br />
'''[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3565059&group_id=76834 whole plant fruit ripening stage] (PO:0007042):''' A sporophyte reproductive stage (PO:0007130) during which a fruit (PO:0009001) on a whole plant (PO:0000003) is undergoing ripening (GO:0009835).<br />
<br />
comment: This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit ripening stage in its life, which is generally followed by a sporophyte senescent stage (PO:0007017), while a perennial may have one fruit ripening stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant has begun.<br />
<br />
<br />
''has_part'' fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)<br />
<br />
subset for angiosperms<br />
<br />
GO:ripening is defined as a type of senescence. Should the term ripening be used only for fleshy fruits? Fruit drying also probably involves cell death, so perhaps it is type of ripening as well.<br />
<br />
''Add comment that ripening is a type of senescence and a comment to distinguish this stage from senescent stage of whole plant.''<br />
<br />
<br />
''Note: the different fruits on a plant may be in different stages, but the whole plant can only be in one stage.''<br />
<br />
''When does the ripening stage end? For annuals, ripening stage is followed by senescence of whole plant in annuals, but for perennials, maybe different. We need to incorporate this into the definition.''<br />
<br />
''PJ: Some pear varieties do not ripen on the plant. Have to be picked and treated. In that case, the plant never enters the whole plant fruit ripening stage, but the individual fruits to.''<br />
<br />
''We be good to tie this to seed development. Make the connection as part of the fruit development stages, and then link fruit stages to whole plant stages. Seeds may regulate development of fruit. Interaction between progeny and maternal tissue.''<br />
<br />
=Upcoming meetings and Presentations 2012-2013:=<br />
<br />
<br />
==[http://phenotypercn.org/ Phenotype RCN meeting], Oct 26-29th 2012==<br />
<br />
Asilomar, CA<br />
<br />
LC is going and has been working with LM to compile EQ statemnts to describe ~100 rice mutants. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.<br />
<br />
Will be combining the mutants with similar E and Q and looking at the genes and if they are othologs.<br />
<br />
==[http://www.intlpag.org/ PAG 2013], San Diego, CA; January 12-16, 2013==<br />
* Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6<br />
<br />
We will be running a workshop focusing on:<br />
<br />
[https://pag.confex.com/pag/xxi/webprogram/Session1596.html Applications of Ontologies for Plant and Animal Genomics]<br />
<br />
Three speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud. PJ present the Ref Plant Ontology Vision? <br />
<br />
* Would like to invite someone from Textpresso and AgiGO. <br />
<br />
''PJ: Suggestions- someone from GO in Berkeley, Nigam Shaw'' <br />
<br />
* Can we offer something to entice the speakers, in addition to the $100 discount on registration offered by the conference?<br />
<br />
* Need to submit list of speakers by November 1, 2012. <br />
<br />
''PJ will check with DW about Gramene involvement''<br />
<br />
Deadline for computer demo- Nov 1st<br />
<br />
==PRO-PO-GO meeting, ~May 2013==<br />
<br />
Location: Buffalo, NY <br />
<br />
Goals:<br />
<br />
# To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination<br />
# To identify potentially fruitful applications which such enhanced coordination might bring <br />
# To enhance the Protein Ontology treatment of plant-related proteins <br />
# To address coordination issues between the GO and PO, for example as concerns treatment of development stages<br />
# To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP] <br />
<br />
<br />
Tentative participant list: <br />
<br />
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others? <br />
<br />
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?<br />
<br />
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)</div>Preecejhttps://wiki.plantontology.org/index.php?title=Crop_Plant_Trait_Ontology_Workshop_OSU_2012&diff=19527Crop Plant Trait Ontology Workshop OSU 20122012-09-13T18:20:17Z<p>Preecej: /* Software Tools for Ontology Development and Annotations */</p>
<hr />
<div>This page has a TinyURL: http://tinyurl.com/Trait-Ontology<br />
<br />
=Background- What is an Ontology?=<br />
<br />
An ontology is a structured vocabulary that provides a consensus set of terms (or classes) to describe the types of entities within a given domain of reality and the relationships among these types. In the age of genomics and big data, ontologies have become indispensable tools for data annotation by suing the same standardized reference vocabulary (ontology). Once the entities are annotated in a consistent manner it is possible to compare the annotations and perform analysis. The analysis of large data sets from molecular, genetic, and genomic diversity studies has the potential to improve our current understanding of phenotype traits of economic relevance, how plants of different and similar species develop respond to various biotic and abiotic stresses.<br />
<br />
=Goals of the Workshop=<br />
<br />
To establish a semantic framework for meaningful cross-species queries across gene expression and phenotype data sets from plant genomics, genetics experiments and annotation of the crop germplasm. <br />
<br />
Vision statement on the Common Reference Trait Ontology for all plants will be presented at the [http://www.keod.ic3k.org/ Knowledge Engineering and Ontology Development] which is part of the International Conference on Knowledge Discovery and Information Retrieval ([http://www.ic3k.org/ IC3K2012]) to be held in Barcelona, Spain, October 4-7th, 2012. <br />
<br />
Vision Paper [[Media:Ref_TO_KEOD_2012.pdf]]<br />
<br />
Primary targets are: <br />
# Poaceae family crops (e.g. wheat, barley, rice, maize, sorghum, Miscanthus)<br />
# Solanaceae (e.g. potato and tomato)<br />
# Leguminosae (e.g. soybean and Medicago)<br />
# Grapes<br />
<br />
The strategy would be to develop Ontology terms and definitions to describe and annotate <br />
# Morphological and anatomical features of the major crops <br />
# Developmental stages of crop plants<br />
# Crop plant traits and phenotypes, as an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO)<br />
<br />
Additional discussions and efforts will be on developing applications to help:<br />
# Annotate data in a consistent manner by developing community standards<br />
# Integrate ontologies and annotations in various plant genomics and genetics resources<br />
# Develop analysis tools<br />
<br />
=Ontologies for Plant Biology=<br />
Here are some links to more information<br />
==Plant Ontology==<br />
* [http://www.plantontology.org/ Plant Ontology] home page<br />
* [[Relations_in_the_Plant_Ontology]]<br />
* [[How_to_use_the_SourceForge_tracker]]<br />
* See this recent publication for more information about the PO and ontologies for plant sciences: [http://www.amjbot.org/content/99/8/1263.abstract?etoc Walls et al (2012)] Ontologies as integrative tools for plant science. American Journal of Botany<br />
<br />
==Trait Ontology==<br />
An ontology of phenotype traits<br />
* Link to: [http://www.gramene.org/plant_ontology/ontology_browse.html browser at Gramene]<br />
* Link to development browser at OSU: [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi Plant Trait Ontology]<br />
* [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc Workshop Trait List]<br />
<br />
==CROP: Common Reference Ontology for Plants==<br />
The broader vision is to develop a reference set of ontologies for all plants.<br />
<br />
The biological ontologies useful for Plant Biology are:<br />
<br />
# PO*: [http://www.plantontology.org Plant Ontology]<br />
# GO: [http://www.geneontology.org Gene Ontology]<br />
# PRO: [http://pir.georgetown.edu/pro/pro.shtml Protein Ontology]<br />
# TO*: Plant Trait Ontology [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi TO browser]<br />
# EO*: Environment Ontology (plant treatments) [http://www.gramene.org/db/ontology/search?id=EO:0007359 browse at Gramene]<br />
# ENVO: [http://www.obofoundry.org/cgi-bin/detail.cgi?id=envo Ontology of environmental features and habitats]<br />
# PATO: [http://www.obofoundry.org/cgi-bin/detail.cgi?id=quality Phenotype Quality Ontology]<br />
# Taxonomy- [http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl USDA-GRIN] / [http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy NCBI] / New? <br />
# GAZ: [http://bioportal.bioontology.org/ontologies/1397 Gazetteer (geographical locations)]<br />
# Plant IDO*: Plant Infectious Disease Ontology [http://kr-med.org/icbofois2012/proceedings/ICBO2012/ICBO2012PapersSingleFiles/ICBO-2012-session1-paper01-walls.pdf A White Paper in PDF format]<br />
# Plant Diseases*: [http://wiki.plantontology.org/index.php/Plant_Disease_Ontology List of plant diseases]<br />
# CHEBI: [http://www.ebi.ac.uk/chebi/ dictionary of molecular entities]<br />
<br />
[* CROP group may adopt their development]<br />
<br />
=Software Tools for Ontology Development and Annotations=<br />
<br />
* [http://oboedit.org/ OBO-Edit]<br />
* [http://protege.stanford.edu/ Protégé]<br />
* Semantic Image Annotator (SIA)<br />
*: - pre-release; the public release will be announced on the PO mailing list and available for download at the [http://jaiswallab.cgrb.oregonstate.edu Jaiswal Lab web site] soon<br />
<br />
=Meeting Agenda=<br />
==Arrival and attendance note==<br />
* Attendees should plan to arrive by Sept 12th- Note all times listed are LOCAL- US Pacific Daylight Time<br />
<br />
==Meeting venue==<br />
# All sessions will be held in the Willamette Room; [http://oregonstate.edu/conferences/ch2m-hill-alumni-center CH2M Hill Alumni Center] (725 SW 26th Street, Oregon State University, Corvallis, OR)<br />
# Rooms for break-out sessions: Trysting Tree and Elle/Burlingham Conference Rooms<br />
<br />
Links to:<br />
<br />
[http://oregonstate.edu/ Oregon State University] Home Page<br />
<br />
[http://oregonstate.edu/campusmap/ Campus Map]<br />
<br />
==Meeting agenda details==<br />
<br />
Visit detailed agenda page at: [[Crop Plant Trait Ontology Workshop Agenda]]<br />
# [[Crop_Plant_Trait_Ontology_Workshop_Agenda#Thursday_September_13]]<br />
# [[Crop_Plant_Trait_Ontology_Workshop_Agenda#Friday_September_14]]<br />
# [[Crop_Plant_Trait_Ontology_Workshop_Agenda#Saturday_September_15]]<br />
<br />
=Attendees=<br />
<br />
==Organizing Committee:==<br />
* Laurel Cooper- Plant Ontology and Trait Ontology Projects, Oregon State University, Corvallis, Oregon (cooperl@science.oregonstate.edu)<br />
* Pankaj Jaiswal, Plant Ontology, Trait Ontology and Gramene Projects, Oregon State University, Corvallis, Oregon (jaiswalp@science.oregonstate.edu)<br />
* Ruth Bastow, GARNet Coordinator, University of Warwick (ruth@garnetcommunity.org.uk)<br />
* Elizabeth Arnaud, Crop Ontology, Generation Challenge Program, Bioversity International, Rome, Italy (e.arnaud@cgiar.org)<br />
* Naama Menda, Sol Genomics Network, Boyce Thompson institute for Plant Research, Ithaca NY (nm249@cornell.edu)<br />
* Rex Nelson, SoyBase, USDA-ARS, Ames, IA (nelsonrt@iastate.edu)<br />
* Paul Kersey, European Bioinformatics Institute, Hinxton, UK (pkersey@ebi.ac.uk) (not attending)<br />
<br />
==From the Plant Ontology Consortium:==<br />
* Laurel Cooper- Plant Ontology and Trait Ontology Projects, Oregon State University, Corvallis, Oregon (cooperl@science.oregonstate.edu)<br />
<br />
* Pankaj Jaiswal, Plant Ontology, Trait Ontology and Gramene Projects, Oregon State University, Corvallis, Oregon (jaiswalp@science.oregonstate.edu)<br />
<br />
* Justin Preece, Bioinformatics and Software Development, POC/OSU<br />
<br />
* Justin Elser, Bioinformatics and Software Development, POC/OSU<br />
<br />
* Laura Moore, Undergrad researcher- Trait Ontology<br />
<br />
* Barry Smith, University at Buffalo [http://ontology.buffalo.edu/smith/ Ontology site], [http://philosophy.buffalo.edu/people/faculty/smith/ Department of Philosophy site]- ''will attend remotely''<br />
<br />
==Invited Expert Guests:==<br />
<br />
* Pawel Krajewski; Leading the standards WP in [http://transplantdb.eu/node/17 transPLANT] <br />
<br />
* Cyril Pommier INRA France; [http://urgi.versailles.inra.fr/Projects/URGI-softwares/Ephesis Ephesis]<br />
<br />
* Jacques Legouis; curator of the Wheat trait lists for INRA, France [http://www4.clermont.inra.fr/umr1095_eng/Staff/Business-cards/LE-GOUIS-Jacques]<br />
<br />
* C Tom Hash- Sorghum GCP challenge initiative, Mali; Representative for ICRISAT’s sorghum (and pearl millet) breeding teams (and the genebanks) <br />
<br />
* Reinhard Simon; Integrated IT and Computational Research [http://cipotato.org/ potato trait ontology CIP][http://www.cropontology.org/ontology/CO_330] <br />
<br />
* Sonia Dias; Medicago [http://agrobiodiversityplatform.org/database/?expert=sonia-dias Trait Information Portal] [http://www.pgrsecure.bham.ac.uk/home PGRSecure]<br />
<br />
* Dan Bosler; EBI, Ensembl Plants Project Leader, potato genomics; [http://plants.ensembl.org/index.html] <br />
<br />
* John Doonan; UK phenomics centre, all crops, EU phenomics network; [http://www.aber.ac.uk/en/ibers/staff/staff-list/doonan,-prof.-john/ IBERS, Aberystwyth University, Wales]<br />
<br />
* Mary Schaeffer; USDA, Missouri [http://www.maizegdb.org/ MaizeGDB]<br />
<br />
* Victoria Blake; USDA, ARS, CA [http://wheat.pw.usda.gov/GG2/index.shtml GrainGenes] Bioinformatics and Triticeae Genomics<br />
<br />
* Ken McNally; [http://irri.org/ IRRI]<br />
<br />
* Melissa Haendel; Ontology Development Group, [http://www.ohsu.edu/library/ OHSU Library]<br />
<br />
* Sunita Kumari, [http://genomicscience.energy.gov/compbio/ KBase]<br />
<br />
* Luke Ramsay; Barley [http://www.hutton.ac.uk/staff/luke-ramsay Hutton Institute]<br />
<br />
* Sharon Lewis Syngenta; Information governance<br />
<br />
* Bob Bensen- Trait Genetics Lead, Quantitative Genetics<br />
<br />
* Michael Dingkuhn; [http://irri.org/ IRRI]<br />
<br />
* Alice Clara Augustine, Biotech Ontology Lead, Monsanto<br />
<br />
==Invited Experts OSU:==<br />
Botany and Plant Pathology Dept:<br />
* Brett Tyler [http://bpp.oregonstate.edu/tyler link]<br />
* Lynda Ciuffetti ''tentative''<br />
* John Fowler <br />
* Joyce E. Loper ''tentative''<br />
<br />
Crop and Soil Science Dept:<br />
* Jenny Kling ''tentative''<br />
* Russell Karow ''tentative''<br />
* Robert S Zemetra ''tentative''<br />
* John A. Henning ''tentative''<br />
<br />
Horticulture Dept:<br />
* Laurent Deluc <br />
* Sushma Naithani <br />
* Shawn Mehlenbacher ''tentative''<br />
<br />
=Meeting Logistics:=<br />
==Transportation==<br />
The two nearest airports for coming to Corvallis, OR are:<br />
# Portland (PDX) about 96 miles N of Corvallis. ~1.5 hours away, but more convenient in terms of connections, prices and shuttle<br />
# Eugene (EUG) about 35 miles S of Corvallis.<br />
<br />
Note: Prepaid shuttles and rental car options are available at both the airports<br />
<br />
===Arriving from Portland, OR===<br />
* '''HUT Shuttle from Portland Airport (PDX) to Corvallis '''- Arrive at the shuttle stop '''Hilton Garden Inn'''<br />
** Shuttle contact Phone# (541) 926-2525<br />
** Link to shuttle arrival/departure schedules: [http://www.hutshuttle.com/ HUT Shuttle] Runs every 2 hours<br />
** '''At PDX''': HUT shuttle picks up in front of the 'Scheduled Buses and Vans' sign in Ground Transportation. Directly across from baggage claim carousel #8.<br />
===Arriving from Eugene, OR===<br />
There is smaller regional airport in Eugene, OR, which is about 45 minutes away and is serviced by [http://www.omnishuttle.com/offer.htm Omnishuttle]<br />
<br />
Phone: 541 461-7959<br />
<br />
Fax: 541 461-7981<br />
<br />
Omnishuttle will drop you right at Finley Hall<br />
<br />
==Directions==<br />
===Walk: If you arrive by HUT shuttle from Portland===<br />
* '''ATTENTION: HUT shuttle will not be stopping at the OSU Bookstore from Monday September 10th through Monday September 17th''' due to the roadway closure on Jefferson Way. Reservations for those times will need to be made for our stop at the Corvallis Hilton Garden Inn.<br />
<br />
<br />
'''Walking directions to Finley Hall from Hilton Garden Inn'''<br />
<br />
* It is a ~7 minute walk to Finley Hall, about 0.4 mile (~ 1 km)<br />
<br />
[[File:Hilton to Finley map.png]]<br />
<br />
<br />
Finley Hall, 2100 Southwest May Way, Corvallis, OR 97333<br />
<br />
1. Head northeast on SW Western Blvd toward SW <br />
<br />
2. Turn left onto SW 26th St 0.2 mi<br />
<br />
3. Turn right onto SW Stadium Ave 0.2 mi<br />
<br />
4. Turn left 112 ft<br />
<br />
5. Slight left Finley Hall will be on the left<br />
<br />
Finley Hall 2100 Southwest May Way, Corvallis, OR<br />
<br />
===Driving Directions from Portland airport (PDX)===<br />
Link to Google map: [http://goo.gl/maps/8FfwY map]<br />
# Head southwest on NE Airport Way 0.4 mi<br />
# Keep right at the fork 0.1 mi<br />
# Slight right to stay on NE Airport Way 1.7 mi<br />
# Take the Interstate 205 S ramp to Interstate 84/Portland/salem 0.5 mi<br />
# Merge onto I-205 S 23.4 mi<br />
# Keep left at the fork and merge onto I-5 S 60.7 mi<br />
# Take exit 228 for Oregon 34 toward Lebanon/Corvallis 0.2 mi<br />
# Turn right onto OR-34 W/Corvallis-Lebanon Hwy Continue to follow OR-34 W 9.6 mi<br />
# Turn left onto OR-34 Bypass W/Corvallis-Newport Hwy/Newport-Corvallis Hwy Continue to follow OR-34 Bypass W 1.1 mi<br />
# Continue onto OR-34 W 0.6 mi<br />
# Turn right onto SW 26th St 0.5 mi<br />
# Turn right onto SW Washington Way 0.2 mi<br />
# Turn right onto SW 17th St 207 ft<br />
# Turn right Finley Hall, will be on the left 348 ft<br />
<br />
== Parking on OSU Campus==<br />
* You can park in any Student/Visitor lots, during the workshop- no permit required.<br />
* OSU [http://oregonstate.edu/campusmap/Map with parking]<br />
* There is a parking structure just west of Finley and two small parking lots to the north.<br />
* [http://oregonstate.edu/uhds/finley Finley Hall], Location: 2100 SW May Way. <br />
* See [http://oregonstate.edu/campusmap/ campus map]<br />
<br />
==Accommodation==<br />
===Accommodation on OSU campus===<br />
====Accommodation at Finley Hall====<br />
[http://oregonstate.edu/uhds/finley Finley Hall], Location: 2100 SW May Way. <br />
<br />
* Guests will be accommodated at on-campus dorm-style housing at OSU; Reasonably priced, close and convenient<br />
* Floors 3 to 7 are reserved to host visiting scholars, researchers, INTO OSU monthly after hours arrivals, and conference groups similar to what many institutions throughout the region provide. (we are all on floor 7)<br />
* Single or double rooms (not shared unless requested) with shared bathroom facilities in the wing<br />
* Internet access- <br />
<br />
See [http://oregonstate.edu/campusmap/ campus map]<br />
<br />
====Check-in instructions====<br />
* When guests arrive they will call the conferences phone at +1-(541) 230-4071 to receive their keys. There are yellow call boxes outside of the entrance in case anyone doesn’t have a cell phone. <br />
* In their room they will have linens provided and Monday-Friday from 7:30a-5:30p the front desk will be open should anyone want to switch out their bath towel for a new towel. <br />
<br />
====Check-out instructions====<br />
As people are ready to checkout on they can leave their room keys with the conferences staff at the Finley front desk, or drop key and fob in the Mail slot if the office is closed. <br />
<br />
* Check-out time: We request that people '''check out by 11.00am on their scheduled check out date'''.<br />
<br />
* On-site contact for the conference: Chris Anderson (anderch2@onid.orst.edu)<br />
<br />
====For after hours access====<br />
Finley Hall Conference duty phone# +1-541 230-4071. There are yellow call boxes outside of the entrance in case anyone doesn’t have a cell phone.<br />
<br />
===Other accommodations (non-OSU)===<br />
Also: If attendees prefer not to stay on campus they can '''stay at their own cost''' at: [http://hiltongardeninn3.hilton.com/en/hotels/oregon/hilton-garden-inn-corvallis-CVOCHGI/index.html Hilton Garden Inn]<br />
<br />
'''* As of Aug 24th, the Hilton was fully booked for Weds Sept 13th, but other nights may be available'''<br />
<br />
[http://book.bestwestern.com/bestwestern/US/OR/Corvallis-hotels/BEST-WESTERN-Grand-Manor-Inn---Suites/Hotel-Overview.do?propertyCode=38111 Best Western Grand Manor Inn & Suites]<br />
<br />
=Campus Visitor Information- Oregon state University and Corvallis, OR=<br />
<br />
[http://oregonstate.edu/ Oregon State University] Link to: [http://oregonstate.edu/campusmap/ Campus Map]<br />
<br />
[http://oregonstate.edu/conferences/ch2m-hill-alumni-center CH2M Hill Alumni Center]<br />
<br />
Corvallis, OR<br />
<br />
[http://visitcorvallis.com/?action=events_info&rowid=1882 Corvallis Visitor Center]<br />
<br />
<br />
[http://www.weather.com/weather/tenday/Corvallis+OR+97333:4:US Weather in Corvallis]<br />
<br />
==OSU is a Smoke-Free Campus==<br />
A reminder that '''smoking is no longer permitted anywhere on the Oregon State University Corvallis campus''' and select OSU property within Benton County signed as nonsmoking. Smoking is permissible on sidewalks that border OSU's boundaries. Smoking receptacles are being installed in strategic, high-traffic areas around the periphery of the Corvallis campus for disposal of smoking-related litter. Their locations will be updated soon on the policy’s website at http://oregonstate.edu/smokefree.<br />
<br />
The smoke-free policy is in effect year-round, including game days, so visitors to campus who are participating in tailgating activities will also be prohibited from smoking.<br />
<br />
Enforcement will focus on educating students, staff and visitors about the policy, but those who refuse to abide by the campus’ smoke-free policy may be cited by OSU Department of Public Safety. Students will be held accountable under the student conduct code and employees under OSU employment policies. Contractors, vendors, event attendees, those who rent or lease university property and other visitors to OSU could be subject to exclusion from campus for violation of the new policy.<br />
<br />
Smoking also is not permitted inside personal vehicles on campus.<br />
<br />
Among the prohibited smoking devices are cigars, cigarettes, pipes, electronic cigarettes or other devices intended to simulate smoking.<br />
<br />
<br />
==Optional activities taking place Saturday Sept. 15th in and around Corvallis==<br />
<br />
These are from your personal expenses and are not covered by the meeting sponsors. Please contact Laurel Cooper for making arrangements.<br />
<br />
* [http://visitcorvallis.com/ai1ec_event/rhapsody-in-the-vineyard-a-downtown-wine-walk/?instance_id=31939 Downtown Wine Walk]<br />
<br />
* [http://www.corvallisenvironmentalcenter.org/enjoy-supper-at-sage-this-september/ Supper at Sage]<br />
<br />
* Possible excursion destination: [http://www.oregonstateparks.org/park_211.php Silver Falls State Park] or [http://discovernewport.com/ Newport, Oregon Coast]<br />
<br />
= Meeting Sponsors and Organizers=<br />
Co-organized by: [http://www.plantontology.org/ The Plant Ontology], the [http://www.bbsrc.ac.uk/home/home.aspx BBSRC] and the [http://www.generationcp.org/ Generation Challenge Programme]. <br />
<br />
Travel Funds provided by: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0822201 NSF Award #0822201] (Plant Ontology) and BB/H531519/1 (BBSRC), as well as by most participants.<br />
<br />
Additional support has been provided for the workshop by: [http://www.generationcp.org/ Generation Challenge Programme] and [http://www.syngenta.com Syngenta]</div>Preecejhttps://wiki.plantontology.org/index.php?title=Crop_Plant_Trait_Ontology_Workshop_Agenda&diff=19524Crop Plant Trait Ontology Workshop Agenda2012-09-13T01:17:24Z<p>Preecej: /* Thursday September 13 */</p>
<hr />
<div>'''Dates:''' Sept 13-15th, 2012 (Thursday through Saturday)<br />
<br />
'''Location:''' Oregon State University<br />
<br />
Return to the main [[Crop_Plant_Trait_Ontology_Workshop_OSU_2012]] page<br />
<br />
=Weds Sept. 12th, 6-8pm=<br />
Dinner on your own those who arrive early<br />
<br />
Snack and refreshments will be available at Finley Hall or Arnold dining center will be open until 7pm<br />
<br />
=Thursday September 13=<br />
Location: [http://oregonstate.edu/conferences/ch2m-hill-alumni-center CH2M Hill Alumni Center] Williamette Room<br />
<br />
The wireless internet username and password is:<br />
<br />
Login User: 25Sept8<br />
<br />
Password: shakyDove<br />
<br />
<br />
'''* 8:00- 9am Continental Breakfast in Williamette Room'''<br />
<br />
* 9:00- 9:15 Welcome and Introduction - Pankaj Jaiswal, OSU<br />
<br />
* 9:15- 9:30 Ruth Bastow: Insights and follow-up from [http://transplantdb.eu/node/68 EBI Crop Ontology Meeting]<br />
<br />
* 9:30- 10:00 Melissa Haendel; "Introduction to Ontologies" <br />
<br />
* 10:00- 10:30 The Plant Ontology and the Trait Ontology- Laurel Cooper, OSU<br />
<br />
'''* 10:30- 10:45 coffee break'''<br />
<br />
* 10:45- 11:00 Elizabeth Arnaud, Bioversity /GCP<br />
<br />
* 11:00- 11:15 Naama Menda- Sol Genomics Network<br />
<br />
* 11:15- 11:30 Rex Nelson- SoyBase<br />
<br />
* 11:30- 11:45 Mary Schaeffer- MaizeGDB<br />
<br />
* 11:45- 12:00 0pen time for questions and discussion<br />
<br />
'''* 12:00- 1:00 Lunch: Soup and Salad Buffet; Elle/Burlingham Room #111'''<br />
<br />
* 1:00- 1:10 Bob Benson, Syngenta traits<br />
<br />
* 1:10- 1:20 Sharon Lewis; Syngenta- Information governance<br />
<br />
* 1:20- 1:30 Alice Clara Augustine, Monsanto<br />
<br />
* 1:30- 1:40 Sonia Dias- Trait Information Portal, PGR secure<br />
<br />
* 1:40- 1:50 Pawel Krajewski, transPLANT<br />
<br />
* 1:50- 2:00 Jacques Legouis; INRA, France<br />
<br />
* 2:00- 2:10 Cyril Pommier, INRA France; Ephesis<br />
<br />
* 2:10- 2:20- John Doonan, UK Phenomics Center<br />
<br />
* 2:20- 2:30- Dan Bolser, EBI, Ensemble, potato genomics<br />
<br />
* 2:30- 2:40 Reinhard Simon, CIP<br />
<br />
'''* 2:40- 3:00 coffee break'''<br />
<br />
* 3:00- 3:10- Victoria Blake, USDA, ARS, CA GrainGenes<br />
<br />
* 3:10- 3:20 Luke Ramsay, Barley traits<br />
<br />
* 3:20- 3:30 C Tom Hash, ICRISAT, sorghum<br />
<br />
* 3:30- 3:40 Ken McNally, IRRI<br />
<br />
* 3:40- 3:50 Michael Dingkuhn, IRRI<br />
<br />
* 3:50- 4:00 Sunita Kumari, KBase<br />
<br />
* 4:00- 4:30 Justin Preece, OSU - Plant Ontology Tools for Annotation: <br />
:*Semantic Image Annotator (SIA)<br />
:*Plant Annotation Wiki<br />
:*PO Web Services<br />
<br />
* 4:30- 5:00 Open time for questions and discussion<br />
<br />
'''* 5:00- 6:00 break, free time'''<br />
<br />
'''* 6:00- 7:00 Pizza dinner- Elle/Burlingham Room #111'''<br />
<br />
<br />
==* 7:00 to 9:00pm 'Hands-on' Ontology Session==<br />
<br />
===Requesting terms using the SourceForge trackers===<br />
Please see the link: [[How to use the Source Forge tracker]]<br />
<br />
Before using the PO Source Forge tracker you should:<br />
<br />
# Register (create a login) <br />
# Log in to your account <br />
# Search the tracker for existing items on the same topic<br />
<br />
<br />
===Ontology editing: Using OBO Edit- tutorial and practice===<br />
<br />
=Friday September 14=<br />
'''* 8:00- 9am Continental Breakfast in Williamette Room'''<br />
<br />
9:00- 9:20 TBA<br />
<br />
9:20- 9:30 Sushma Naithani, OSU Horticulture<br />
<br />
9:30-9:40 Laurent DeLuc, OSU Horticulture, grape research<br />
<br />
<br />
'''* 9:40- 10:00 coffee break'''<br />
<br />
* 10:00- 11:00 Creating the 'CROP Initiative' (Common Reference Ontologies for Plants)<br />
** Pankaj: Introduction<br />
** [http://ontology.buffalo.edu/smith/ Barry Smith]: Webex presentation<br />
*** [http://wiki.plantontology.org/index.php/Crop_Plant_Trait_Ontology_Workshop_OSU_2012#CROP:_Common_Reference_Ontology_for_Plants List of Ontologies]<br />
*** [http://obofoundry.org/ OBO Foundry website]<br />
*** [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Background reading on the OBO Foundry]<br />
<br />
11:00- 12:00 discussion<br />
<br />
'''* 12:00-1:00 Lunch: Assorted Wraps with Soup and Salad; Elle/Burlingham Room #111'''<br />
<br />
1:00- 1:15 breakout groups are organized and task is explained<br />
<br />
1:15- 2:45 breakout group session: "Find your trait of Interest"<br />
<br />
<br />
<br />
<br />
'''* 2:45- 3:00 coffee break'''<br />
<br />
3:00- 3:30- breakout groups report on progress, discussion<br />
<br />
3:30- 5:00 breakout groups<br />
<br />
5:00- 5:30 breakout groups report on progress, discussion<br />
<br />
'''* 5:30- 6:30 break, free time'''<br />
<br />
'''* 6:30- 9:00 Dinner and Social -Elle/Burlingham Room #111'''<br />
<br />
=Saturday September 15=<br />
<br />
'''* 8:00- 9am Continental Breakfast in Williamette Room'''<br />
<br />
9:00- 9:30 Biological examples and ontology applications; Pankaj Jaiswal, OSU<br />
<br />
9:30- 10:30 Breakout groups and group discussion<br />
<br />
'''* 10:30- 10:45 Coffee break'''<br />
<br />
10:45 Summary and conclusions<br />
<br />
Wrap and to-do lists for follow-up<br />
<br />
'''12:00 Boxed Lunches'''</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Outreach_Events&diff=19209POC Outreach Events2012-08-24T20:15:00Z<p>Preecej: /* Genome Informatics 2012 */</p>
<hr />
<div>Workshops, Presentations, Posters, etc<br />
<br />
=Year 2012=<br />
==Genome Informatics 2012==<br />
[https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296 Genome Informatics 2012]<br />
<br />
[http://wiki.plantontology.org/index.php/File:Abstract_GI_2012_PO_poster.pdf Abstract]<br />
<br />
September 6th-9th, Robinson College, Cambridge, UK<br />
<br />
JP will attend<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission: [http://precis.preciscentral.com/utils/ip/ShowSummary.asp?AbstractId=521&Presenter= Poster Number: P28002]<br />
<br />
[[Media:Poster_ASPB_2012_(LC_7-18-12).pdf]]<br />
<br />
[http://my.aspb.org/default.asp?page=Meetings_PB12Wrkshps Plant Informatics Workshop] was held with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 9:00 PM<br />
<br />
Link to Plant Ontology workshop presentation: [[Media:Cooper_PO_ASPB_2012.pdf]]<br />
<br />
LC attended<br />
<br />
[[Outreach booth- ASPB Plant Biology 2012]]<br />
<br />
==[http://purl.bioontology.org/ICBO/ ICBO 2012]==<br />
International Conference on Biomedical Ontologies, July 22nd-25th, Graz, Austria, co-located with the 7th International Conference on Formal Ontologies in Information Systems [http://www.kr-med.org/icbofois2012/ (FOIS 2012)].<br />
<br />
A paper describing a plant disease extension of the Infectious Disease Ontology was presented at this meeting, as well as a poster on the PO-FNA collaboration.<br />
<br />
*Link to IDOPlant paper: [[Media:idoplant_paper.pdf]]<br />
*Wiki page for notes on [[Plant Disease Ontology]]<br />
*Link to abstract for PO-FNA mapping poster: [[Media:PO_FNA_ICBO_abstract.pdf]]<br />
*Link to PO-FNA mapping poster: [[Media:PO_FNA_ICBO_poster.pdf]]<br />
*Link to PO-FNA mapping: http://tinyurl.com/FNAPOmapping<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
The PO will host a [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 Plant Ontology workshop] on Sunday, July 8th, 9:00AM - 12:00PM, to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
Wiki page for workshop: [[Plant Ontology Workshop, Botany 2012]]<br />
<br />
==[http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]==<br />
<br />
April 2-4, 2012, Washington DC<br />
<br />
Poster Presentation: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf]]<br />
<br />
==[http://www.maizegdb.org/maize_meeting/2012/index.php Maize Genetics Meeting 2012]==<br />
<br />
March 15-18, 2012 in Portland, OR <br />
<br />
LC submitted an abstract for a short talk [http://maizemeeting.maizegdb.org/mm2012/see_abstract.php?id=302 abstract] Friday March 16th, 5:45pm, which was presented by PJ.<br />
<br />
[[File:Maize_meeting_2012_v2.pdf]]<br />
<br />
==[http://www.intl-pag.org/ PAG 2012] San Diego, CA==<br />
<br />
PO was represented at the following events:<br />
<br />
PO organized an Ontology workshop: Using Ontologies for Organizing Plant and Animal Genomics Data, Saturday January 14th from 10:20am-12:30pm. <br />
<br />
We had 5 speakers and a panel discussion at the end.<br />
<br />
* [http://pag.confex.com/pag/xx/webprogram/Session1272.html Ontology Workshop page] <br />
<br />
[[File:Cooper_PO_(LC_4-4-12).pdf]] <br />
<br />
For more info, see the [[PAG 2012 Ontology workshop]] wiki page<br />
<br />
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1046.html Non-Seed Plant Workshop] on Saturday, Jan 14th, (3:50pm-6pm) <br />
Link to [http://pag.confex.com/pag/xx/webprogram/Paper1640.html abstract] and presentation: <br />
<br />
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes] workshop on Sunday, Jan. 15th, (8:00am - 10:10am)<br />
Link to [http://pag.confex.com/pag/xx/webprogram/Paper1878.html abstract] and presentation: [[Media: Cooper_Phenos_PAG2012.pdf]].<br />
<br />
* Computer demo Monday 12:50 pm for the PO.<br />
Link to [http://pag.confex.com/pag/xx/webprogram/Paper3536.html abstract] and presentation: <br />
<br />
* The PO also took part in an [http://www.agron.missouri.edu/mnl/pgoPAG.htm Outreach booth] organized by MaizeGDB<br />
<br />
=Year 2011=<br />
<br />
* '''[http://www.swat4ls.org/workshops/london2011/ Semantic Web Applications and Tools for Life Sciences Workshop]''' Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), Dec 6-9<br />
<br />
JP will present a poster entitled "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes". (abstract: [[Media:SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf|SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf]]). He will also participate in a "hackathon" software development session meant to spur innovation in semantic web applications.<br />
<br />
<br />
* '''[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: from Genes to Networks]''' Cold Spring Harbor Laboratory, November 30 - December 3, 2011<br />
<br />
RW will present a poster entitled "Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets". (link to abstract: [[Media:PO_abstract_PGB_CSHL2011.pdf]]<br />
<br />
<br />
* '''Departmental seminar: Facultad de Ciencis Naturales y Museo , Universidad Nacional de La Plata, Argentina''', Nov. 1, 2011<br />
MAG presented: 'El valor de las fosiles para descrifar la historia evolutiva de las angiospermas y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany Laboratory- Dr. Ari Iglesias.<br />
<br />
* '''Departmental seminar: Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Argentina''', Oct. 31, 2011<br />
MAG presented: "Paleobotanica en la era de la Biologia Molecular y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany and Palynology laboratory- Dr. Maria del Carmen Zamaloa.<br />
<br />
<br />
* '''12th Genomic Standards Consortium Meeting''' ([http://gensc.org/gc_wiki/index.php/GSC_12 GSC 12]), Max Planck Institute for Marine Microbiology, Bremen, September 28-29, 2011<br />
<br />
Barry Smith addressed Plant Ontology issues in two presentations, on “An Introduction to Ontology as a Strategy for Data Integration”, and on “The Structure of the Environment Ontology”)<br />
<br />
<br />
* '''Syngenta Presentation'''. Global webinar, September 26, 2011<br />
<br />
PJ and JP presented our current work on the Planteome Annotation Wiki to the IT Research and Development Dept. at Syngenta. (presentation: [[Media:Jaiswal_Lab_-_Semantic_Wiki_Presentation_-_2011.pdf|Jaiswal Lab - Semantic Wiki Presentation - 2011.pdf]])<br />
<br />
<br />
* '''[http://conference.cgrb.oregonstate.edu/ 2011 CGRB Fall Conference]''' Oregon State University, September 18th-19th, 2011.<br />
<br />
Two posters related to the Plant Ontology were presented.<br />
<br />
LC presented the poster: "[[Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa]]".<br />
<br />
JP presented a poster: "[[Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes]]". This explains the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service and includes an initial data set built from PO GAF (.assoc) files for ''Oryza sativa''. <br />
<br />
<br />
<br />
* '''Moss 2011 PO presentation''' (Black Forest, September 11th - 15th, 2011, done via Webex) [[Moss 2011 Meeting- PO presentation]] Sept 12, 2011<br />
<br />
<br />
* '''NSF Plant Genome Awardee meeting''' Sept, 2011. Washington, DC. Submission: [[Media:2-pager_plant_ontology-2011.pdf]]<br />
<br />
<br />
* '''ASPB Plant Biology meeting 2011,''' [http://my.aspb.org/?page=Meetings_PB2011 PB2011], Minneapolis, Minn. Aug 6th-10th, 2011<br />
<br />
PO and [http://www.gramene.org/ Gramene] hosted a [http://outreach.gramene.org/gramene-outreach/index.php/Main_Page Data Curation Workshop] <br />
<br />
LC presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster] and we took part in an [[Plant Biology 2011 Outreach Booth]]<br />
<br />
<br />
* '''International Botanical Congress''' [http://www.ibc2011.com/Default.htm (IBC2011)],Melbourne, Australia. July 23rd – 30th 2011<br />
Symposium hosted: [[Bio-Ontologies for the Plant Sciences]] under the Genetics, Genomics and Bioinformatics theme. <br />
<br />
Please see the [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details.<br />
<br />
Press release about the PO at IBC 2011: [[Media:IBC_2011_Congress_News_Thursday_28_July_WEB.pdf]]<br />
<br />
POC presented talks:<br />
<br />
Pankaj Jaiswal, Oregon State University, [[Ontologies for Plant Biology - IBC 2011]]<br />
<br />
Dennis Stevenson, Genomics of Seed Plants and Ontologies.<br />
<br />
Ramona Walls, The New York Botanical Garden, [[The Plant Ontology: an updated tool for all plant biologists - IBC 2011]]. Link to PDF of presentation: [[Media:Walls_PO_presentation_IBC11.pdf]]<br />
<br />
<br />
<br />
* '''International Conference on Biomedical Ontologies''' [http://icbo.buffalo.edu IBCO 2011] Buffalo, NY. July 26-30, 2011<br />
LC co-organized the session on [http://icbo.buffalo.edu/2011/WorkshopD_Program.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability"]<br />
and presented a flash talk "The Plant Ontology: Development of a Reference Ontology for all Plants"<br />
<br />
LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership [http://icbo.buffalo.edu/2011/slides/Thursday%20OBO_Foundry_Panel/ link]<br />
<br />
<br />
<br />
'''*Plant Working Group Meeting of the Phenotype Ontology RCN''', Google Campus in Boulder, CO; June 1-3, 2011 <br />
[http://www.phenotypercn.org/?page_id=542 RCN, June 2011]<br />
<br />
All four (Plants, Arthropoda, Vertebrates and Bioinformatics) Working Group sessions ran concurrently to maximize the benefits of emerging results, group experiences and collective synergy.<br />
<br />
<br />
<br />
'''*Semantic Web Workshop''', June 6-7, 2011, Santa Fe, NM.<br />
<br />
The Plant Ontology was represented at the 2011 [http://www.iplantcollaborative.org/learn/events/2011/04/22/2011-semantic-web-workshop Semantic Web Workshop]. Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop focused on biological applications for semantic web services. JP and JE attended. <br />
<br />
<br />
'''* Presentation to Physcomitrella Collaborators''' May 2011 [[Plant Ontology Webinar- May 2011 release]]<br />
<br />
<br />
*'''Phenotype RCN Meeting Durham, NC''', February 25-27, 2011 [http://www.phenotypercn.org/?page_id=289]<br />
The Plant Ontology attended the inaugural meeting of the newly-funded [http://phenotypercn.org Phenotype Ontology RCN] at the National Evolutionary Synthesis Center in Durham, NC. <br />
<br />
<br />
<br />
<br />
==Plant and Animal Genome XIX Conference==<br />
[http://intl-pag.org/ PAG 2011], San Diego, CA. January 15-19, 2011<br />
<br />
LC, RW, JP and DWS presented a [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_887.html PO poster and a computer demo].<br />
<br />
LC took part in the [http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes workshop] and panel discussion<br />
<br />
We also hosted a [http://wiki.plantontology.org:8080/index.php/PAG_2011_Collaborators_Workshop PO Collaborators workshop] on Sunday, Jan 16th, 2011.<br />
<br />
=Year 2010=<br />
<br />
* [http://www.nettab.org/2010/ NETTAB 2010 conference on Biological Wikis], Nov 29-Dec 1, 2010, Naples, Italy<br />
Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" [[File:NETTAB 2010 poster proposal.pdf]]<br />
<br />
* Seminar, Department of Botany and Plant Pathology, Oregon State University- Thurs, Oct 14th, 2010.<br />
Laurel presented a seminar: Bridging Plant Anatomy and Genomics in the Digital Era: Recent Advances at The Plant Ontology<br />
[[File:Cooper_BPP_final_(LC_10-14-10).pdf]]<br />
<br />
*Seminar, New York Botanical Garden. October 6, 2010. Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'<br />
<br />
*[http://www.aspb.org/pb-2010/ American Society of Plant Biologists], Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010<br />
Laurel Cooper and Pankaj Jaiswal attended. Laurel presented a poster:[http://abstracts.aspb.org/pb2010/public/P14/P14010.html The Plant Ontology: A Database for Plant Genomics].<br />
<br />
''Cooper, L., Elser, J., Walls, R., Stevenson, Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Database for Plant Genomics. American Society of Plant Biologists, Quebec, Montreal, Canada''<br />
<br />
<br />
We also organized a Plant Biology 2010 Outreach Booth: [[Plant Genome Resources Outreach Booth]].<br />
<br />
*PO-Gramene Annotation Workshop at Plant Biology 2010 [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop PO-Gramene Annotation Workshop]<br />
A workshop to demonstrate the Phenote Annotation Tool was held at the ASPB Plant Biology Meeting in Montreal, Quebec, Canada. <br />
<br />
You can find a link to the workshop page at: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop Phenote Workshop] <br />
<br />
*[http://www.botanyconference.org/ Botany 2010], Providence, RI. Jul. 31 - Aug. 4, 2010. Dennis Stevenson, Alejandra Gandolfo, and Ramona Walls attended.<br />
Ramona Walls gave a presentation for the Developmental and Structural Section [[Abstract-BSA2010]] [[File:Presentation-BSA2010.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Stevenson Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: a tool for structural, developmental, and molecular plant biologists. Providence, RI.''<br />
<br />
<br />
*[http://sites.google.com/site/bioontologiessig2010/ Bio-Ontologies 2010: Semantic Applications in Life Sciences] July 9th-10th, 2010<br />
Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk' <br />
<br />
[[File:PO_Poster_BioOntologies2010.pdf]]<br />
<br />
[[File:PO_FlashTalk_BioOntologies2010.pdf]]<br />
<br />
[[File:Walls_Cooper_BioOntologies29.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Dennis W. Stevenson, Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Common Reference Ontology for Plants. Boston, MA.''<br />
<br />
<br />
*[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology Workshop],Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010 <br />
Laurel Cooper and Ramona Walls attended and Laurel presented a talk [http://obofoundry.org/wiki/images/9/95/Plant_Ontology_CL_Workshop.ppt "Introduction to the Plant Ontology™"]<br />
<br />
*[http://intl-pag.org/ Plant and Animal Genome XVIII Conference], San Diego, CA. Jan. 9-13, 2010<br />
Laurel Cooper and Justin Elser [[Poster and Computer Demonstration]]<br />
<br />
''Elser, J., Cooper, L., and Jaiswal, P. (2010). Plant Ontology: Databases And Applications. San Diego, CA.''<br />
<br />
=Year 2009=<br />
* [http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=582&Itemid=283/ GCP Ontology Workshop] Rome, Italy, April 20-22, 2009<br />
** Chih-Wei Tung, Gave a talk on "Plant and Trait Ontology"<br />
<br />
* [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html/ 3rd International Biocuration Conference] Berlin, Germany, April 16-19, 2009<br />
** Chih-Wei Tung, POC poster presentation<br />
<br />
* [http://www.intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 10-14, 2009<br />
** Chih-Wei Tung, [http://www.intl-pag.org/17/abstracts/P08a_PAGXVII_807.html/ POC poster presentation]<br />
<br />
=Year 2008=<br />
* [http://bti.cornell.edu/ MetaCyc database workshop] Ithaca, Oct 21, 2008<br />
** Chih-Wei Tung, present a talk "An Introduction to the Plant Ontology Database "<br />
* [http://intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 12, 2008<br />
** Chih-Wei Tung, [http://intl-pag.org/16/abstracts/PAG16_C01_931.html POC poster presentation]<br />
<br />
=Year 2007=<br />
<br />
* [http://www.aspb.org/plantbiology/events.cfm ASPB 2007] Chicago, July 7-11, 2007<br />
** Chih-Wei Tung, [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/ASPB2007_PO_cw.ppt presentation], [http://2007.botanyconference.org/engine/search/index.php?func=detail&aid=2127 poster abstract]<br /><br />
<br />
* [http://www.gramene.org/workshop/rcn/ontology/rcn_onto-cshl07.html RCN Plant and Trait Ontology Workshop], CSHL, NY, June 10-11<br />
** Doreen Ware, Pankaj Jaiswal, Shuly Avraham, Chih-Wei Tung<br /><br />
<br />
* AGRONOMICS workshop " Ontologies, Standards and Best Practices", Gent, Belgium, May 21-23<br />
** Chih-Wei Tung, [http://www.agron-omics.eu/index.php/resource_center/workshops presentation]<br />
<br />
* [http://itmi.haifa.ac.il/06.html ITMI] Israel, April 16-20, 2007<br />
** Shuly Avraham, poster<br />
<br />
* [http://www.intl-pag.org/15/15-pag.html PAG XV] CA, January 13-17, 2007<br />
** Chih-Wei Tung, poster [http://www.intl-pag.org/pag/15/abstracts/PAG15_P08a_841.html abstract]<br />
<br />
=Year 2006=<br />
<br />
* [http://www.intl-pag.org/14/ PAG XIV] Ontology Workshop (2006): Ontologies for Databases<br />
** Anuradha Pujar: [http://www.intl-pag.org/14/abstracts/PAG14_W406.html Development of a generic plant growth stage ontology]<br />
** Katica Ilic: [http://www.intl-pag.org/14/abstracts/PAG14_P871.html Application of plant ontologies]<br />
<br />
=Year 2005=<br />
<br />
* [http://www.intl-pag.org/13/ PAG XIII] Ontology Workshop (2005): Development and Implementation of Ontologies in the Database<br />
** Leonore Reiser: [http://www.intl-pag.org/13/abstracts/PAG13_W244.html Using the Plant Ontologies]<br />
** Katica Ilic: [http://www.intl-pag.org/13/abstracts/PAG13_W242.html Controlled vocabularies for describing and cmparing phenotypes and gene expression]<br /><br />
** Pankaj: [http://www.intl-pag.org/cgi-bin/swish-bin/SwishPAGXIII.pl posters]<br />
<br />
* The 16th International Conference on Arabidopsis Research, Madison, WI, June 18, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_ki2005.ppt Katica Ilic] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_lr2005.ppt Leonore] presentations<br />
** [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_arabfnl_2005ki.ppt Poster]<br />
<br />
* The [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0010077 8th Annual Bio-Ontologies Meeting] at the [http://www.iscb.org/ismb2005/index.html ISMB], June 24, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/poc-ismb_pj2005.ppt Pankaj Jaiswal], presentation<br />
<br />
* The [http://www.maizegdb.org/maize_meeting/2005/ 47th Maize Genetic Conference], WI, March 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocpostermaizegenetics2005_mp.ppt Poster]<br />
<br />
* Frontiers in Plant Biology, MO, April 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_missouri2005ki.ppt Poster]<br />
<br />
* [http://www.ibc2005.ac.at The XVII International Botanical Congress], Vienna, Austria, July, 2005. Felipe, poster<br />
<br />
=Year 2004=<br />
<br />
* [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/annotationdemo_april2004.ppt Annotation Demo, 04/07/2004]<br />
* [http://www.botanyconference.org/ Botany 2004], Abstract #347 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_tk2004.ppt Toby.ppt]) and #351 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_fz2004.ppt Felipe.ppt])<br />
* [https://www.aspb.org/meetings/ ASPB 2004], FL, July, Abstract #864, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/aspbposter_ki23072004.ppt KI]), Workshop ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_pj2004.ppt PJ] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_lr2004.ppt LR])<br />
* [http://www.intl-pag.org/12/ PAG XII 2004], CA, January, Abstract # 927, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/pag_poster_pj2004.ppt Pankaj]), [http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html abstract]<br />
<br />
=Year 2002=<br />
<br />
* PAG X Bioinformatics: Database<br />
** Leszek Vincent: The POC and Plant ontologies ([http://www.intl-pag.org/pag/10/abstracts/PAGX_P815.html poster])<br />
** Leszek Vincent: The POC and Plant ontologies - silk purpose from a maize ear ([http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html workshop: ontology])<br />
<br />
[[Category:Documents]]<br />
[[Category:Outreach]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:Abstract_GI_2012_PO_poster.pdf&diff=19196File:Abstract GI 2012 PO poster.pdf2012-08-24T18:16:35Z<p>Preecej: PO abstract for Genome Informatics 2012 (Cambridge)</p>
<hr />
<div>PO abstract for Genome Informatics 2012 (Cambridge)</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_6-5-12&diff=18071POC Conf. Call 6-5-122012-06-05T22:16:33Z<p>Preecej: /* Image annotation software demo */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday June 6th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:''Laurel Cooper (OSU), Ramona Walls (NYBG), Marie Alejandra Gandolfo (Cornell), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG)''<br />
<br />
Absent:''Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)''<br />
<br />
<br />
<br />
Collaborators: none<br />
<br />
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=65565392&rKey=0c7d839ea1cb7310<br />
<br />
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=65565392&rKey=8aee18c021fa41e0 <br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_5-29-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
=Image annotation software demo=<br />
<br />
Justin Preece will give an updated demo of the ontology-enabled image annotation desktop application and also review these '''[[POC_Conf._Call_4-10-12#Demo_-_Integrating_Annotated_Images_with_PO_terms|HTML mock-ups]]''' (intended for future database and web development) for those who missed the previous demos.<br />
<br />
''JP demo'd the OEIA desktop application for the group. Thanks to all for their good questions and helpful feedback.''<br />
<br />
* '''Main idea:''' Markup and annotate images of botanical species w/ ontology terms, and store that data in such a way (structured zip files) that we can transfer it to a database in the future and serve it out to other applications. The application allows you to open an image, highlight individual parts of that image, label those parts with Plant Ontology terms, and save the annotated image accompanied by add'l metadata such as a curator, independent identifier, species, etc.<br />
* '''Future use-case example:''' Build a database to store this annotated image data and write an import utility to pull in .zip files and other annotated images (i.e. from ''plantsystematics.org''). Integrate this database with external web applications, such as the Plant Ontology AmiGO browser.<br />
* '''Usage and testing:''' The Cornell group is invited to begin using the app and providing feedback when it's ready (in a couple of weeks). We will set up a feature request and bug report submission system.<br />
* '''Presentation:''' RW has graciously agreed to demo it at the Botany 2012 conference (July 7-11)<br />
* ''Credits:'' Nikhil Lingutla: software adaptation and development, Justin Preece: software and systems architecture, design, development, and technical oversight. Pankaj: The bright ideas and the funding to make it happen.<br />
<br />
There are many UI and usability improvements we would like to make -- we already have a long list of things we look forward to adding or enhancing -- but we've been very focused on getting the fundamental image segmentation functionality, web service integration and data architecture ready. We welcome your feedback and suggestions, and we will prioritize those and implement them in incremental releases. - JP<br />
<br />
=Updating the pages on the PO website=<br />
Some of these changes like the tutorials are nb for the BSA workshop<br />
<br />
We will have a separate meeting to go over web site changes. Please fill out <br />
[http://www.doodle.com/vcpdceau6maratsp Doodle Poll]<br />
<br />
''This poll will be updated- maybe the week of June 18th we should follow-up on the changes''<br />
<br />
==Tutorials and presentations:==<br />
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.<br />
<br />
See [[Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date]]<br />
<br />
<br />
<br />
==Mistakes on website and wiki==<br />
See [[Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes]]<br />
<br />
''The website refresh (change to Drupal6) will probably take place late summer, early fall 2012, but in the meantime, we will start fixing the out of date pages''<br />
<br />
==Booklet for the BSA Workshop==<br />
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website. Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.<br />
<br />
Might be good to make it as a PDF, so it can include web links if people open it on screen.<br />
<br />
''We did not discuss this on today's call''<br />
<br />
=New upper level terms for PO=<br />
This section has moved back to [[Items_for_future_meetings#background_-_CARO]]- will go on the next meeting agenda.<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[http://www.regonline.com/builder/site/Default.aspx?EventID=1015479 MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes]==<br />
<br />
Thursday, June 14, 2012 - Friday, June 22, 2012<br />
<br />
The New York Botanical Garden<br />
<br />
Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).<br />
<br />
RW submitted an abstract for a poster [[File:PO_poster_Moss_2012.pdf]].<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
[http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on '''Sunday, July 8th, 9:00AM - 12:00PM'''<br />
<br />
see: link on [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops schedule] to view the abstract.<br />
<br />
Wiki page for workshop: [[Plant Ontology Workshop, Botany 2012]]<br />
<br />
Goal of workshop: To teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
Announcement has been posted on the PO home page and FB page.<br />
<br />
===exhibitor's booth===<br />
We had considered hosting an [http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth]. (Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference)<br />
<br />
''We decided that there were not enough people at the conference to man a booth and we could put up a display at the NYBG booth''<br />
<br />
''RW will look into purchasing a TV/monitor (~22") that could display a rotating slideshow. Could also be used for future presentations''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW will present the IDO-Plant paper and a poster on the PO-FNA collaboration.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
Dates TBA: probably Sept. 13-15th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
=Next meeting scheduled for Tuesday, June 12, 2012 at 10am PDT/1pm EDT=<br />
See: [[POC_Conf._Call_6-12-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_6-5-12&diff=18043POC Conf. Call 6-5-122012-06-05T15:49:20Z<p>Preecej: /* Image annotation software demo */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday June 6th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_5-29-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
=Image annotation software demo=<br />
<br />
Justin Preece will give an updated demo of the ontology-enabled image annotation desktop application and also review these '''[[POC_Conf._Call_4-10-12#Demo_-_Integrating_Annotated_Images_with_PO_terms|HTML mock-ups]]''' (intended for future database and web development) for those who missed the previous demos.<br />
<br />
=Preparations for Botany meeting workshop=<br />
We will have a separate meeting to go over web site changes. Please fill out Doodle Poll: <br />
http://www.doodle.com/vcpdceau6maratsp<br />
<br />
The notes below are just for everyone's information -- no need to discuss them at today's meeting<br />
<br />
==Updated tutorials and presentations==<br />
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.<br />
<br />
See [[Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date]]<br />
<br />
==Mistakes on website and wiki==<br />
See [[Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes]]<br />
<br />
==Booklet==<br />
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website. Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.<br />
<br />
Might be good to make it as a PDF, so it can include web links if people open it on screen.<br />
<br />
=New upper level terms for PO=<br />
This came up with the need to describe things that are part of a seed (and therefore not cardinal organ parts), along with some other problems.<br />
==structures that are located other organisms==<br />
The located_in relation has been to the PO file. Right now it is only used for embryo sac located in plant ovary ovule, but should be applied whenever there are two plant structures that are parts of different organisms.<br />
<br />
Located_in replaces contained_in. Located_in can be used for both part_of and contained_in.<br />
<br />
Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.<br />
<br />
Need to check with CM about correct xrefs for located_in.<br />
==Background==<br />
At the [[POC Conf. Call 5-8-12]] we discussed the need for a general term for collective plant structures that are collections of things other than organs. This general term would be parent of collective plant organ structure, collective organ part structure and other types of collective structures.<br />
<br />
If we want this term to be parent to seed, we need to define it broadly. What is a seed? It has as parts a mature ovule, some accessory structures like an aril, and parts derived from the ovule like the seed funicle. It also contains endosperm and an embryo. (See below about located in relation.) Is this a collective plant structure? What does it collect? Maybe seed coat, endosperm, and embryo.<br />
<br />
We also need a term to cover structures that are part of a seed (like arilloid and seed funicle) and terms like ovary that are parts of a plant, but do not fit any of the other categories. These are not necessarily collections. Could use something like CARO term '''multi-tissue structure'''.<br />
<br />
<br />
''Note from earlier meeting:'' If we include seed under the new CPS, we should mention that some of the parts of this new CPS are part of the mother plant and some are new organism. Some of the cells may be from the mother plant, but they take on a new developmental pathways, function, etc.<br />
<br />
==New proposed term [https://sourceforge.net/tracker/?func=detail&aid=3530843&group_id=76834&atid=835555 multi-tissue plant structure]==<br />
'''CARO:multi-tissue structure:''' Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component. <br />
<br />
This is very similar to PO plant organ, but does not come with the baggage of being called an organ so it can be applied more broadly. See below for definition of plant organ.<br />
<br />
<br />
'''proposed definition, multi-tissue plant structure:''' A plant structure that has as parts two or more portions of plant tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.<br />
<br />
Not sure about the bona-fide boundaries part.<br />
<br />
Seed could be a child of multi-tissue plant structure, as would plant organ, or we could make plant organ a synonym of multi-tissue plant structure.<br />
<br />
If we keep a separate term for plant organ, we could also add a term for "cardinal part of a multi-tissue structure", to go along with "cardinal organ part". If we decide to merge plant organ with multi-tissue structure, then cardinal organ part should be merged with cardinal part of a multi-tissue structure. Even if we keep plant organ (because it is such a commonly used term), we could still merge cardinal organ part with cardinal part of a multi-tissue structure. It seems confusing to have them as two separate classes.<br />
<br />
RW: I think this terms could be interpreted to be a parent to collective plant organ structure (CPOS), since CPOS's have two or more tissue and form a distinct structural unit (think of a flower or a gynoecium or a shoot system as a structural unit). In that case, if we create the term "cardinal part of multi-tissue structure", it could include things like ovary, which are part of either an organ or a CPOS. Cardinal organ part (and/or cardinal part of multi-tissue structure), however, would be outside this class, because not all cardinal organ parts are distinct structural units and have bona-fide boundaries.<br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=3530834&group_id=76834&atid=835555 collective plant structure (new)]===<br />
<br />
Do we still want a general term for collective plant structure, parent to collective plant organ structure and collective organ part structure?<br />
<br />
The important part of a collective plant structure is that it is a collection of two or more similar structures that are not tissues (e.g., two organs, two cardinal organ parts). If we add multi-tissue structure to cover seed, we may not need a new term for collective plant structure.<br />
<br />
proposed definition: A plant structure that is a proper part of a whole plant...<br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=2954382&group_id=76834&atid=835555 collective plant organ structure] (PO:0025007)===<br />
This is currently named '''collective plant structure'''. At the POC meeting on 5-?-12, we discussed renaming it "collective plant organ structure", which is clearer.<br />
<br />
Changed name, and slight change to clarify that the two organs must be adjacent, not one part of the other. Otherwise, a sporophyll would be a collective plant organ structure.<br />
<br />
New proposed def.: A collective plant structure (PO:id) that is a proper<br />
part of a whole plant (PO:0000003) and is composed of two or more '''adjacent'''<br />
plant organs (PO:0009008) and the associated portions of plant tissue<br />
(PO:0009007).<br />
<br />
comment: A collective plant organ structure must have as parts at least two<br />
organs that do not have a part of relation between them, that is, one must<br />
be adjacent to the other, rather than one part of the other. The organs in<br />
a collective plant structure can be of the same type, such as a corolla<br />
(PO:0009059) composed of multiple petals (PO:0009032), or of different<br />
types, such as a shoot system (PO:0009006) composed of shoot axes<br />
(PO:0025029) and phyllomes (PO:0006001). Other examples include flower<br />
(PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See<br />
also collective organ part structure (PO:0025269), for collective plant<br />
structures composed of parts of multiple organs, but no complete organs.<br />
<br />
===Modified comment for plant organ:===<br />
<br />
plant organ (PO:0009008), current def.: A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.<br />
<br />
new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.<br />
<br />
comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an ovule.<br />
<br />
<br />
===Slight modification to cardinal organ part===<br />
<br />
Add comment to see also COPS, add ids:<br />
<br />
'''cardinal organ part (PO:0025001), proposed def.:''' A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.<br />
<br />
comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.<br />
<br />
'''From discussion on 5-8-12:''' <br />
<br />
Maybe it would be better to say '''cardinal part of collective plant organ'''.<br />
<br />
FMA has "regional parts". It is like a "zone", which PO uses in a few terms. We also have terms like leaf tip or leaf lobe that are regional parts.<br />
<br />
This is what we call a cardinal part. BS: Biological significance is not all of the story for cardinal parts. They should also have their own boudaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.<br />
<br />
===collective organ part structure===<br />
<br />
Current def.: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.<br />
<br />
comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths. Unlike a collective plant structure, a collective organ part structure does not contain any complete organs.<br />
<br />
Add PO ids. Say "plant organs" instead of "organs".<br />
<br />
===cardinal part of collective plant structure===<br />
<br />
Do we still need this term? Maybe replace with cardinal part of multi-tissue plant structure.<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[http://www.regonline.com/builder/site/Default.aspx?EventID=1015479 MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes]==<br />
<br />
Thursday, June 14, 2012 - Friday, June 22, 2012<br />
<br />
The New York Botanical Garden<br />
<br />
Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).<br />
<br />
RW submitted an abstract for a poster [[File:PO_poster_Moss_2012.pdf]].<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
This is a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
An announcement has been posted on the PO home page and FB page.<br />
<br />
Goal of workshop: Will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW will present the IDO-Plant paper and a poster on the PO-FNA collaboration.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
Dates TBA: probably Sept. 13-15th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
=Next meeting scheduled for Tuesday, June 12, 2012 at 10am PDT/1pm EDT=<br />
See: [[POC_Conf._Call_6-12-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_6-5-12&diff=18031POC Conf. Call 6-5-122012-06-04T23:51:27Z<p>Preecej: /* Image annotation software demo */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday June 6th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_5-29-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
=Image annotation software demo=<br />
<br />
Justin Preece will give an updated demo of the image annotation desktop application and also review these '''[[POC_Conf._Call_4-10-12#Demo_-_Integrating_Annotated_Images_with_PO_terms|HTML mock-ups]]''' (intended for future database and web development) for those who missed the previous demos.<br />
<br />
=Preparations for Botany meeting workshop=<br />
We will have a separate meeting to go over web site changes. Please fill out Doodle Poll: <br />
http://www.doodle.com/vcpdceau6maratsp<br />
<br />
The notes below are just for everyone's information -- no need to discuss them at today's meeting<br />
<br />
==Updated tutorials and presentations==<br />
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.<br />
<br />
See [[Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date]]<br />
<br />
==Mistakes on website and wiki==<br />
See [[Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes]]<br />
<br />
==Booklet==<br />
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website. Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.<br />
<br />
Might be good to make it as a PDF, so it can include web links if people open it on screen.<br />
<br />
=New upper level terms for PO=<br />
This came up with the need to describe things that are part of a seed (and therefore not cardinal organ parts), along with some other problems.<br />
<br />
==Background==<br />
At the [[POC Conf. Call 5-8-12]] we discussed the need for a general term for collective plant structures that are collections of things other than organs. This general term would be parent of collective plant organ structure, collective organ part structure and other types of collective structures.<br />
<br />
If we want this term to be parent to seed, we need to define it broadly. What is a seed? It has as parts a mature ovule, some accessory structures like an aril, and parts derived from the ovule like the seed funicle. It also contains endosperm and an embryo. (See below about located in relation.) Is this a collective plant structure? What does it collect? Maybe seed coat, endosperm, and embryo.<br />
<br />
We also need a term to cover structures that are part of a seed (like arilloid and seed funicle) and terms like ovary that are parts of a plant, but do not fit any of the other categories. These are not necessarily collections. Could use something like CARO term '''multi-tissue structure'''.<br />
<br />
<br />
''Note from earlier meeting:'' If we include seed under the new CPS, we should mention that some of the parts of this new CPS are part of the mother plant and some are new organism. Some of the cells may be from the mother plant, but they take on a new developmental pathways, function, etc.<br />
<br />
==structures that are located other organisms==<br />
The located_in relation has been to the PO file. Right now it is only used for embryo sac located in plant ovary ovule, but should be applied whenever there are two plant structures that are parts of different organisms.<br />
<br />
Located_in replaces contained_in. Located_in can be used for both part_of and contained_in.<br />
<br />
Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.<br />
<br />
Need to check with CM about correct xrefs for located_in.<br />
<br />
==New proposed term [https://sourceforge.net/tracker/?func=detail&aid=3530843&group_id=76834&atid=835555 multi-tissue plant structure]==<br />
'''CARO:multi-tissue structure:''' Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component. <br />
<br />
This is very similar to PO plant organ, but does not come with the baggage of being called an organ so it can be applied more broadly. See below for definition of plant organ.<br />
<br />
<br />
'''proposed definition, multi-tissue plant structure:''' A plant structure that has as parts two or more portions of plant tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.<br />
<br />
Not sure about the bona-fide boundaries part.<br />
<br />
Seed could be a child of multi-tissue plant structure, as would plant organ, or we could make plant organ a synonym of multi-tissue plant structure.<br />
<br />
If we keep a separate term for plant organ, we could also add a term for "cardinal part of a multi-tissue structure", to go along with "cardinal organ part". If we decide to merge plant organ with multi-tissue structure, then cardinal organ part should be merged with cardinal part of a multi-tissue structure. Even if we keep plant organ (because it is such a commonly used term), we could still merge cardinal organ part with cardinal part of a multi-tissue structure. It seems confusing to have them as two separate classes.<br />
<br />
RW: I think this terms could be interpreted to be a parent to collective plant organ structure (CPOS), since CPOS's have two or more tissue and form a distinct structural unit (think of a flower or a gynoecium or a shoot system as a structural unit). In that case, if we create the term "cardinal part of multi-tissue structure", it could include things like ovary, which are part of either an organ or a CPOS. Cardinal organ part (and/or cardinal part of multi-tissue structure), however, would be outside this class, because not all cardinal organ parts are distinct structural units and have bona-fide boundaries.<br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=3530834&group_id=76834&atid=835555 collective plant structure (new)]===<br />
<br />
Do we still want a general term for collective plant structure, parent to collective plant organ structure and collective organ part structure?<br />
<br />
The important part of a collective plant structure is that it is a collection of two or more similar structures that are not tissues (e.g., two organs, two cardinal organ parts). If we add multi-tissue structure to cover seed, we may not need a new term for collective plant structure.<br />
<br />
proposed definition: A plant structure that is a proper part of a whole plant...<br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=2954382&group_id=76834&atid=835555 collective plant organ structure] (PO:0025007)===<br />
This is currently named '''collective plant structure'''. At the POC meeting on 5-?-12, we discussed renaming it "collective plant organ structure", which is clearer.<br />
<br />
Changed name, and slight change to clarify that the two organs must be adjacent, not one part of the other. Otherwise, a sporophyll would be a collective plant organ structure.<br />
<br />
New proposed def.: A collective plant structure (PO:id) that is a proper<br />
part of a whole plant (PO:0000003) and is composed of two or more '''adjacent'''<br />
plant organs (PO:0009008) and the associated portions of plant tissue<br />
(PO:0009007).<br />
<br />
comment: A collective plant organ structure must have as parts at least two<br />
organs that do not have a part of relation between them, that is, one must<br />
be adjacent to the other, rather than one part of the other. The organs in<br />
a collective plant structure can be of the same type, such as a corolla<br />
(PO:0009059) composed of multiple petals (PO:0009032), or of different<br />
types, such as a shoot system (PO:0009006) composed of shoot axes<br />
(PO:0025029) and phyllomes (PO:0006001). Other examples include flower<br />
(PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See<br />
also collective organ part structure (PO:0025269), for collective plant<br />
structures composed of parts of multiple organs, but no complete organs.<br />
<br />
===Modified comment for plant organ:===<br />
<br />
plant organ (PO:0009008), current def.: A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.<br />
<br />
new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.<br />
<br />
comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an ovule.<br />
<br />
<br />
===Slight modification to cardinal organ part===<br />
<br />
Add comment to see also COPS, add ids:<br />
<br />
'''cardinal organ part (PO:0025001), proposed def.:''' A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.<br />
<br />
comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.<br />
<br />
'''From discussion on 5-8-12:''' <br />
<br />
Maybe it would be better to say '''cardinal part of collective plant organ'''.<br />
<br />
FMA has "regional parts". It is like a "zone", which PO uses in a few terms. We also have terms like leaf tip or leaf lobe that are regional parts.<br />
<br />
This is what we call a cardinal part. BS: Biological significance is not all of the story for cardinal parts. They should also have their own boudaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.<br />
<br />
===collective organ part structure===<br />
<br />
Current def.: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.<br />
<br />
comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths. Unlike a collective plant structure, a collective organ part structure does not contain any complete organs.<br />
<br />
Add PO ids. Say "plant organs" instead of "organs".<br />
<br />
===cardinal part of collective plant structure===<br />
<br />
Do we still need this term? Maybe replace with cardinal part of multi-tissue plant structure.<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[http://www.regonline.com/builder/site/Default.aspx?EventID=1015479 MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes]==<br />
<br />
Thursday, June 14, 2012 - Friday, June 22, 2012<br />
<br />
The New York Botanical Garden<br />
<br />
Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).<br />
<br />
RW submitted an abstract for a poster [[File:PO_poster_Moss_2012.pdf]].<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
This is a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
An announcement has been posted on the PO home page and FB page.<br />
<br />
Goal of workshop: Will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW will present the IDO-Plant paper and a poster on the PO-FNA collaboration.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
Dates TBA: probably Sept. 13-15th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
=Next meeting scheduled for Tuesday, June 12, 2012 at 10am PDT/1pm EDT=<br />
See: [[POC_Conf._Call_6-12-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=18008Plant Ontology Web Site Update: 20132012-06-01T21:08:27Z<p>Preecej: </p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under <br />
"/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link<br />
to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not<br />
their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking<br />
you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email<br />
notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Current PO Site Map===<br />
<br />
Screenshots of site content (''circa'' Spring 2012) have been collected, mapped to URLs, and tagged with summary descriptions. You can download the site map '''[[media:PO Site Map Spring 2012.pdf|here]]'''. This is a clickable PDF: the screenshots are linked to the actual site.<br />
<br />
Or, if you would rather just look at the pretty picture...<br />
<br />
[[image:PO Site Map Spring 2012.png|400px|PO Site Map - Spring 2012]]<br />
<br />
This document is intended to capture the state of affairs on the site ''as they are'', not necessarily as we wish them to be. The grouping and categorization of pages is arbitrary and meant to be a discussion starter about how you would like the site content to be organized going forward. If corrections are needed, just let us know.<br />
<br />
For the moment, please feel free to leave your comments and suggestions about site content organization here. If that discussion becomes substantial, we can move it to its own page.<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
* GARNet has a clean, fresh look- I like it: [http://www.garnetcommunity.org.uk/ GARNet] LC<br />
<br />
* MosDB: http://mips.helmholtz-muenchen.de/plant/rice/index.jsp<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our Palea web server (''currently in progress'').<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
See also the items listed on the [[POC_Technical_Issues_Page]]- some of which are AmiGO specific<br />
<br />
==High priority fixes==<br />
<br />
RW has marked these as high priority to fix before the Botany meeting (by mid-June).<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to log in to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
RW (4/2012): Maybe this has been fixed? Seems to work. I have created a wiki page for [[How_to_use_the_Source_Forge_tracker]].<br />
<br />
This could be made into a web page, as part of the browser, rather than leaving it on the wiki. Perhaps the "Request term" page link here, instead of directly to Source Forge.<br />
<br />
===Plant Ontology Browser Users Guide===<br />
http://plantontology.org/amigo_user_guide/index.html#intro<br />
<br />
- No images show up. Text not displaying correctly (missing spaces).<br />
<br />
===Web pages that are out of date - high priority===<br />
<br />
*http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date.<br />
*http://plantontology.org/docs/growth/growth_stages.html - Out of date. Should merge with page for development stages.<br />
*http://plantontology.org/docs/faq/growth_faq.html - Out of date. Should merge with page for development stages.<br />
*http://plantontology.org/docs/development/developmental_stages.html - Out of date. Should merge with page for growth stages.<br />
<br />
*http://plantontology.org/docs/otherdocs/ontology_doc.html Developers' guide. Content is not too bad, but this should be only on the wiki, and not on the web page since it is only for developers -- most users never need to see this.<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
Presentations/tutorials that need to be updated:<br />
<br />
*[http://plantontology.org/docs/presentations/demo/poc-demo-1.html Introduction to the project] - Slide show. There are links to this from both the web page and the wiki. Much of it is still valid, so it could be updated, rater than replaced. [http://palea.cgrb.oregonstate.edu/viewsvn/plantontology/html/docs/presentations/demo/ link to svn folder]<br />
<br />
*http://wiki.plantontology.org/index.php/Plant_Ontology_Tutorials and http://plantontology.org/docs/otherdocs/tutorials.html<br />
<br />
'''There is a problem opening or downloading the following quicktime movies and the ppt files.''' JE is looking into this right now.<br />
<br />
*Introduction to ontologies: http://plantontology.org/docs/presentations/tutorials/poc_intro.mov, http://plantontology.org/docs/presentations/tutorials/poc_intro.ppt Powerpoint slides<br />
*Development of ontologies: http://plantontology.org/docs/presentations/tutorials/ontology.mov, http://plantontology.org/docs/presentations/tutorials/ontology.ppt<br />
*Annotations: http://plantontology.org/docs/presentations/tutorials/annotation.mov, http://plantontology.org/docs/presentations/tutorials/annotation.ppt<br />
*Plant ontology browser and POC web site: http://plantontology.org/docs/presentations/tutorials/website.mov, http://plantontology.org/docs/presentations/tutorials/website.ppt<br />
<br />
===Out of date wiki pages===<br />
Principles, Rationales and Key Organizing Rules of the PO (These correspond to the out of date web pages).:<br />
* [[Plant_Structure_Principles_Rules|Plant Structure Ontology]] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure. <br />
* [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked questions]]<br />
* [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]]<br />
<br />
<br />
*Wiki home page: under Formats of the Ontology Files, needs info on OWL (provide link).<br />
<br />
===Developers guide -Download SVN Page===<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
http://www.plantontology.org/download/svn_doc.html Developers guide<br />
<br />
RW: Thanks for adding instructions for Mac users!<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an images for all these relations.''<br />
<br />
''RW: Minor point, but perhaps the list of icons could be have is_a first (as it is now) and then list the rest of them in alphabetical order.''<br />
<br />
==Medium priority fixes==<br />
These fixes are important, but can wait until after June.<br />
<br />
===Web pages that are out of date - medium priority===<br />
*http://plantontology.org/docs/otherdocs/poc_project.html - Was updated in the past year, but needs new updates. Still refers to "Plant Growth and Developmental Stages". Could use more detail on the project.<br />
*http://plantontology.org/docs/otherdocs/charter.html POC charter is out of date.<br />
*http://plantontology.org/docs/otherdocs/resources.html out of date<br />
*http://plantontology.org/docs/references/pub.html out of date<br />
<br />
==Feature requests==<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
RW: Yes! This would be really great.</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=18007Plant Ontology Web Site Update: 20132012-06-01T20:48:48Z<p>Preecej: /* Current PO Site Map */</p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under <br />
"/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link<br />
to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not<br />
their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking<br />
you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email<br />
notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
* GARNet has a clean, fresh look- I like it: [http://www.garnetcommunity.org.uk/ GARNet] LC<br />
<br />
* MosDB: http://mips.helmholtz-muenchen.de/plant/rice/index.jsp<br />
<br />
===Current PO Site Map===<br />
<br />
Screenshots of site content (''circa'' Spring 2012) have been collected, mapped to URLs, and tagged with summary descriptions. You can download the site map '''[[media:PO Site Map Spring 2012.pdf|here]]'''.<br />
<br />
Or, if you would rather just look at the pretty picture...<br />
<br />
[[image:PO Site Map Spring 2012.png|400px|PO Site Map - Spring 2012]]<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our Palea web server (''currently in progress'').<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
See also the items listed on the [[POC_Technical_Issues_Page]]- some of which are AmiGO specific<br />
<br />
==High priority fixes==<br />
<br />
RW has marked these as high priority to fix before the Botany meeting (by mid-June).<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to log in to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
RW (4/2012): Maybe this has been fixed? Seems to work. I have created a wiki page for [[How_to_use_the_Source_Forge_tracker]].<br />
<br />
This could be made into a web page, as part of the browser, rather than leaving it on the wiki. Perhaps the "Request term" page link here, instead of directly to Source Forge.<br />
<br />
===Plant Ontology Browser Users Guide===<br />
http://plantontology.org/amigo_user_guide/index.html#intro<br />
<br />
- No images show up. Text not displaying correctly (missing spaces).<br />
<br />
===Web pages that are out of date - high priority===<br />
<br />
*http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date.<br />
*http://plantontology.org/docs/growth/growth_stages.html - Out of date. Should merge with page for development stages.<br />
*http://plantontology.org/docs/faq/growth_faq.html - Out of date. Should merge with page for development stages.<br />
*http://plantontology.org/docs/development/developmental_stages.html - Out of date. Should merge with page for growth stages.<br />
<br />
*http://plantontology.org/docs/otherdocs/ontology_doc.html Developers' guide. Content is not too bad, but this should be only on the wiki, and not on the web page since it is only for developers -- most users never need to see this.<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
Presentations/tutorials that need to be updated:<br />
<br />
*[http://plantontology.org/docs/presentations/demo/poc-demo-1.html Introduction to the project] - Slide show. There are links to this from both the web page and the wiki. Much of it is still valid, so it could be updated, rater than replaced. [http://palea.cgrb.oregonstate.edu/viewsvn/plantontology/html/docs/presentations/demo/ link to svn folder]<br />
<br />
*http://wiki.plantontology.org/index.php/Plant_Ontology_Tutorials and http://plantontology.org/docs/otherdocs/tutorials.html<br />
<br />
'''There is a problem opening or downloading the following quicktime movies and the ppt files.''' JE is looking into this right now.<br />
<br />
*Introduction to ontologies: http://plantontology.org/docs/presentations/tutorials/poc_intro.mov, http://plantontology.org/docs/presentations/tutorials/poc_intro.ppt Powerpoint slides<br />
*Development of ontologies: http://plantontology.org/docs/presentations/tutorials/ontology.mov, http://plantontology.org/docs/presentations/tutorials/ontology.ppt<br />
*Annotations: http://plantontology.org/docs/presentations/tutorials/annotation.mov, http://plantontology.org/docs/presentations/tutorials/annotation.ppt<br />
*Plant ontology browser and POC web site: http://plantontology.org/docs/presentations/tutorials/website.mov, http://plantontology.org/docs/presentations/tutorials/website.ppt<br />
<br />
===Out of date wiki pages===<br />
Principles, Rationales and Key Organizing Rules of the PO (These correspond to the out of date web pages).:<br />
* [[Plant_Structure_Principles_Rules|Plant Structure Ontology]] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure. <br />
* [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked questions]]<br />
* [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]]<br />
<br />
<br />
*Wiki home page: under Formats of the Ontology Files, needs info on OWL (provide link).<br />
<br />
===Developers guide -Download SVN Page===<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
http://www.plantontology.org/download/svn_doc.html Developers guide<br />
<br />
RW: Thanks for adding instructions for Mac users!<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an images for all these relations.''<br />
<br />
''RW: Minor point, but perhaps the list of icons could be have is_a first (as it is now) and then list the rest of them in alphabetical order.''<br />
<br />
==Medium priority fixes==<br />
These fixes are important, but can wait until after June.<br />
<br />
===Web pages that are out of date - medium priority===<br />
*http://plantontology.org/docs/otherdocs/poc_project.html - Was updated in the past year, but needs new updates. Still refers to "Plant Growth and Developmental Stages". Could use more detail on the project.<br />
*http://plantontology.org/docs/otherdocs/charter.html POC charter is out of date.<br />
*http://plantontology.org/docs/otherdocs/resources.html out of date<br />
*http://plantontology.org/docs/references/pub.html out of date<br />
<br />
==Feature requests==<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
RW: Yes! This would be really great.</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:PO_Site_Map_Spring_2012.png&diff=18006File:PO Site Map Spring 2012.png2012-06-01T20:47:17Z<p>Preecej: uploaded a new version of "File:PO Site Map Spring 2012.png":&#32;added an internal border</p>
<hr />
<div>Screenshot of map, links, and content descriptions for the Plant Ontology web site, as of Spring 2012.</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:PO_Site_Map_Spring_2012.png&diff=18005File:PO Site Map Spring 2012.png2012-06-01T20:37:47Z<p>Preecej: Screenshot of map, links, and content descriptions for the Plant Ontology web site, as of Spring 2012.</p>
<hr />
<div>Screenshot of map, links, and content descriptions for the Plant Ontology web site, as of Spring 2012.</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:PO_Site_Map_Spring_2012.pdf&diff=18004File:PO Site Map Spring 2012.pdf2012-06-01T20:29:05Z<p>Preecej: Map, links, and content descriptions for the Plant Ontology web site, as of Spring 2012.</p>
<hr />
<div>Map, links, and content descriptions for the Plant Ontology web site, as of Spring 2012.</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_6-5-12&diff=18003POC Conf. Call 6-5-122012-06-01T20:12:02Z<p>Preecej: /* Mistakes on website and wiki */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday June 6th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_5-29-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
=Preparations for Botany meeting workshop=<br />
==Updated tutorials and presentations==<br />
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.<br />
<br />
See [[Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date]]<br />
<br />
==Mistakes on website and wiki==<br />
See [[Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes]]<br />
<br />
==Booklet==<br />
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website. Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.<br />
<br />
Might be good to make it as a PDF, so it can include web links if people open it on screen.<br />
<br />
=New upper level terms for PO=<br />
This came up as the need to describe things that are part of a seed, along with some other problems.<br />
<br />
==Background==<br />
At the [[POC Conf. Call 5-8-12]] we discussed the need for a general term for collective plant structures that are collections of things other than organs. This general term would be parent of collective plant organ structure, collective organ part structure and other types of collective structures.<br />
<br />
If we want this term to be parent to seed, we need to define it broadly. What is a seed? It has as parts a mature ovule, some accessory structures like an aril, and parts derived from the ovule like the seed funicle. It also contains endosperm and an embryo. (See below about located in relation.) Is this a collective plant structure? What does it collect? Maybe seed coat, endosperm, and embryo.<br />
<br />
We also need a term to cover structures that are part of a seed (like arilloid and seed funicle) and terms like ovary that are parts of a plant, but do not fit any of the other categories. These are not necessarily collections. Could use something like CARO term '''multi-tissue structure'''. This would be parent to CPS, but also plant organ, cardinal organ part, and things like arilloid.<br />
<br />
<br />
''Note from earlier meeting:'' If we include seed under the new CPS, we should mention that some of the parts of this new CPS are part of the mother plant and some are new organism. Some of the cells may be from the mother plant, but they take on a new developmental pathways, function, etc.<br />
<br />
==structures that are located other organisms==<br />
The located_in relation has been to the PO file. Right now it is only used for embryo sac located in plant ovary ovule, but should be applied whenever there are two plant structures that are parts of different organisms.<br />
<br />
Located_in replaces contained_in. Located_in can be used for both part_of and contained_in.<br />
<br />
Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.<br />
<br />
==New proposed term [https://sourceforge.net/tracker/?func=detail&aid=3530843&group_id=76834&atid=835555 multi-tissue plant structure]==<br />
'''CARO:multi-tissue structure:''' Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component. <br />
<br />
This is very similar to PO plant organ, but does not come with the baggage of being called an organ so it can be applied more broadly. See below for definition of plant organ.<br />
<br />
<br />
'''proposed definition, multi-tissue plant structure:''' A plant structure that has as parts two or more portions of plant tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.<br />
<br />
Not sure about the bona-fide boundaries part.<br />
<br />
Seed could be a child of multi-tissue plant structure, as would plant organ, or we could make plant organ a synonym of multi-tissue plant structure.<br />
<br />
If we keep a separate term for plant organ, we could also add a term for "cardinal part of a multi-tissue structure", to go along with "cardinal organ part". If we decide to merge plant organ with multi-tissue structure, then cardinal organ part should be merged with cardinal part of a multi-tissue structure. Even if we keep plant organ (because it is such a commonly used term), we could still merge cardinal organ part with cardinal part of a multi-tissue structure. It seems confusing to have them as two separate classes.<br />
<br />
RW: I think this terms could be interpreted to be a parent to collective plant organ structure (CPOS), since CPOS's have two or more tissue and form a distinct structural unit (think of a flower or a gynoecium or a shoot system as a structural unit). In that case, if we create the term "cardinal part of multi-tissue structure", it could include things like ovary, which are part of either an organ or a CPOS. <br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=3530834&group_id=76834&atid=835555 collective plant structure (new)]===<br />
<br />
Do we still want a general term for collective plant structure, parent to collective plant organ structure and collective organ part structure?<br />
<br />
The important part of a collective plant structure is that it is a collection of two or more similar structures that are not tissues (e.g., two organs, two cardinal organ parts). If we add multi-tissue structure to cover seed, we may not need a new term for collective plant structure.<br />
<br />
proposed definition: A plant structure that is a proper part of a whole plant...<br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=2954382&group_id=76834&atid=835555 collective plant organ structure]===<br />
Changed name, and slight change to clarify that the two organs must be adjacent, not one part of the other. Otherwise, a sporophyll would be a collective plant organ structure.<br />
<br />
New proposed def.: A collective plant structure (PO:id) that is a proper<br />
part of a whole plant (PO:0000003) and is composed of two or more '''adjacent'''<br />
plant organs (PO:0009008) and the associated portions of plant tissue<br />
(PO:0009007).<br />
<br />
comment: A collective plant organ structure must have as parts at least two<br />
organs that do not have a part of relation between them, that is, one must<br />
be adjacent to the other, rather than one part of the other. The organs in<br />
a collective plant structure can be of the same type, such as a corolla<br />
(PO:0009059) composed of multiple petals (PO:0009032), or of different<br />
types, such as a shoot system (PO:0009006) composed of shoot axes<br />
(PO:0025029) and phyllomes (PO:0006001). Other examples include flower<br />
(PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See<br />
also collective organ part structure (PO:0025269), for collective plant<br />
structures composed of parts of multiple organs, but no complete organs.<br />
<br />
<br />
===Modified comment for plant organ:===<br />
<br />
plant organ (PO:0009008), current def.: A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.<br />
<br />
new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.<br />
<br />
comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an ovule.<br />
<br />
<br />
===Slight modification to cardinal organ part===<br />
<br />
Add comment to see also COPS, add ids:<br />
<br />
'''cardinal organ part (PO:0025001), proposed def.:''' A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.<br />
<br />
comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.<br />
<br />
'''From discussion on 5-8-12:''' <br />
<br />
Maybe it would be better to say "cardinal part of collective plant structure" and "cardinal part of plant organ.<br />
<br />
FMA has "regional parts". It is like a "zone", which PO uses in a few terms. We also have terms like leaf tip or leaf lobe that are regional parts.<br />
<br />
This is what we call a cardinal part. BS: Biological significance is not all of the story for cardinal parts. They should also have their own boudaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.<br />
<br />
===collective organ part structure===<br />
<br />
Current def.: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.<br />
<br />
comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths. Unlike a collective plant structure, a collective organ part structure does not contain any complete organs.<br />
<br />
Add PO ids. Say "plant organs" instead of "organs".<br />
<br />
===cardinal part of collective plant structure===<br />
<br />
Do we still need this term? Maybe replace with cardinal part of multi-tissue plant structure.<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[http://www.regonline.com/builder/site/Default.aspx?EventID=1015479 MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes]==<br />
<br />
Thursday, June 14, 2012 - Friday, June 22, 2012<br />
<br />
The New York Botanical Garden<br />
<br />
Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).<br />
<br />
RW submitted an abstract for a poster [[File:PO_poster_Moss_2012.pdf]].<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
Dates TBA: probably Sept. 13-15th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
This is a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
An announcement has been posted on the PO home page and FB page.<br />
<br />
Goal of workshop: Will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW will present the IDO-Plant paper and a poster on the PO-FNA collaboration.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
=Next meeting scheduled for Tuesday, June 12, 2012 at 10am PDT/1pm EDT=<br />
See: [[POC_Conf._Call_6-12-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Technical_Issues_Page&diff=18002POC Technical Issues Page2012-06-01T20:11:28Z<p>Preecej: /* Plant Ontology Web site issues: */</p>
<hr />
<div>This page provides a record of the technical issues and software needs of the POC. When requesting new software, please provide an example of why the software is needed. Also provide the date that the request was first made. If the problem has been solved (either by creation of new software, or through some other means, please provide information on the solution here.<br />
<br />
website issues- link from downlooad page goes to index page. Need a direct link to the live tag.<br />
<br />
<br />
<br />
==Need new DBxRef Links:==<br />
<br />
* Link to ISBN#s- [http://openisbn.com/ OpenISBN] or page with list of ISBN refs [[PO_references]]<br />
<br />
* [[PO_references]] page for POC curators or something similar<br />
<br />
* Need to fix dbxref for Fragaria<br />
<br />
<br />
(LC 2-18-12)<br />
<br />
==Database structure==<br />
From Chris Mungall:<br />
<br />
It makes things a little easier if the directory is laid out consistently with other ontologies. Perhaps<br />
<br />
ontology/<br />
<br />
>po-edit.obo<br />
<br />
>po.obo # derived<br />
<br />
>po.owl # derived<br />
<br />
>...<br />
<br />
(RW 3-7-12)<br />
<br />
=AmiGo 2 Wishlist:=<br />
==More reasons to switch to AmiGO 2==<br />
Recent email from CM:<br />
<br />
Note that AmiGO1 will give curious answers to gene expression queries if you leave in has_part. AmiGO2 will handle cycles and answering questions appropriately.<br />
<br />
(RW05-03-12)<br />
==Idea for PO Graphical Viewer==<br />
suggested at wood ontology meeting 2-6-12:<br />
<br />
Customize the graph- for example, make the part_of relation a dotted line to differentiate it from the is_a relation<br />
<br />
==Idea for advanced filter==<br />
suggested at wood ontology meeting 2-6-12:<br />
<br />
Would be good to be able to filter by relation type<br />
<br />
==Redirect from search to GO==<br />
How is the best way to redirect users to terms that are in GO? For example; casparian strip or pit membranes? <br />
<br />
We need a means of redirection from the search- could we have a list of GO terms specific to the PO that the browser could redirect to?<br />
<br />
(LC Feb 2012)<br />
<br />
==sort the child terms numerically==<br />
<br />
It would be great if the tree would sort the child terms numerically, rather than alphabetically by term name. This came up in the discussion of the seed trichome dev stage terms [[POC_Conf._Call_11-29-11]]. Then we would not have to prefix the names with numbers or letters.<br />
<br />
==Link on Homepage to Source Forge tracker==<br />
submitted 9-28-11- LC<br />
Now that people need to login to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
==Color coding the Anatomy and Development terms differently?==<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
==filter translation==<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
<br />
email: schaefferm@missouri.edu<br />
<br />
organization: MaizeGDB<br />
<br />
==Download annotations from the PO website==<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
==New images needed for browser==<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We now have icons for all relations. Remove this item? (RW05-03-12)''<br />
<br />
=Translations=<br />
New subsets for Spanish and Japanese synonyms are ready to be added to the PO, with the scope exact synonym. All plant anatomy terms now have Spanish synonyms, and most have Japanese synonyms. Spanish and Japanese synonyms will not be incorporated into the live version of the PO for this release, but will be available to users on request.<br />
<br />
Just need the script to insert them, will include in the next release<br />
<br />
==Need script for inserting the translations as synonyms into the obo file==<br />
<br />
Also, it would be helpful to be able to generate a list of the new terms whenever we are ready for a new release. <br />
<br />
It should contain the ID, English name, foreign name, and definition. There would be blank spaces under the foreign name for any new term. If we also could make it flag terms whose names have changed since the last release, that would be great.<br />
<br />
=Version information=<br />
(posted 11-14-11)<br />
<br />
We have been numbering releases sequentially (e.g., 1 -16)<br />
<br />
CM suggests another system:<br />
<br />
Many people use YYYY-MM-DD<br />
<br />
See http://www.obofoundry.org/id-policy.shtml<br />
<br />
This has the advantage of making automated releases easier - just use the date and don't worry about what the previous version# is. Oort should do this for you.<br />
<br />
It's up to you how you do it. You could have names like apple, except cute plants rather than cute animals.<br />
<br />
If you are using incremental versions, I recommend a minor-major system with a dash separator. E.g. 1-16.<br />
<br />
If you are manually assigning releases then you can add this to the data-version tag in the obo, where it will propagate to versionInfo in OWL<br />
<br />
=Plant Ontology Web site issues:=<br />
Please go to: [[Plant Ontology Web Site Update: 2012]]<br />
<br />
==Tutorials and Demos out-of-date==<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
=Problem on the dev browser- can't filter by the new 'plant anatomy' name=<br />
<br />
''Looked at filtering problem on dev browser. It does not seem to be related to differences in capitalization or word form, as these also exist on the live browser, with no problem. JE is looking into it. ''<br />
<br />
=Problems displaying AmiGO Browser in Internet Explorer:=<br />
<br />
PJ sent a note out by email that some users are having problems displaying AmiGO Browser in Internet Explorer: IE views are not similar to the ones in Firefox.<br />
<br />
-See the comment at:[https://sites.google.com/site/liveplantimagegroup/ontologies-and-identifier-structure/plant-ontology link] "On my computer, this displays correctly in FireFox 3.6.13, but not Internet Explorer 8.0.6' on this page." <br />
<br />
<br />
- RW confirmed it: "The Amigo browser tree view does not display correctly in Internet Explorer on my PC either. All of the terms at one level of the tree are displayed on one line, instead of in a hierarchy. I'm sure I've griped about this before, but don't know if I have a written record. It works fine on Safari and Firefox on my Mac."<br />
<br />
<br />
JE looked into this and it seems to be just with the newest version of the IE. We will put a note on our browser site: "Best viewed using Firefox" or something to that effect.<br />
<br />
=Problem: Loading ''has_part'' relations in the Plant Ontology File=<br />
<br />
'''Original request''': This became a problem with with the January 2011 release, as the has_part relation had to be stripped out. <br />
<br />
==The Problem:== <br />
<br />
-The ''has_part'' relation causes a 'circularity or cycle' when loading the Ontology file into the database (not onto the browser as we originally thought?).<br />
<br />
-Note: Our collaborators (eg; SGN), who uses a Chado schema, also have to remove them (LC). <br />
<br />
-What exactly is causing the problem with loading? Is it actually the has_part relations themselves? (note: removing them allows the file to be loaded with no problems)<br />
<br />
<br />
==Questions:==<br />
<br />
*Do the problems arise when we have reciprocal part_of and has_part relations (or reciprocal part_of and develops_from relations) ? <br />
<br />
For example, embryo sac egg cell is ''part_of'' egg apparatus and egg apparatus ''has_part'' embryo sac egg cell. <br />
<br />
[[File:Egg apparatus.jpg]]<br />
<br />
* JP: In general, which relations are treated as "reciprocally coupled"? Does this differ amongst different reasoners?<br />
<br />
-Example: Does the OBO-Edit reasoner recognize these as "reciprocally coupled"? (Is the OE reasoner on when these are being added?)<br />
<br />
<br />
* Uberon has a similar situation with mammary gland secretes milk and milk secreted_by mammary gland. Does that cause a problem?<br />
<br />
*Also, PO has reciprocal disjoint_from relations, and they don't seem to cause a problem<br />
<br />
*Question for JE: Are the disjoints being stripped from the live plant_ontology.obo file? They do not show up in the AmiGO browser either.<br />
<br />
**(JE) I am not taking them explicitly out, but there is no trace of them in the database. Not sure why.<br />
<br />
==Definition of has_part relation vs the part_of relation:==<br />
<br />
'''*definition of has_part:''' <br />
<br />
"In GO: The relationship A ''has_part'' B means that A necessarily (always) has B as a part"; <br />
<br />
i.e., if A exists then B also exists as a part of A. If A does not exist, B may or may not exist. <br />
<br />
For example, ‘cell envelope’ ''has_part'' ‘plasma membrane’ means that a cell envelope always has a plasma membrane as a part but a plasma membrane may exist without being a part of a cell envelope. "<br />
<br />
(Reference: The Gene Ontology Consortium The Gene Ontology in 2010: extensions and refinements. Nucl. Acids Res. 38, D331-335 (2010)). <br />
<br />
You can also see the example on their site:<br />
<br />
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0005886&session_id=5992amigo1297726982 GO example]<br />
<br />
This is also defined on the [http://www.geneontology.org/GO.ontology-ext.relations.shtml GO Extended Relations Page] <br />
<br />
'''* def'n of Part-of:'''<br />
<br />
* PJ raised the point (by email) that the developers guide on the PO website: [http://plantontology.org/docs/otherdocs/ontology_doc.html] defines the<br />
part_of relation as follows: <br />
<br />
"This relationship is used in the plant structure ontology to indicate a subpart/part relationship within a tissue or organ."<br />
<br />
for example: Ectocarp is part-of pericarp, which in turn is part-of fruit<br />
<br />
[relationship type - part of]<br />
PO id: part_of<br />
name: part of<br />
definition: It indicates a subpart/part relationship within a tissue or organ. <br />
<br />
Used in a '''non-restrictive manner''', i.e., the parent '''may or may not have the child as a part''', and the '''child may or may not be a part of the parent'''. Therefore, a child is sometimes part of its parent and not necessarily always part of a parent term.<br />
<br />
''We should be using the definitions based on RO. Think of them this way:''<br />
<br />
''A part_of B can be read "Every A is part of some B."''<br />
<br />
''A has_part B can be read "Every B has as a part some B."''<br />
<br />
''A pair of classes may have either one of these relations or both. Having one does not imply the other.''<br />
<br />
<br />
==Example- why it is needed:==<br />
Below is an example of how the has_part relation would be used in the PO to deal with the parts of the sporangium wall:<br />
<br />
[[File:sporangium_anther_pollensac5_suggested2.jpg]]<br />
<br />
The sporangium wall is basically the same throughout vascular plants, so this proposal creates a new general term "microsporangium wall". The part_of children are part of microsporangium wall (sort of like the part_of children of leaf). Anther wall has_part sporangium wall, since an anther is composed of multiple sporangia. In the current version of the PO, parts of the microsporangium wall are parts of the anther wall, but that only works for angiosperms.<br />
<br />
Note: With this approach, we not only need the software to be able to handle the relations, we need a way to assure that annotations move through has_part relations<br />
<br />
==Possible Solutions:==<br />
'''3-16-11 test''' <br />
RW: Removed the has_part relations from the reciprocal has_part and part_of relations from about 15 terms in the '''plant_anatomy.obo''' file.<br />
<br />
JE loaded the file into the database and the onto the AmiGO browser with no problems.<br />
<br />
<br />
'''3-17-11:''' RW removed the following relations from the developers' version of '''plant_ontology.obo''' and put it on SVN (version#1050):<br />
<br />
'''Removed has_part (left in reciprocal part_of) relations from:'''<br />
<br />
abscission zone > protective layer, separation layer<br />
<br />
basal endosperm transfer layer > basal endosperm transfer cell<br />
<br />
egg apparatus > embryo sac egg cell, synergid<br />
<br />
Leaf stomatal complex > leaf guard cell, leaf stomatal pore<br />
<br />
phyllome stomatal complex > phyllome guard cell, phyllome stomatal pore<br />
<br />
Shoot apex > shoot apical meristem, leaf primordium<br />
<br />
stomatal complex > guard cell, stomatal pore<br />
<br />
<br />
'''Removed develops_from relations from (left in reciprocal has_part):'''<br />
<br />
megaspore > tetrad of megaspores<br />
<br />
microspore > tetrad of microspores<br />
<br />
*Note: We will need to check into which way would have been better biologically.<br />
<br />
* ''From BS (by email): Please make sure that if you delete these assertions, then you keep them at least as comments.''<br />
<br />
<br />
'''The following has_part relations are still in the file:'''<br />
<br />
collective organ part structure > cardinal organ part<br />
<br />
collective plant structure > plant organ<br />
<br />
coma > seed trichome<br />
<br />
embryo axis > hypocotyl, root meristem<br />
<br />
first order inflorescence axis > peduncle<br />
<br />
fused collective tepal structure > fused tepal<br />
<br />
inflorescence > flower<br />
<br />
infructescence > fruit<br />
<br />
meristem > meristematic cell<br />
<br />
second order inflorescence > flower, second order inflorescence axis<br />
<br />
second order infructescence > fruit, second order infructescence axis<br />
<br />
tetrad of megaspores > megaspore<br />
<br />
tetrad of microspores > microspore<br />
<br />
theca > pollen sac<br />
<br />
<br />
'''3-17-11 test:''' <br />
*JE loaded the modified '''plant_ontology.obo''' from the SVN (version#1050) onto the beta browser and LC loaded onto the dev browser. It works fine on both sites. <br />
[http://dev.plantontology.org:8080/amigo/go.cgi?action=dotty&view=details&search_constraint=terms&query=PO:0009049&session_id=6934b1300392307 dev: inflorescence has_part flower]<br />
<br />
*Still need to determine if this fix works for Chado users. LC will send the modified version to Naama and Lucas and ask them to test it.<br />
<br />
''We will try to load the file that has has_part relations but no reciprocal has_part/part_of relations into the beta browser with annotations, to see if that works. Also need to try loading a file into the dev browser with a pair of reciprocal relations to see if it works without annotations.''<br />
<br />
===Possible solutions discussed at the meeting on 3-17-11/action items for being able load the file with has_part relations===<br />
<br />
'''POC meeting, Webex Conference Call; Date: Thursday Mar 17th, 2011 1 (PDT)'''<br />
<br />
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)<br />
<br />
Absent: Marie Alejandra Gandolfo; (Cornell University, Barry Smith (University at Buffalo, NY)<br />
<br />
1. Confirm that the reciprocal part_of and has_part relations were what was actually cause the problem with loading the obo file onto our browser.<br />
<br />
''To do this, we should: a) Try loading the file without the reciprocal relations but with some has_part relations onto the beta browser with annotations (this will require that I edit a version of the live file, since the annotation files currently match the live file), b) try loading a version of the file that has maybe one or two reciprocal relations, but no annotations on to the dev browser (to see if the reciprocal relations cause a problem when there are no annotations).''<br />
<br />
2. If the reciprocal relations are causing the problem, we can deal with them in one of two ways: a) remove all reciprocal relations from the ontology file, that is, only use part_of or has_part, but not both, or b) include reciprocal relations when they are appropriate, but write a script that searches the files for reciprocal relations and removes the has_part relation from classes that have both.''<br />
<br />
<br />
''If PO is going to modify the Amigo code to treat different relations differently, CM suggested that we first switch to the newest version of Amigo. That way, any changes we make could be shared with other users in the community.''<br />
<br />
''GO consortium is working on new software that uses Java on top of OWL (not sure it that is exactly what he said). Also moving toward greater interoperability of OBO and OWL, so it may not be necessary to switch to OWL at this point.''<br />
<br />
===Alternative solutions to using has_parts===<br />
<br />
1. Have all of the part_of shildren a structure be only part of the most general class, then write a script so annotations to any part_of child of that class also go to the correct specific is_a child (as describe above for [http://wiki.plantontology.org:8080/index.php/POC_software_requests#Algorithm_for_gathering_annotations_from_parts_of_leaf_to_either_vascular_leaf_or_non-vascular_leaf leaf]).<br />
<br />
This would allow us to use the current software such as AmiGO and Chado, but would require additional software and possibly special coding in the obo file for all terms that need special treatment.<br />
<br />
''This is probably not feasible at this time.''<br />
<br />
2. Have specific part_of children for all of the specific is_a children. This would not require any changes to the existing software or new scripts. However, it would quickly lead to term inflation. Also, it would not be biologically accurate, since the is_a children would be based largely on the taxon in which they occur, not on real differences in the structure.<br />
<br />
''There was general opposition to this approach, particularly for terms with many part_of children, because of the resulting term inflation.''<br />
<br />
3. Use the PO as an uber-ontology for plants, then create taxon-specific sub-ontologies that cross-reference the main ontology. This would create a similar number of terms as solution number 2, but they would not all be in one ontology, so it may be more manageable. Would create problems in syncing the ontologies, and could make cross-species comparisons more difficult. Of course, even within a single taxon (like angiosperms) there may be a need to use the has_part relation (like inflorescence has_part flower).<br />
<br />
''We did not discuss this possibility.''<br />
<br />
==Treating different relations differently when dealing with annotations==<br />
Recent email from CM:<br />
<br />
''Note that AmiGO1 will give curious answers to gene expression queries if you leave in has_part. AmiGO2 will handle cycles and answering questions appropriately.'' (RW05-03-12) <br />
<br />
<br />
Original request: March 9, 2011, but has been discussed earlier.<br />
<br />
* Under the current rules, all relations are treated equally, so '''all annotations get passed up from any child to its parent, regardless of the relation'''.<br />
<br />
This works fine for is_a and part_of, but is problem for other relations.<br />
<br />
<br />
'''has_part:''' <br />
<br />
*Annotations should pass '''from parent to child''', in the opposite direction of the arrow (through has_part backwards, that is). <br />
<br />
*Furthermore, they should only pass through has_part relations when the instance for which the annotation was created comes from a taxon in which the parent term is part_of the child term.<br />
<br />
For example: <br />
<br />
In theca has_part pollen sac, theca is the child, and pollen sac is the parent. <br />
<br />
Annotation should never go from theca to pollen sac. Annotations should go from pollen sac to theca, but only if they come from an angiosperms.<br />
<br />
[[File:theca.jpg]]<br />
<br />
<br />
In order for this to work, the conditions under which annotations should pass through will have to be specified every time a has_part relation is added to the ontology. That means that any class in the PO that has a has_part tag will have to have additional tags specifying the conditions under which annotation should pass through the has_part relation. We would have to create a custom tag for this, perhaps a custom relation, that is conditional. Something along the lines of: if taxon_id=xxxx then treat parent term as part_of child term.<br />
<br />
'''Option: Should we just have the annotation not move through the has_part relations?'''<br />
<br />
What are the implications of this?<br />
<br />
''At a minimum, annotations should not pass forward through has_part relations. Possible solution is to have two versions of PO Amigo (similar to what GO does). One with all of the relations visible, for those who want to explore the ontology and definitions, and one with has_part and develops_from relations stripped out, to be used for gene expression queries.''<br />
<br />
''It may be possible to create a schema to assign the annotations to the correct terms, similar to the one described below for parts of leaf, using the only_in taxon relation. This would only work when the has_part relation is specific to a larger taxon. Would not work for something like inflorescence has_part flower, which is highly variable among close relatives. We will probably not be able to implement this solution in the short term.''<br />
<br />
<br />
'''develops_from:''' Annotations should not pass through the develops from relation. For example, leaf develops_from leaf meristem. If a gene is expressed in a leaf, this does not mean it is expressed in the leaf meristem that it developed from.<br />
<br />
''Did not discuss this at length. Best solution is probably to modify the code (in Amigo or elsewhere) to not allow annotations to pass through develops_from relation. Alternative is to use two versions of Amigo, as described above.''<br />
<br />
=Need: Script or an Algorithm for Assigning Annotations=<br />
<br />
'''Original request:''' March 1, 2011<br />
<br />
Example: For gathering annotations from parts of leaf to either vascular leaf or non-vascular leaf<br />
<br />
[[File:leaf.jpg]]<br />
<br />
'''Why this is needed:'''<br />
<br />
At the [[POC_Conf._Call_3-1-11]] we agreed that in general, it is better to have the part_of children of leaf only be part of the general term leaf, rather than create new terms for vascular parts of and non-vascular parts of. Terms that only occur in one or the other (like leaf endodermis or costa) will only be the child of the appropriate term.<br />
<br />
If someone puts an annotation on leaf epidermis for rice, it will be collected by leaf, but not by vascular leaf, even though it should also be on vascular leaf. <br />
<br />
<br />
==Solutions:==<br />
- We will suggest to users that in cases like this, they annotate to both leaf epidermis and vascular leaf. <br />
<br />
- Also, we will need to write an algorithm or script that will automatically add the annotations to vascular leaf, in case the curators miss it. <br />
<br />
- It should search for annotations for parts of leaf, then check the taxon ID, and then add the appropriate annotation to either vascular leaf or non-vascular leaf. <br />
<br />
- This will assure that annotations end up on the correct terms, but reduce term inflation.<br />
<br />
It is likely that the same issue will come up for other classes, as we add terms and annotations for more taxa.<br />
<br />
''We can implement this by using the "only_in_taxon" relation. For example, we would add the relations vascular leaf only_in_taxon vascular plants and non-vascular leaf only_in_taxon bryophytes. Then we would have a script that looked at all annotations for the part_of children of leaf, determine if the taxon id is for vascular plants or bryophytes, and then move the annotation to either vascular leaf or non-vascular leaf.''<br />
<br />
''CM asked us to send him a sample file with a few only_in_taxon relations, so he can send us an example of how the script would work.''<br />
<br />
''In order to add these relations, we will need to:''<br />
<br />
''-Create PO slim for plant taxonomy, based on NCBI ontology. Include all plant species currently in GO?''<br />
<br />
''-Create union classes for Bryophytes, pteridophytes, others''<br />
<br />
''-Import or mireot PO plant taxonomy slim into PO''<br />
<br />
''-Add the relations''<br />
<br />
=Problem with OWL File Generation=<br />
-OBO to OWL file generator is creating OWL file without the term definitions. Needed for interaction with SSWAP services.<br />
<br />
-- We currently create the OWL file manually using OBO-Edit. This works as long as we only do it (and remember to do it) when we have a release.<br />
<br />
-- Trying to create an automated way to do this I turned to using go2fmt.pl to do it.<br />
<br />
Both of the above methods result in a valid OWL file, but valuable info such as the definitions is lost.<br />
<br />
- I found a paper that says they have a method to do a OBO 2 OWL -> OWL 2 OBO round trip with no loss of info, but can not find the actual program to do this. Paper:ftp://ftp.cs.utexas.edu/pub/techreports/tr06-47.pdf<br />
<br />
''CM said not to use that software, because it is out of date. He sent a link to the correct code:''<br />
http://code.google.com/p/oboformat/<br />
<br />
<br />
<br />
=Linking images to PO=<br />
<br />
'''Original request:''' March 9, 2011, but this has been discussed on and off since 2010, including at the POC meeting at the NYBG in Nov. 2010.<br />
<br />
Need to register Plantsystematics.org in the GO dbxref database so we can create shortcut links to their pages.<br />
<br />
=Register OBO_SF_PO in Go.xrf_abbs=<br />
<br />
We have a number of xrefs to OBO_SF_PO, which refer to the SourceForge tracker items associated with terms.</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_4-10-12&diff=18001POC Conf. Call 4-10-122012-06-01T20:10:58Z<p>Preecej: /* Plant Ontology Web Site and Browser Update: */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Apr 10th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members: ''Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Barry Smith (University at Buffalo, NY), Justin Elser (OSU).''<br />
<br />
Absent: ''Marie Alejandra Gandolfo (Cornell), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)''<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_3-27-12]]? ''no changes, additions, or deletions''<br />
<br />
<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
=Demo - Integrating Annotated Images with PO terms=<br />
<br />
JP gave a short demo with "mock-ups" to display one approach to integrating annotated images with PO terms on the PO web site (screenshots below). This one envisions pop-ups driven from links on PO term information pages -- ''perhaps'' in the External References section, or somewhere else on the page -- we have options and flexibility in this regard.<br />
<br />
The long-term goal: A database on a PO server that stores images annotated with PO terms (internally and externally-generated), and a corresponding web interface to display them online in conjunction with other PO data. Database currently being designed by JP and BA.''<br />
<br />
The desktop image annotation tool that allows curators to generate annotated images for future integration with web sites and other applications will be available for testing within a few weeks, but any db storage and web-based display of annotated images in conjunction with the PO site is not currently scheduled for active development and is a few months away, at a minimum.<br />
<br />
'''Screenshots''' (click to see full resolution)<br />
<br />
{|<br />
|[[File:PO_image_annotation_mockup_1.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_2.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_3.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_4.png|150px|thumb|left]]<br />
|}<br />
<br />
'''Suggestions'''<br />
<br />
* Give the "secondary" annotation terms a more prominent location, perhaps on the left or right instead of the bottom. <br />
* field for annotators on the desktop app, also can zoom on the segmentation tool.<br />
* Keeping things up to date- will not be an issue, as they will go through the webservices. All the parts will draw from from the database.<br />
<br />
''Pop-up (eg. shown above) would pull out any annotations to all images with that key words.'' <br />
<br />
''Discussions about the options for linking to keywords and the level of curation needed: One approach is to link to keywords, but their def'n may or may not match our def'n, or the curate the images themselves. May also mirror ale's images at OSU and those would be curated. Could apply for curating other images such as the foxtail images. Would be attributed back to source site.''<br />
<br />
''Desktop application could most likely be ready to demo for the workshop at the BSA meeting. Will pull taxonomy terms from UBio and could in the future pull terms from TO or GO. Database should be developed for fall. Will plan to do another demo when Ale and KS can take part. RW will coordinate it. ''<br />
<br />
=Other notes about Images=<br />
<br />
* Journal Bioinformatics- new section called "[http://bioinformatics.oxfordjournals.org/content/28/8/1057.extract?etoc Bioimage informatics]<br />
<br />
Might be able to put together a publication about this new tool? LC would be interested in taking part.<br />
<br />
*From the BioCuration meeting: David Orloff, Senior Manager, Image Library, The American Society for Cell Biology.<br />
"I would welcome a conversation to discuss presenting your images, videos, or animations in The Cell: An Image Library www.cellimagelibrary.org, and then linking back to your websites so that researchers can easily interact with the data. "<br />
<br />
See link to image of [http://cellimagelibrary.org/images/40589 Hibiscus Pollen grain] on their site.<br />
<br />
''Should see if we can get permission to Link to or mirror their images on PO and add annotations. See if they can list PO ids as a source on their web page, like they do for GO and NCBI.''<br />
<br />
* Ale got the ok to use the [http://www.agron.iastate.edu/~weeds/Fox/FoxSeed/germination.html Setaria germination] images: we need to give credit to Drs. John Dekker and Mitt Haar.<br />
<br />
=Update on the Release #17, April 2012=<br />
<br />
* Review and Assessments:<br />
<br />
* Issue of files on Bioportal all "PO"- are we going to keep posting the separate aspect files?<br />
<br />
* Updates to the SOP page: [[PO_Release_SOP_Page]]<br />
''Need to clarify where the various files go''<br />
<br />
* What do we need to do better next time?<br />
<br />
''Now that we can use Oort, we can easily generate the asserted file earlier in the process and test load it onto Dev or beta. That way if we run into problems, it will not hold up the database loading. I suggest adding this conversion step to the dev loading script. That will make it easier to diagnose any issues early.''<br />
<br />
''This is a good idea, although at this point, the creation of the asserted file cannot be done automatically and will have to be hand tweaked by the editors each time.''<br />
<br />
''BS suggested that using "plant_ontology_assert" was misleading, and because this is the inferred file. RW pointed out that it was called "assert" based on the OboEdit function "assert implied links".''<br />
<br />
''BS: Users should see the file with inferred relations asserted (They do, since that is what is on AmiGO).''<br />
<br />
''We will look at the naming scheme that CM suggested (what GO uses) and see if that makes sense for PO.''<br />
<br />
=Goals and Timeline for the next Release #18=<br />
Timeline: End of june to Mid- July- '''before''' BSA and ASPB meetings?<br />
<br />
''Agreed''<br />
<br />
==Continue major revision of PSDS==<br />
Focus on the revisions on:<br />
<br />
'''PO:0007033 : whole plant development stage'''<br />
<br />
'''> PO:0028002 : sporophyte development stage'''<br />
<br />
>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)<br />
<br />
>>> PO:0007047 : 3 inflorescence detectable stage [29131]<br />
<br />
>>>PO:0007016 : 4 flowering [28057]<br />
<br />
>>>PO:0007042 : 5 fruit formation [31009]<br />
<br />
>>>PO:0007010 : 6 ripening [37642]<br />
<br />
<br />
'''>> PO:0007134 : sporophyte vegetative stage [60370]:''' (Some still have the numbers preceding them, others don't)<br />
<br />
>>>PO:0007057 : 0 seed germination stage [29568]<br />
<br />
>>>PO:0007112 : 1 main shoot growth stage [47411]<br />
<br />
>>>PO:0007131 : seedling development stage [26673]<br />
<br />
<br />
<br />
'''PO:0009012 : plant structure development stage:'''<br />
<br />
> PO:0007615 : flower development stage [48067]<br />
<br />
>PO:0001083 : inflorescence development stage [48067]<br />
<br />
<br />
'''PO:0025339 : plant organ development stage [46618]''' <br />
<br />
>PO:0001050 : leaf development stage [45968]<br />
<br />
>PO:0007520 : root development stage [25208]<br />
<br />
<br />
'''PO:0025338 : collective plant structure development stage [49645]'''<br />
<br />
>PO:0007615 : flower development stage [48067]<br />
<br />
<br />
<br />
==Continue revisions and adding new terms for wood ontology==<br />
''Most terms are in the PAE branch or for GO.''<br />
<br />
''Can continue to add annotations as we go along, as well.''<br />
<br />
==New or expanded association files:==<br />
* wood genes [http://dendrome.ucdavis.edu/treegenes/ TreeGenes] and [http://www.fagaceae.org/ Fagaceae Genomics Web]<br />
<br />
* cotton- [http://www.agbase.msstate.edu/ AgBase]<br />
<br />
* soybean- [http://soybase.org/ SoyBase]<br />
<br />
* potato<br />
<br />
* rice<br />
<br />
* grape<br />
<br />
''RW will email Stefan and Daniel to find out if either of them are planning to attend the moss meeting at NYBG this summer.''<br />
<br />
==Plant Ontology Web Site and Browser Update:==<br />
<br />
Please see [[Plant_Ontology_Web_Site_Update:_2012]] for more details<br />
<br />
*Items on the [http://palea.cgrb.oregonstate.edu/trac/report/1 tracker]: <br />
<br />
PO:IDs in definitions working as links, fixes to web page headers<br />
<br />
*Browser update- what is the status of this?<br />
<br />
==Complete old user requests/SF tracker items==<br />
Ongoing process....<br />
<br />
priorities<br />
<br />
=Report from the [http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]=<br />
<br />
April 2-4, 2012, Washington DC<br />
<br />
Link to poster Abstract: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf]]<br />
<br />
* LC attended and took part in the BioCreative workshop<br />
<br />
<br />
==Main topics:==<br />
<br />
* Community annotation<br />
<br />
* Functional annotation and pathways<br />
<br />
* Databases & Journals – How to have a sustainable long term plan for journals and databases? <br />
<br />
* Careers in biocuration<br />
<br />
* Curation workflows and tools<br />
<br />
* Integrating text mining into biocuration workflows<br />
<br />
* Ontologies and standards<br />
<br />
==Biocreative-2012 Workshop==<br />
<br />
Interactive Text Mining in the Biocuration Workflow<br />
<br />
Textpresso<br />
<br />
[http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ Pubtator]<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[https://docs.google.com/document/d/1rb_VbdteXujvm1gXLky1YDtaDNCFguxYdFBeZiQkI04/edit?pli=1 Semantics of Biodiversity Workshop]==<br />
May 16 - 18, 2012<br />
<br />
University of Kansas Biodiversity Institute, Lawrence, Kansas<br />
<br />
The goals of this workshop (still being refined): 1) Clarification of terms used in the biodiversity, genomics, and ecological communities, and 2) Steps to take in building a Biocollections Ontology.<br />
<br />
BS, MAG, and RW are attending.<br />
<br />
==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==<br />
Annual meeting of the Society for the Preservation of Natural History Collections <br />
<br />
Yale University, New Haven Connecticut<br />
June 11-16, 2012 <br />
<br />
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).<br />
<br />
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).<br />
<br />
''From PJ: If we can show progress in the FNA work or Morphobank yes we should''<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
Ruth Bastow is contacting some of the interested people to see which of these dates work best.<br />
<br />
Can we consider September? RB is available 12th -25th September<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
RW will prepare an announcement for the PO home page and FB page.<br />
<br />
Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, early Bird Registration: by May 11<br />
<br />
Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW sent around a draft of an abstract for a poster summarizing the PO-FNA collaboration, with the folks from FNA.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
''LC will forward email to PO announce list and post on PO Facebook page.''<br />
<br />
=Next meeting scheduled for Tuesday, April. 17th, 2012 at 10am PDT/1pm EDT=<br />
[[POC_Conf._Call_4-17-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=July_2012_Release&diff=18000July 2012 Release2012-06-01T20:10:29Z<p>Preecej: /* Plant Ontology Web Site and Browser Update: */</p>
<hr />
<div>=Goals and Timeline for the next Release #18=<br />
Timeline: End of june to Mid- July- '''before''' BSA and ASPB meetings?<br />
<br />
''Agreed''<br />
<br />
==Continue major revision of PSDS==<br />
Focus on the revisions on:<br />
<br />
'''PO:0007033 : whole plant development stage'''<br />
<br />
'''> PO:0028002 : sporophyte development stage'''<br />
<br />
>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)<br />
<br />
>>> PO:0007047 : 3 inflorescence detectable stage [29131]<br />
<br />
>>>PO:0007016 : 4 flowering [28057]<br />
<br />
>>>PO:0007042 : 5 fruit formation [31009]<br />
<br />
>>>PO:0007010 : 6 ripening [37642]<br />
<br />
<br />
'''>> PO:0007134 : sporophyte vegetative stage [60370]:''' (Some still have the numbers preceding them, others don't)<br />
<br />
>>>PO:0007057 : 0 seed germination stage [29568]<br />
<br />
>>>PO:0007112 : 1 main shoot growth stage [47411]<br />
<br />
>>>PO:0007131 : seedling development stage [26673]<br />
<br />
<br />
<br />
'''PO:0009012 : plant structure development stage:'''<br />
<br />
> PO:0007615 : flower development stage [48067]<br />
<br />
>PO:0001083 : inflorescence development stage [48067]<br />
<br />
<br />
'''PO:0025339 : plant organ development stage [46618]''' <br />
<br />
>PO:0001050 : leaf development stage [45968]<br />
<br />
>PO:0007520 : root development stage [25208]<br />
<br />
<br />
'''PO:0025338 : collective plant structure development stage [49645]'''<br />
<br />
>PO:0007615 : flower development stage [48067]<br />
<br />
==Continue revisions and adding new terms for wood ontology==<br />
''Most terms are in the PAE branch or for GO.''<br />
<br />
''Can continue to add annotations as we go along, as well.''<br />
<br />
==New or expanded association files:==<br />
* wood genes [http://dendrome.ucdavis.edu/treegenes/ TreeGenes] and [http://www.fagaceae.org/ Fagaceae Genomics Web]<br />
<br />
* cotton- [http://www.agbase.msstate.edu/ AgBase]<br />
<br />
* soybean- [http://soybase.org/ SoyBase]<br />
<br />
* potato<br />
<br />
* rice<br />
<br />
* grape<br />
<br />
==Plant Ontology Web Site and Browser Update:==<br />
<br />
Please see [[Plant_Ontology_Web_Site_Update:_2012]] for more details<br />
<br />
*Items on the [http://palea.cgrb.oregonstate.edu/trac/report/1 tracker]: <br />
<br />
PO:IDs in definitions working as links, fixes to web page headers<br />
<br />
*Browser update- what is the status of this?<br />
<br />
==Update Tutorials on PO site==<br />
<br />
==Complete old user requests/SF tracker items==<br />
Ongoing process....<br />
<br />
priorities:<br />
<br />
<br />
=Summary of Changes=<br />
<br />
For more information about the release, please visit our wikipage with a [[Summary of Changes to PO July 2012]].<br />
<br />
You can also view a list of [[New terms and obsolete terms July 2012 Release]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_6-5-12&diff=17999POC Conf. Call 6-5-122012-06-01T20:09:55Z<p>Preecej: /* Updated tutorials and presentations */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday June 6th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_5-29-12]]?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
=Preparations for Botany meeting workshop=<br />
==Updated tutorials and presentations==<br />
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.<br />
<br />
See [[Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date]]<br />
<br />
==Mistakes on website and wiki==<br />
See [[Plant_Ontology_Web_Site_Update:_Winter_2012#High_priority_fixes]]<br />
<br />
==Booklet==<br />
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website. Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.<br />
<br />
Might be good to make it as a PDF, so it can include web links if people open it on screen.<br />
<br />
=New upper level terms for PO=<br />
This came up as the need to describe things that are part of a seed, along with some other problems.<br />
<br />
==Background==<br />
At the [[POC Conf. Call 5-8-12]] we discussed the need for a general term for collective plant structures that are collections of things other than organs. This general term would be parent of collective plant organ structure, collective organ part structure and other types of collective structures.<br />
<br />
If we want this term to be parent to seed, we need to define it broadly. What is a seed? It has as parts a mature ovule, some accessory structures like an aril, and parts derived from the ovule like the seed funicle. It also contains endosperm and an embryo. (See below about located in relation.) Is this a collective plant structure? What does it collect? Maybe seed coat, endosperm, and embryo.<br />
<br />
We also need a term to cover structures that are part of a seed (like arilloid and seed funicle) and terms like ovary that are parts of a plant, but do not fit any of the other categories. These are not necessarily collections. Could use something like CARO term '''multi-tissue structure'''. This would be parent to CPS, but also plant organ, cardinal organ part, and things like arilloid.<br />
<br />
<br />
''Note from earlier meeting:'' If we include seed under the new CPS, we should mention that some of the parts of this new CPS are part of the mother plant and some are new organism. Some of the cells may be from the mother plant, but they take on a new developmental pathways, function, etc.<br />
<br />
==structures that are located other organisms==<br />
The located_in relation has been to the PO file. Right now it is only used for embryo sac located in plant ovary ovule, but should be applied whenever there are two plant structures that are parts of different organisms.<br />
<br />
Located_in replaces contained_in. Located_in can be used for both part_of and contained_in.<br />
<br />
Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.<br />
<br />
==New proposed term [https://sourceforge.net/tracker/?func=detail&aid=3530843&group_id=76834&atid=835555 multi-tissue plant structure]==<br />
'''CARO:multi-tissue structure:''' Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component. <br />
<br />
This is very similar to PO plant organ, but does not come with the baggage of being called an organ so it can be applied more broadly. See below for definition of plant organ.<br />
<br />
<br />
'''proposed definition, multi-tissue plant structure:''' A plant structure that has as parts two or more portions of plant tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.<br />
<br />
Not sure about the bona-fide boundaries part.<br />
<br />
Seed could be a child of multi-tissue plant structure, as would plant organ, or we could make plant organ a synonym of multi-tissue plant structure.<br />
<br />
If we keep a separate term for plant organ, we could also add a term for "cardinal part of a multi-tissue structure", to go along with "cardinal organ part". If we decide to merge plant organ with multi-tissue structure, then cardinal organ part should be merged with cardinal part of a multi-tissue structure. Even if we keep plant organ (because it is such a commonly used term), we could still merge cardinal organ part with cardinal part of a multi-tissue structure. It seems confusing to have them as two separate classes.<br />
<br />
RW: I think this terms could be interpreted to be a parent to collective plant organ structure (CPOS), since CPOS's have two or more tissue and form a distinct structural unit (think of a flower or a gynoecium or a shoot system as a structural unit). In that case, if we create the term "cardinal part of multi-tissue structure", it could include things like ovary, which are part of either an organ or a CPOS. <br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=3530834&group_id=76834&atid=835555 collective plant structure (new)]===<br />
<br />
Do we still want a general term for collective plant structure, parent to collective plant organ structure and collective organ part structure?<br />
<br />
The important part of a collective plant structure is that it is a collection of two or more similar structures that are not tissues (e.g., two organs, two cardinal organ parts). If we add multi-tissue structure to cover seed, we may not need a new term for collective plant structure.<br />
<br />
proposed definition: A plant structure that is a proper part of a whole plant...<br />
<br />
===[https://sourceforge.net/tracker/?func=detail&aid=2954382&group_id=76834&atid=835555 collective plant organ structure]===<br />
Changed name, and slight change to clarify that the two organs must be adjacent, not one part of the other. Otherwise, a sporophyll would be a collective plant organ structure.<br />
<br />
New proposed def.: A collective plant structure (PO:id) that is a proper<br />
part of a whole plant (PO:0000003) and is composed of two or more '''adjacent'''<br />
plant organs (PO:0009008) and the associated portions of plant tissue<br />
(PO:0009007).<br />
<br />
comment: A collective plant organ structure must have as parts at least two<br />
organs that do not have a part of relation between them, that is, one must<br />
be adjacent to the other, rather than one part of the other. The organs in<br />
a collective plant structure can be of the same type, such as a corolla<br />
(PO:0009059) composed of multiple petals (PO:0009032), or of different<br />
types, such as a shoot system (PO:0009006) composed of shoot axes<br />
(PO:0025029) and phyllomes (PO:0006001). Other examples include flower<br />
(PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See<br />
also collective organ part structure (PO:0025269), for collective plant<br />
structures composed of parts of multiple organs, but no complete organs.<br />
<br />
<br />
===Modified comment for plant organ:===<br />
<br />
plant organ (PO:0009008), current def.: A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.<br />
<br />
new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.<br />
<br />
comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an ovule.<br />
<br />
<br />
===Slight modification to cardinal organ part===<br />
<br />
Add comment to see also COPS, add ids:<br />
<br />
'''cardinal organ part (PO:0025001), proposed def.:''' A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.<br />
<br />
comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.<br />
<br />
'''From discussion on 5-8-12:''' <br />
<br />
Maybe it would be better to say "cardinal part of collective plant structure" and "cardinal part of plant organ.<br />
<br />
FMA has "regional parts". It is like a "zone", which PO uses in a few terms. We also have terms like leaf tip or leaf lobe that are regional parts.<br />
<br />
This is what we call a cardinal part. BS: Biological significance is not all of the story for cardinal parts. They should also have their own boudaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.<br />
<br />
===collective organ part structure===<br />
<br />
Current def.: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.<br />
<br />
comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths. Unlike a collective plant structure, a collective organ part structure does not contain any complete organs.<br />
<br />
Add PO ids. Say "plant organs" instead of "organs".<br />
<br />
===cardinal part of collective plant structure===<br />
<br />
Do we still need this term? Maybe replace with cardinal part of multi-tissue plant structure.<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[http://www.regonline.com/builder/site/Default.aspx?EventID=1015479 MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes]==<br />
<br />
Thursday, June 14, 2012 - Friday, June 22, 2012<br />
<br />
The New York Botanical Garden<br />
<br />
Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).<br />
<br />
RW submitted an abstract for a poster [[File:PO_poster_Moss_2012.pdf]].<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
Dates TBA: probably Sept. 13-15th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
This is a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
An announcement has been posted on the PO home page and FB page.<br />
<br />
Goal of workshop: Will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW will present the IDO-Plant paper and a poster on the PO-FNA collaboration.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
=Next meeting scheduled for Tuesday, June 12, 2012 at 10am PDT/1pm EDT=<br />
See: [[POC_Conf._Call_6-12-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_Winter_2012&diff=17998Plant Ontology Web Site Update: Winter 20122012-06-01T20:09:00Z<p>Preecej: moved Plant Ontology Web Site Update: Winter 2012 to Plant Ontology Web Site Update: 2012</p>
<hr />
<div>#REDIRECT [[Plant Ontology Web Site Update: 2012]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=17997Plant Ontology Web Site Update: 20132012-06-01T20:09:00Z<p>Preecej: moved Plant Ontology Web Site Update: Winter 2012 to Plant Ontology Web Site Update: 2012</p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under <br />
"/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link<br />
to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not<br />
their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking<br />
you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email<br />
notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
* GARNet has a clean, fresh look- I like it: [http://www.garnetcommunity.org.uk/ GARNet] LC<br />
<br />
* MosDB: http://mips.helmholtz-muenchen.de/plant/rice/index.jsp<br />
<br />
===Current PO Site Map===<br />
<br />
''Screenshots of current content have been catalogued and URLs have been mapped. Diagram of PO's current site map will be posted shortly...''<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our Palea web server (''currently in progress'').<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
See also the items listed on the [[POC_Technical_Issues_Page]]- some of which are AmiGO specific<br />
<br />
==High priority fixes==<br />
<br />
RW has marked these as high priority to fix before the Botany meeting (by mid-June).<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to log in to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
RW (4/2012): Maybe this has been fixed? Seems to work. I have created a wiki page for [[How_to_use_the_Source_Forge_tracker]].<br />
<br />
This could be made into a web page, as part of the browser, rather than leaving it on the wiki. Perhaps the "Request term" page link here, instead of directly to Source Forge.<br />
<br />
===Plant Ontology Browser Users Guide===<br />
http://plantontology.org/amigo_user_guide/index.html#intro<br />
<br />
- No images show up. Text not displaying correctly (missing spaces).<br />
<br />
===Web pages that are out of date - high priority===<br />
<br />
*http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date.<br />
*http://plantontology.org/docs/growth/growth_stages.html - Out of date. Should merge with page for development stages.<br />
*http://plantontology.org/docs/faq/growth_faq.html - Out of date. Should merge with page for development stages.<br />
*http://plantontology.org/docs/development/developmental_stages.html - Out of date. Should merge with page for growth stages.<br />
<br />
*http://plantontology.org/docs/otherdocs/ontology_doc.html Developers' guide. Content is not too bad, but this should be only on the wiki, and not on the web page since it is only for developers -- most users never need to see this.<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
Presentations/tutorials that need to be updated:<br />
<br />
*[http://plantontology.org/docs/presentations/demo/poc-demo-1.html Introduction to the project] - Slide show. There are links to this from both the web page and the wiki. Much of it is still valid, so it could be updated, rater than replaced. [http://palea.cgrb.oregonstate.edu/viewsvn/plantontology/html/docs/presentations/demo/ link to svn folder]<br />
<br />
*http://wiki.plantontology.org/index.php/Plant_Ontology_Tutorials and http://plantontology.org/docs/otherdocs/tutorials.html<br />
<br />
'''There is a problem opening or downloading the following quicktime movies and the ppt files.''' JE is looking into this right now.<br />
<br />
*Introduction to ontologies: http://plantontology.org/docs/presentations/tutorials/poc_intro.mov, http://plantontology.org/docs/presentations/tutorials/poc_intro.ppt Powerpoint slides<br />
*Development of ontologies: http://plantontology.org/docs/presentations/tutorials/ontology.mov, http://plantontology.org/docs/presentations/tutorials/ontology.ppt<br />
*Annotations: http://plantontology.org/docs/presentations/tutorials/annotation.mov, http://plantontology.org/docs/presentations/tutorials/annotation.ppt<br />
*Plant ontology browser and POC web site: http://plantontology.org/docs/presentations/tutorials/website.mov, http://plantontology.org/docs/presentations/tutorials/website.ppt<br />
<br />
===Out of date wiki pages===<br />
Principles, Rationales and Key Organizing Rules of the PO (These correspond to the out of date web pages).:<br />
* [[Plant_Structure_Principles_Rules|Plant Structure Ontology]] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure. <br />
* [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked questions]]<br />
* [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]]<br />
<br />
<br />
*Wiki home page: under Formats of the Ontology Files, needs info on OWL (provide link).<br />
<br />
===Developers guide -Download SVN Page===<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
http://www.plantontology.org/download/svn_doc.html Developers guide<br />
<br />
RW: Thanks for adding instructions for Mac users!<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an images for all these relations.''<br />
<br />
''RW: Minor point, but perhaps the list of icons could be have is_a first (as it is now) and then list the rest of them in alphabetical order.''<br />
<br />
==Medium priority fixes==<br />
These fixes are important, but can wait until after June.<br />
<br />
===Web pages that are out of date - medium priority===<br />
*http://plantontology.org/docs/otherdocs/poc_project.html - Was updated in the past year, but needs new updates. Still refers to "Plant Growth and Developmental Stages". Could use more detail on the project.<br />
*http://plantontology.org/docs/otherdocs/charter.html POC charter is out of date.<br />
*http://plantontology.org/docs/otherdocs/resources.html out of date<br />
*http://plantontology.org/docs/references/pub.html out of date<br />
<br />
==Feature requests==<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
RW: Yes! This would be really great.</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_4-10-12&diff=16711POC Conf. Call 4-10-122012-04-13T18:03:34Z<p>Preecej: /* Demo - Integrating Annotated Images with PO terms */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Apr 10th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members: ''Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Barry Smith (University at Buffalo, NY), Justin Elser (OSU).''<br />
<br />
Absent: ''Marie Alejandra Gandolfo (Cornell), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)''<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_3-27-12]]? ''no changes, additions, or deletions''<br />
<br />
<br />
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=63898157&rKey=b1cc4800e2b264be<br />
<br />
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=63898157&rKey=119a3285353e0d57<br />
<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
=Demo - Integrating Annotated Images with PO terms=<br />
<br />
JP gave a short demo with "mock-ups" to display one approach to integrating annotated images with PO terms on the PO web site (screenshots below). This one envisions pop-ups driven from links on PO term information pages -- ''perhaps'' in the External References section, or somewhere else on the page -- we have options and flexibility in this regard.<br />
<br />
The long-term goal: A database on a PO server that stores images annotated with PO terms (internally and externally-generated), and a corresponding web interface to display them online in conjunction with other PO data. Database currently being designed by JP and BA.''<br />
<br />
The desktop image annotation tool that allows curators to generate annotated images for future integration with web sites and other applications will be available for testing within a few weeks, but any db storage and web-based display of annotated images in conjunction with the PO site is not currently scheduled for active development and is a few months away, at a minimum.<br />
<br />
'''Screenshots''' (click to see full resolution)<br />
<br />
{|<br />
|[[File:PO_image_annotation_mockup_1.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_2.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_3.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_4.png|150px|thumb|left]]<br />
|}<br />
<br />
'''Suggestions'''<br />
<br />
* Give the "secondary" annotation terms a more prominent location, perhaps on the left or right instead of the bottom. <br />
<br />
Feel free to add more...<br />
<br />
=Other notes about Images=<br />
<br />
* Journal Bioinformatics- new section called "[http://bioinformatics.oxfordjournals.org/content/28/8/1057.extract?etoc Bioimage informatics]<br />
<br />
Might be able to put together a publication about this new tool? LC would be interested in taking part.<br />
<br />
*From the BioCuration meeting: David Orloff, Senior Manager, Image Library, The American Society for Cell Biology.<br />
"I would welcome a conversation to discuss presenting your images, videos, or animations in The Cell: An Image Library www.cellimagelibrary.org, and then linking back to your websites so that researchers can easily interact with the data. "<br />
<br />
See link to image of [http://cellimagelibrary.org/images/40589 Hibiscus Pollen grain] on their site.<br />
<br />
''Should see if we can get permission to mirror their images on PO and add annotations. See if they can list PO ids as a source on their web page, like they do for GO and NCBI.''<br />
<br />
* Ale got the ok to use the [http://www.agron.iastate.edu/~weeds/Fox/FoxSeed/germination.html Setaria germination] images: we need to give credit to Drs. John Dekker and Mitt Haar.<br />
<br />
=Update on the Release #17, April 2012=<br />
<br />
* Review and Assessments:<br />
<br />
* Issue of files on Bioportal all "PO"- are we going to keep posting the separate aspect files?<br />
<br />
* Updates to the SOP page: [[PO_Release_SOP_Page]]<br />
''Need to clarify where the various files go''<br />
<br />
* What do we need to do better next time?<br />
<br />
''Now that we can use Oort, we can easily generate the asserted file earlier in the process and test load it onto Dev or beta. That way if we run into problems, it will not hold up the database loading. I suggest adding this conversion step to the dev loading script. That will make it easier to diagnose any issues early.''<br />
<br />
''This is a good idea, although at this point, the creation of the asserted file cannot be done automatically and will have to be hand tweaked by the editors each time.''<br />
<br />
''BS suggested that using "plant_ontology_assert" was misleading, and because this is the inferred file. RW pointed out that it was called "assert" based on the OboEdit function "assert implied links".''<br />
<br />
''BS: Users should see the file with inferred relations asserted (They do, since that is what is on AmiGO).''<br />
<br />
''We will look at the naming scheme that CM suggested (what GO uses) and see if that makes sense for PO.''<br />
<br />
=Goals and Timeline for the next Release #18=<br />
Timeline: End of june to Mid- July- '''before''' BSA and ASPB meetings?<br />
<br />
''Agreed''<br />
<br />
==Continue major revision of PSDS==<br />
Focus on the revisions on:<br />
<br />
'''PO:0007033 : whole plant development stage'''<br />
<br />
'''> PO:0028002 : sporophyte development stage'''<br />
<br />
>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)<br />
<br />
>>> PO:0007047 : 3 inflorescence detectable stage [29131]<br />
<br />
>>>PO:0007016 : 4 flowering [28057]<br />
<br />
>>>PO:0007042 : 5 fruit formation [31009]<br />
<br />
>>>PO:0007010 : 6 ripening [37642]<br />
<br />
<br />
'''>> PO:0007134 : sporophyte vegetative stage [60370]:''' (Some still have the numbers preceding them, others don't)<br />
<br />
>>>PO:0007057 : 0 seed germination stage [29568]<br />
<br />
>>>PO:0007112 : 1 main shoot growth stage [47411]<br />
<br />
>>>PO:0007131 : seedling development stage [26673]<br />
<br />
<br />
<br />
'''PO:0009012 : plant structure development stage:'''<br />
<br />
> PO:0007615 : flower development stage [48067]<br />
<br />
>PO:0001083 : inflorescence development stage [48067]<br />
<br />
<br />
'''PO:0025339 : plant organ development stage [46618]''' <br />
<br />
>PO:0001050 : leaf development stage [45968]<br />
<br />
>PO:0007520 : root development stage [25208]<br />
<br />
<br />
'''PO:0025338 : collective plant structure development stage [49645]'''<br />
<br />
>PO:0007615 : flower development stage [48067]<br />
<br />
<br />
<br />
==Continue revisions and adding new terms for wood ontology==<br />
''Most terms are in the PAE branch or for GO.''<br />
<br />
''Can continue to add annotations as we go along, as well.''<br />
<br />
==New or expanded association files:==<br />
* wood genes [http://dendrome.ucdavis.edu/treegenes/ TreeGenes] and [http://www.fagaceae.org/ Fagaceae Genomics Web]<br />
<br />
* cotton- [http://www.agbase.msstate.edu/ AgBase]<br />
<br />
* soybean- [http://soybase.org/ SoyBase]<br />
<br />
* potato<br />
<br />
* rice<br />
<br />
* grape<br />
<br />
''RW will email Stefan and Daniel to find out if either of them are planning to attend the moss meeting at NYBG this summer.''<br />
<br />
==Plant Ontology Web Site and Browser Update:==<br />
<br />
Please see [[Plant_Ontology_Web_Site_Update:_Winter_2012]] for more details<br />
<br />
*Items on the [http://palea.cgrb.oregonstate.edu/trac/report/1 tracker]: <br />
<br />
PO:IDs in definitions working as links, fixes to web page headers<br />
<br />
*Browser update- what is the status of this?<br />
<br />
==Complete old user requests/SF tracker items==<br />
Ongoing process....<br />
<br />
priorities<br />
<br />
=Report from the [http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]=<br />
<br />
April 2-4, 2012, Washington DC<br />
<br />
Link to poster Abstract: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf]]<br />
<br />
* LC attended and took part in the BioCreative workshop<br />
<br />
<br />
==Main topics:==<br />
<br />
* Community annotation<br />
<br />
* Functional annotation and pathways<br />
<br />
* Databases & Journals – How to have a sustainable long term plan for journals and databases? <br />
<br />
* Careers in biocuration<br />
<br />
* Curation workflows and tools<br />
<br />
* Integrating text mining into biocuration workflows<br />
<br />
* Ontologies and standards<br />
<br />
==Biocreative-2012 Workshop==<br />
<br />
Interactive Text Mining in the Biocuration Workflow<br />
<br />
Textpresso<br />
<br />
[http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ Pubtator]<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[https://docs.google.com/document/d/1rb_VbdteXujvm1gXLky1YDtaDNCFguxYdFBeZiQkI04/edit?pli=1 Semantics of Biodiversity Workshop]==<br />
May 16 - 18, 2012<br />
<br />
University of Kansas Biodiversity Institute, Lawrence, Kansas<br />
<br />
The goals of this workshop (still being refined): 1) Clarification of terms used in the biodiversity, genomics, and ecological communities, and 2) Steps to take in building a Biocollections Ontology.<br />
<br />
BS, MAG, and RW are attending.<br />
<br />
==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==<br />
Annual meeting of the Society for the Preservation of Natural History Collections <br />
<br />
Yale University, New Haven Connecticut<br />
June 11-16, 2012 <br />
<br />
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).<br />
<br />
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).<br />
<br />
''From PJ: If we can show progress in the FNA work or Morphobank yes we should''<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
Ruth Bastow is contacting some of the interested people to see which of these dates work best.<br />
<br />
Can we consider September? RB is available 12th -25th September<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
RW will prepare an announcement for the PO home page and FB page.<br />
<br />
Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, early Bird Registration: by May 11<br />
<br />
Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW sent around a draft of an abstract for a poster summarizing the PO-FNA collaboration, with the folks from FNA.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
''LC will forward email to PO announce list and post on PO Facebook page.''<br />
<br />
=Next meeting scheduled for Tuesday, April. 17th, 2012 at 10am PDT/1pm EDT=<br />
[[POC_Conf._Call_4-17-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_4-10-12&diff=16710POC Conf. Call 4-10-122012-04-13T18:02:49Z<p>Preecej: /* Demo - Integrating Annotated Images with PO terms */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Apr 10th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members: ''Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Barry Smith (University at Buffalo, NY), Justin Elser (OSU).''<br />
<br />
Absent: ''Marie Alejandra Gandolfo (Cornell), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)''<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_3-27-12]]? ''no changes, additions, or deletions''<br />
<br />
<br />
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=63898157&rKey=b1cc4800e2b264be<br />
<br />
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=63898157&rKey=119a3285353e0d57<br />
<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
=Demo - Integrating Annotated Images with PO terms=<br />
<br />
JP gave a short demo with "mock-ups" to display one approach to integrating annotated images with PO terms on the PO web site (screenshots below). This one envisions pop-ups driven from links on PO term information pages -- ''perhaps'' in the External References section, or somewhere else on the page -- we have options and flexibility in this regard.<br />
<br />
The long-term goal: A database on a PO server that stores images annotated with PO terms (internally and externally-generated), and a corresponding web interface to display them online in conjunction with other PO data. Currently being designed by JP and BA.''<br />
<br />
The desktop image annotation tool that allows curators to generate annotated images for future integration with web sites and other applications will be available for testing within a few weeks, but any db storage and web-based display of annotated images in conjunction with the PO site is not currently scheduled for active development and is a few months away, at a minimum.<br />
<br />
'''Screenshots''' (click to see full resolution)<br />
<br />
{|<br />
|[[File:PO_image_annotation_mockup_1.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_2.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_3.png|150px|thumb|left]]<br />
|[[File:PO_image_annotation_mockup_4.png|150px|thumb|left]]<br />
|}<br />
<br />
'''Suggestions'''<br />
<br />
* Give the "secondary" annotation terms a more prominent location, perhaps on the left or right instead of the bottom. <br />
<br />
Feel free to add more...<br />
<br />
=Other notes about Images=<br />
<br />
* Journal Bioinformatics- new section called "[http://bioinformatics.oxfordjournals.org/content/28/8/1057.extract?etoc Bioimage informatics]<br />
<br />
Might be able to put together a publication about this new tool? LC would be interested in taking part.<br />
<br />
*From the BioCuration meeting: David Orloff, Senior Manager, Image Library, The American Society for Cell Biology.<br />
"I would welcome a conversation to discuss presenting your images, videos, or animations in The Cell: An Image Library www.cellimagelibrary.org, and then linking back to your websites so that researchers can easily interact with the data. "<br />
<br />
See link to image of [http://cellimagelibrary.org/images/40589 Hibiscus Pollen grain] on their site.<br />
<br />
''Should see if we can get permission to mirror their images on PO and add annotations. See if they can list PO ids as a source on their web page, like they do for GO and NCBI.''<br />
<br />
* Ale got the ok to use the [http://www.agron.iastate.edu/~weeds/Fox/FoxSeed/germination.html Setaria germination] images: we need to give credit to Drs. John Dekker and Mitt Haar.<br />
<br />
=Update on the Release #17, April 2012=<br />
<br />
* Review and Assessments:<br />
<br />
* Issue of files on Bioportal all "PO"- are we going to keep posting the separate aspect files?<br />
<br />
* Updates to the SOP page: [[PO_Release_SOP_Page]]<br />
''Need to clarify where the various files go''<br />
<br />
* What do we need to do better next time?<br />
<br />
''Now that we can use Oort, we can easily generate the asserted file earlier in the process and test load it onto Dev or beta. That way if we run into problems, it will not hold up the database loading. I suggest adding this conversion step to the dev loading script. That will make it easier to diagnose any issues early.''<br />
<br />
''This is a good idea, although at this point, the creation of the asserted file cannot be done automatically and will have to be hand tweaked by the editors each time.''<br />
<br />
''BS suggested that using "plant_ontology_assert" was misleading, and because this is the inferred file. RW pointed out that it was called "assert" based on the OboEdit function "assert implied links".''<br />
<br />
''BS: Users should see the file with inferred relations asserted (They do, since that is what is on AmiGO).''<br />
<br />
''We will look at the naming scheme that CM suggested (what GO uses) and see if that makes sense for PO.''<br />
<br />
=Goals and Timeline for the next Release #18=<br />
Timeline: End of june to Mid- July- '''before''' BSA and ASPB meetings?<br />
<br />
''Agreed''<br />
<br />
==Continue major revision of PSDS==<br />
Focus on the revisions on:<br />
<br />
'''PO:0007033 : whole plant development stage'''<br />
<br />
'''> PO:0028002 : sporophyte development stage'''<br />
<br />
>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)<br />
<br />
>>> PO:0007047 : 3 inflorescence detectable stage [29131]<br />
<br />
>>>PO:0007016 : 4 flowering [28057]<br />
<br />
>>>PO:0007042 : 5 fruit formation [31009]<br />
<br />
>>>PO:0007010 : 6 ripening [37642]<br />
<br />
<br />
'''>> PO:0007134 : sporophyte vegetative stage [60370]:''' (Some still have the numbers preceding them, others don't)<br />
<br />
>>>PO:0007057 : 0 seed germination stage [29568]<br />
<br />
>>>PO:0007112 : 1 main shoot growth stage [47411]<br />
<br />
>>>PO:0007131 : seedling development stage [26673]<br />
<br />
<br />
<br />
'''PO:0009012 : plant structure development stage:'''<br />
<br />
> PO:0007615 : flower development stage [48067]<br />
<br />
>PO:0001083 : inflorescence development stage [48067]<br />
<br />
<br />
'''PO:0025339 : plant organ development stage [46618]''' <br />
<br />
>PO:0001050 : leaf development stage [45968]<br />
<br />
>PO:0007520 : root development stage [25208]<br />
<br />
<br />
'''PO:0025338 : collective plant structure development stage [49645]'''<br />
<br />
>PO:0007615 : flower development stage [48067]<br />
<br />
<br />
<br />
==Continue revisions and adding new terms for wood ontology==<br />
''Most terms are in the PAE branch or for GO.''<br />
<br />
''Can continue to add annotations as we go along, as well.''<br />
<br />
==New or expanded association files:==<br />
* wood genes [http://dendrome.ucdavis.edu/treegenes/ TreeGenes] and [http://www.fagaceae.org/ Fagaceae Genomics Web]<br />
<br />
* cotton- [http://www.agbase.msstate.edu/ AgBase]<br />
<br />
* soybean- [http://soybase.org/ SoyBase]<br />
<br />
* potato<br />
<br />
* rice<br />
<br />
* grape<br />
<br />
''RW will email Stefan and Daniel to find out if either of them are planning to attend the moss meeting at NYBG this summer.''<br />
<br />
==Plant Ontology Web Site and Browser Update:==<br />
<br />
Please see [[Plant_Ontology_Web_Site_Update:_Winter_2012]] for more details<br />
<br />
*Items on the [http://palea.cgrb.oregonstate.edu/trac/report/1 tracker]: <br />
<br />
PO:IDs in definitions working as links, fixes to web page headers<br />
<br />
*Browser update- what is the status of this?<br />
<br />
==Complete old user requests/SF tracker items==<br />
Ongoing process....<br />
<br />
priorities<br />
<br />
=Report from the [http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]=<br />
<br />
April 2-4, 2012, Washington DC<br />
<br />
Link to poster Abstract: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf]]<br />
<br />
* LC attended and took part in the BioCreative workshop<br />
<br />
<br />
==Main topics:==<br />
<br />
* Community annotation<br />
<br />
* Functional annotation and pathways<br />
<br />
* Databases & Journals – How to have a sustainable long term plan for journals and databases? <br />
<br />
* Careers in biocuration<br />
<br />
* Curation workflows and tools<br />
<br />
* Integrating text mining into biocuration workflows<br />
<br />
* Ontologies and standards<br />
<br />
==Biocreative-2012 Workshop==<br />
<br />
Interactive Text Mining in the Biocuration Workflow<br />
<br />
Textpresso<br />
<br />
[http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ Pubtator]<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[https://docs.google.com/document/d/1rb_VbdteXujvm1gXLky1YDtaDNCFguxYdFBeZiQkI04/edit?pli=1 Semantics of Biodiversity Workshop]==<br />
May 16 - 18, 2012<br />
<br />
University of Kansas Biodiversity Institute, Lawrence, Kansas<br />
<br />
The goals of this workshop (still being refined): 1) Clarification of terms used in the biodiversity, genomics, and ecological communities, and 2) Steps to take in building a Biocollections Ontology.<br />
<br />
BS, MAG, and RW are attending.<br />
<br />
==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==<br />
Annual meeting of the Society for the Preservation of Natural History Collections <br />
<br />
Yale University, New Haven Connecticut<br />
June 11-16, 2012 <br />
<br />
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).<br />
<br />
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).<br />
<br />
''From PJ: If we can show progress in the FNA work or Morphobank yes we should''<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
Ruth Bastow is contacting some of the interested people to see which of these dates work best.<br />
<br />
Can we consider September? RB is available 12th -25th September<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
RW will prepare an announcement for the PO home page and FB page.<br />
<br />
Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, early Bird Registration: by May 11<br />
<br />
Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW sent around a draft of an abstract for a poster summarizing the PO-FNA collaboration, with the folks from FNA.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
''LC will forward email to PO announce list and post on PO Facebook page.''<br />
<br />
=Next meeting scheduled for Tuesday, April. 17th, 2012 at 10am PDT/1pm EDT=<br />
[[POC_Conf._Call_4-17-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:PO_image_annotation_mockup_4.png&diff=16709File:PO image annotation mockup 4.png2012-04-13T17:55:54Z<p>Preecej: Annotated rice flower</p>
<hr />
<div>Annotated rice flower</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:PO_image_annotation_mockup_3.png&diff=16708File:PO image annotation mockup 3.png2012-04-13T17:55:34Z<p>Preecej: The original, unannotated image</p>
<hr />
<div>The original, unannotated image</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:PO_image_annotation_mockup_2.png&diff=16707File:PO image annotation mockup 2.png2012-04-13T17:55:16Z<p>Preecej: Other segments annotated with PO terms in the same image</p>
<hr />
<div>Other segments annotated with PO terms in the same image</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:PO_image_annotation_mockup_1.png&diff=16706File:PO image annotation mockup 1.png2012-04-13T17:54:34Z<p>Preecej: Segments annotated with PO terms</p>
<hr />
<div>Segments annotated with PO terms</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_4-10-12&diff=16705POC Conf. Call 4-10-122012-04-13T01:18:57Z<p>Preecej: /* Demo of Integrating Annotated Images with PO terms */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Apr 10th, 2012 10am PDT/1pm EDT<br />
<br />
In attendance:<br />
<br />
POC members: ''Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Barry Smith (University at Buffalo, NY), Justin Elser (OSU).''<br />
<br />
Absent: ''Marie Alejandra Gandolfo (Cornell), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)''<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_3-27-12]]? ''no changes, additions, or deletions''<br />
<br />
<br />
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=63898157&rKey=b1cc4800e2b264be<br />
<br />
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=63898157&rKey=119a3285353e0d57<br />
<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
=Demo - Integrating Annotated Images with PO terms=<br />
<br />
JP gave a short demo with "mock-ups" to display one approach to integrating annotated images with PO terms on the PO web site (screenshots below). This one envisions pop-ups driven from links on PO term information pages -- ''perhaps'' in the External References section, or somewhere else on the page -- we have options and flexibility in this regard.<br />
<br />
The long-term goal: A database on a PO server that stores images annotated with PO terms (internally and externally-generated), and a corresponding web interface to display them online in conjunction with other PO data. Currently being designed by JP and BA.''<br />
<br />
The desktop image annotation tool that allows curators to generate annotated images for future integration with web sites and other applications will be available for testing within a few weeks, but any db storage and web-based display of annotated images in conjunction with the PO site is not currently scheduled for active development and is a few months away, at a minimum.<br />
<br />
'''Screenshots'''<br />
<br />
coming soon...<br />
<br />
'''Suggestions'''<br />
<br />
coming soon...<br />
<br />
=Other notes about Images=<br />
<br />
* Journal Bioinformatics- new section called "[http://bioinformatics.oxfordjournals.org/content/28/8/1057.extract?etoc Bioimage informatics]<br />
<br />
Might be able to put together a publication about this new tool? LC would be interested in taking part.<br />
<br />
*From the BioCuration meeting: David Orloff, Senior Manager, Image Library, The American Society for Cell Biology.<br />
"I would welcome a conversation to discuss presenting your images, videos, or animations in The Cell: An Image Library www.cellimagelibrary.org, and then linking back to your websites so that researchers can easily interact with the data. "<br />
<br />
See link to image of [http://cellimagelibrary.org/images/40589 Hibiscus Pollen grain] on their site.<br />
<br />
''Should see if we can get permission to mirror their images on PO and add annotations. See if they can list PO ids as a source on their web page, like they do for GO and NCBI.''<br />
<br />
* Ale got the ok to use the [http://www.agron.iastate.edu/~weeds/Fox/FoxSeed/germination.html Setaria germination] images: we need to give credit to Drs. John Dekker and Mitt Haar.<br />
<br />
=Update on the Release #17, April 2012=<br />
<br />
* Review and Assessments:<br />
<br />
* Issue of files on Bioportal all "PO"- are we going to keep posting the separate aspect files?<br />
<br />
* Updates to the SOP page: [[PO_Release_SOP_Page]]<br />
''Need to clarify where the various files go''<br />
<br />
* What do we need to do better next time?<br />
<br />
''Now that we can use Oort, we can easily generate the asserted file earlier in the process and test load it onto Dev or beta. That way if we run into problems, it will not hold up the database loading. I suggest adding this conversion step to the dev loading script. That will make it easier to diagnose any issues early.''<br />
<br />
''This is a good idea, although at this point, the creation of the asserted file cannot be done automatically and will have to be hand tweaked by the editors each time.''<br />
<br />
''BS suggested that using "plant_ontology_assert" was misleading, and because this is the inferred file. RW pointed out that it was called "assert" based on the OboEdit function "assert implied links".''<br />
<br />
''BS: Users should see the file with inferred relations asserted (They do, since that is what is on AmiGO).''<br />
<br />
''We will look at the naming scheme that CM suggested (what GO uses) and see if that makes sense for PO.''<br />
<br />
=Goals and Timeline for the next Release #18=<br />
Timeline: End of june to Mid- July- '''before''' BSA and ASPB meetings?<br />
<br />
''Agreed''<br />
<br />
==Continue major revision of PSDS==<br />
Focus on the revisions on:<br />
<br />
'''PO:0007033 : whole plant development stage'''<br />
<br />
'''> PO:0028002 : sporophyte development stage'''<br />
<br />
>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)<br />
<br />
>>> PO:0007047 : 3 inflorescence detectable stage [29131]<br />
<br />
>>>PO:0007016 : 4 flowering [28057]<br />
<br />
>>>PO:0007042 : 5 fruit formation [31009]<br />
<br />
>>>PO:0007010 : 6 ripening [37642]<br />
<br />
<br />
'''>> PO:0007134 : sporophyte vegetative stage [60370]:''' (Some still have the numbers preceding them, others don't)<br />
<br />
>>>PO:0007057 : 0 seed germination stage [29568]<br />
<br />
>>>PO:0007112 : 1 main shoot growth stage [47411]<br />
<br />
>>>PO:0007131 : seedling development stage [26673]<br />
<br />
<br />
<br />
'''PO:0009012 : plant structure development stage:'''<br />
<br />
> PO:0007615 : flower development stage [48067]<br />
<br />
>PO:0001083 : inflorescence development stage [48067]<br />
<br />
<br />
'''PO:0025339 : plant organ development stage [46618]''' <br />
<br />
>PO:0001050 : leaf development stage [45968]<br />
<br />
>PO:0007520 : root development stage [25208]<br />
<br />
<br />
'''PO:0025338 : collective plant structure development stage [49645]'''<br />
<br />
>PO:0007615 : flower development stage [48067]<br />
<br />
<br />
<br />
==Continue revisions and adding new terms for wood ontology==<br />
''Most terms are in the PAE branch or for GO.''<br />
<br />
''Can continue to add annotations as we go along, as well.''<br />
<br />
==New or expanded association files:==<br />
* wood genes [http://dendrome.ucdavis.edu/treegenes/ TreeGenes] and [http://www.fagaceae.org/ Fagaceae Genomics Web]<br />
<br />
* cotton- [http://www.agbase.msstate.edu/ AgBase]<br />
<br />
* soybean- [http://soybase.org/ SoyBase]<br />
<br />
* potato<br />
<br />
* rice<br />
<br />
* grape<br />
<br />
''RW will email Stefan and Daniel to find out if either of them are planning to attend the moss meeting at NYBG this summer.''<br />
<br />
==Plant Ontology Web Site and Browser Update:==<br />
<br />
Please see [[Plant_Ontology_Web_Site_Update:_Winter_2012]] for more details<br />
<br />
*Items on the [http://palea.cgrb.oregonstate.edu/trac/report/1 tracker]: <br />
<br />
PO:IDs in definitions working as links, fixes to web page headers<br />
<br />
*Browser update- what is the status of this?<br />
<br />
==Complete old user requests/SF tracker items==<br />
Ongoing process....<br />
<br />
priorities<br />
<br />
=Report from the [http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]=<br />
<br />
April 2-4, 2012, Washington DC<br />
<br />
Link to poster Abstract: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf]]<br />
<br />
* LC attended and took part in the BioCreative workshop<br />
<br />
<br />
==Main topics:==<br />
<br />
* Community annotation<br />
<br />
* Functional annotation and pathways<br />
<br />
* Databases & Journals – How to have a sustainable long term plan for journals and databases? <br />
<br />
* Careers in biocuration<br />
<br />
* Curation workflows and tools<br />
<br />
* Integrating text mining into biocuration workflows<br />
<br />
* Ontologies and standards<br />
<br />
==Biocreative-2012 Workshop==<br />
<br />
Interactive Text Mining in the Biocuration Workflow<br />
<br />
Textpresso<br />
<br />
[http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/ Pubtator]<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==[https://docs.google.com/document/d/1rb_VbdteXujvm1gXLky1YDtaDNCFguxYdFBeZiQkI04/edit?pli=1 Semantics of Biodiversity Workshop]==<br />
May 16 - 18, 2012<br />
<br />
University of Kansas Biodiversity Institute, Lawrence, Kansas<br />
<br />
The goals of this workshop (still being refined): 1) Clarification of terms used in the biodiversity, genomics, and ecological communities, and 2) Steps to take in building a Biocollections Ontology.<br />
<br />
BS, MAG, and RW are attending.<br />
<br />
==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==<br />
Annual meeting of the Society for the Preservation of Natural History Collections <br />
<br />
Yale University, New Haven Connecticut<br />
June 11-16, 2012 <br />
<br />
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).<br />
<br />
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).<br />
<br />
''From PJ: If we can show progress in the FNA work or Morphobank yes we should''<br />
<br />
==Crop Ontology Workshop==<br />
For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]<br />
<br />
We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th<br />
<br />
The focus of the workshop will be on mostly development stages and traits for the crop plants<br />
<br />
Ruth Bastow is contacting some of the interested people to see which of these dates work best.<br />
<br />
Can we consider September? RB is available 12th -25th September<br />
<br />
==[http://www.botanyconference.org/ Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM<br />
<br />
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops] <br />
<br />
The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.<br />
<br />
RW will prepare an announcement for the PO home page and FB page.<br />
<br />
Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices. <br />
<br />
''A desktop version of the image annotation software should be ready to demo at this meeting.''<br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
''We should do the booth. PJ will attend to host the booth for both Gramene and PO.''<br />
<br />
==Bio-Ontologies SIG 2012==<br />
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with [http://www.iscb.org/ismb2012 ISMB 2012]<br />
<br />
When: Submissions Due: April 13th, 2012 (Fri)<br />
<br />
See: [http://www.bio-ontologies.org.uk/call-for-participation Bio-Ontologies SIG 2012]<br />
<br />
Three types of submissions.<br />
<br />
- Short papers, up to 4 pages.<br />
- Poster abstracts, up to 1 page.<br />
- Flash updates, up to 1 page<br />
<br />
Successful papers will be presented at the Bio-Ontologies SIG. <br />
<br />
Poster abstracts: time will be allocated during the 2 days for at least one poster session. <br />
<br />
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.<br />
<br />
==ASPB Plant Biology 2012==<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]<br />
<br />
Abstract was submitted for submission for minisymposia consideration.<br />
<br />
Joint workshop is planned with PO, Gramene and TAIR<br />
<br />
Registration is open, early Bird Registration: by May 11<br />
<br />
Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on [[Plant Disease Ontology]].<br />
<br />
'''Relevant dates'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
RW sent around a draft of an abstract for a poster summarizing the PO-FNA collaboration, with the folks from FNA.<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
==Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012==<br />
Link to: [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]<br />
<br />
from Paula Mabee: Opening are available the Anatomy Ontology course.<br />
<br />
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]<br />
<br />
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).<br />
<br />
Apply here: [https://docs.google.com/spreadsheet/viewform?formkey=dEVyQUJkYjJ4WXIzYUIwaWlNOWRCWGc6MA#gid=0]<br />
<br />
Application deadline is April 4th, 2012 (extended through mid-April)<br />
<br />
''LC will forward email to PO announce list and post on PO Facebook page.''<br />
<br />
=Next meeting scheduled for Tuesday, April. 17th, 2012 at 10am PDT/1pm EDT=<br />
[[POC_Conf._Call_4-17-12]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=16386Plant Ontology Web Site Update: 20132012-03-29T18:07:12Z<p>Preecej: /* Example sites whose design and layout we like */</p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under "/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
* GARNet has a clean, fresh look- I like it: [http://www.garnetcommunity.org.uk/ GARNet] LC<br />
<br />
* MosDB: http://mips.helmholtz-muenchen.de/plant/rice/index.jsp<br />
<br />
===Current PO Site Map===<br />
<br />
''Screenshots of current content have been catalogued and URLs have been mapped. Diagram of PO's current site map will be posted shortly...''<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our Palea web server (''currently in progress'').<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
See also the items listed on the [[POC_Technical_Issues_Page]]- some of which are AmiGO specific<br />
<br />
===Developers guide -Download SVN Page===<br />
<br />
<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
[http://www.plantontology.org/download/svn_doc.html Developers guide]<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to login to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an image for participates_in, still need one for adjacent_to and also has_participant.''</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=14838Plant Ontology Web Site Update: 20132012-02-03T01:36:45Z<p>Preecej: /* Drupal Suggestion */</p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under "/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
===Current PO Site Map===<br />
<br />
''Screenshots of current content have been catalogued and URLs have been mapped. Diagram of PO's current site map will be posted shortly...''<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our Palea web server (''currently in progress'').<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
===Developers guide -Download SVN Page===<br />
<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
[http://www.plantontology.org/download/svn_doc.html Developers guide]<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to login to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an image for participates_in, still need one for adjacent_to and also has_participant.''</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=14837Plant Ontology Web Site Update: 20132012-02-03T01:21:48Z<p>Preecej: /* Drupal Suggestion */</p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under "/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
===Current PO Site Map===<br />
<br />
''Screenshots of current content have been catalogued and URLs have been mapped. Diagram of PO's current site map will be posted shortly...''<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our palea web server (''currently in progress'').<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
===Developers guide -Download SVN Page===<br />
<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
[http://www.plantontology.org/download/svn_doc.html Developers guide]<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to login to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an image for participates_in, still need one for adjacent_to and also has_participant.''</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=14836Plant Ontology Web Site Update: 20132012-02-03T01:03:03Z<p>Preecej: /* Site "Refresh" */</p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under "/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
===Current PO Site Map===<br />
<br />
''Screenshots of current content have been catalogued and URLs have been mapped. Diagram of PO's current site map will be posted shortly...''<br />
<br />
===Drupal Suggestion===<br />
<br />
We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). '''We are merely ''exploring'' the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders.''' ;)<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
===Developers guide -Download SVN Page===<br />
<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
[http://www.plantontology.org/download/svn_doc.html Developers guide]<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to login to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an image for participates_in, still need one for adjacent_to and also has_participant.''</div>Preecejhttps://wiki.plantontology.org/index.php?title=Plant_Ontology_Web_Site_Update:_2013&diff=14835Plant Ontology Web Site Update: 20132012-02-03T00:51:10Z<p>Preecej: </p>
<hr />
<div>Note: To access the page on Plant Ontology web site technical issues, go back to the [[POC_Technical_Issues_Page]]. For changes to site ''content'' and the site design "refresh", read on...<br />
<br />
=Site "Refresh"=<br />
<br />
We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.<br />
<br />
The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.<br />
<br />
* Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features<br />
* Static content: Generally speaking, HTML pages currently maintained in SVN under "/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)<br />
<br />
We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:<br />
<br />
1. If you have a favorite research web site whose design and layout you just love, please add the link to the "Example sites" section (below) so we can check it out.<br />
2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking you for specific thoughts soon. <br />
<br />
This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):<br />
<br />
* Our focus: The aesthetic and static items mentioned above, including the header and navigational elements<br />
* Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email notification features, the "site map" (that is, the location and organization of static pages)<br />
<br />
We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.<br />
<br />
Our next step is to produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)<br />
<br />
===Example sites whose design and layout we like===<br />
<br />
We welcome more suggestions...<br />
<br />
*On the [http://solgenomics.net/ Solanaceae Genomics] site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC<br />
<br />
<br />
<br />
=Requests for Content Change=<br />
<br />
A list of requested content corrections...<br />
<br />
===Developers guide -Download SVN Page===<br />
<br />
submitted: 1-11-12<br />
<br />
Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit<br />
<br />
[http://www.plantontology.org/download/svn_doc.html Developers guide]<br />
<br />
===Link on Homepage to Source Forge tracker===<br />
submitted 9-28-11- LC<br />
Now that people need to login to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in.<br />
Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation<br />
<br />
===Color coding the Anatomy and Development terms differently?===<br />
This was a suggestion raised by PJ a the NYBG meeting Sept 2011 [[Saturday_Sept_10th,_2011]] during the discussion of the cross-ontology relations.<br />
<br />
add more details....<br />
<br />
===filter translation===<br />
Date: 9-13-11<br />
<br />
This was sent as a feedback response on the web page- went to Po-internal.<br />
refer_to_url: http://www.plantontology.org/index.html<br />
<br />
subject: filter translation<br />
<br />
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.<br />
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.<br />
<br />
name: Mary Schaeffer<br />
email: schaefferm@missouri.edu<br />
organization: MaizeGDB<br />
<br />
===Download annotations from the PO website===<br />
-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.<br />
<br />
-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!<br />
<br />
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis]<br />
<br />
===Tutorials and Demos out-of-date===<br />
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials]<br />
The ppt tutorials on this page are severely outdated!<br />
<br />
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo]<br />
<br />
===New images needed for browser===<br />
JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?<br />
<br />
''We have now an image for participates_in, still need one for adjacent_to and also has_participant.''</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Conf._Call_1-24-12&diff=14539POC Conf. Call 1-24-122012-01-24T17:35:57Z<p>Preecej: /* Demonstration of Photo Annotation Tool */</p>
<hr />
<div>POC meeting, Webex Conference Call; Date: Tuesday Jan 24th, 2012 10am (PST)<br />
<br />
In attendance:<br />
<br />
POC members:<br />
<br />
Absent:<br />
<br />
<br />
Collaborators: none<br />
<br />
<br />
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-17-12?<br />
<br />
Back to [[POC Meetings Minutes]]<br />
<br />
<br />
<br />
=Interim Data Release 16A, January 2012=<br />
The Plant Ontology is pleased to announce the availability of the January 2012, Interim Data Release 16A on our web page.<br />
<br />
Through a collaborative effort with the Moss Computational Biology Resource (COSMOSS and University of Freiburg), this interim data release adds approximately 82,000 new annotations for genes expressed in the model moss species; Physcomitrella patens.<br />
<br />
Links from annotations on the PO terms; gametophore (PO:0030018), spore (PO:0025017), protonema (PO:0030003) and protoplast (PO:0030003) will take you to the Cosmoss site (cosmoss.org) for further info.<br />
<br />
This work is the result of a process that has been undergone for the past year, adding more than 80 new terms and revising the structure of the Plant Anatomy branch of the ontology to accommodate non-vascular plants. <br />
<br />
There are no changes to the ontology file relative to version #16.<br />
<br />
=Demonstration of Image Annotation Tool=<br />
<br />
JP and Nikhil (CS student) will demonstrate an image annotation application currently under development. It is intended to be used by curators for segmenting and tagging images of plant specimens with PO terms.<br />
<br />
=Updates from [http://www.intl-pag.org/ PAG 2012]=<br />
January 14-18, 2012, San Diego, California<br />
<br />
'''PO was represented at the following events:'''<br />
<br />
*Ontology workshop, Saturday January 14th from 10:20am-12:30pm: [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1272.html Use of Ontologies for Organizing Plant and Animal Genomics Data]. <br />
<br />
We had 5 speakers and a panel discussion at the end<br />
<br />
For more info, see the [[PAG 2012 Ontology workshop]] wiki page.<br />
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1046.html Non-Seed Plant Workshop] on Saturday, Jan 14th, (3:50pm-6pm) <br />
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes] workshop on Sunday, Jan. 15th, (8:00am - 10:10am)<br />
* Computer demo Monday 12:50 pm for the PO.<br />
<br />
* The PO also took part in an [http://www.agron.missouri.edu/mnl/pgoPAG.htm Outreach booth] organized by MaizeGDB<br />
<br />
=Wood Anatomy Ontology Meeting=<br />
Please see the [[Wood_Anatomy]] and the [[Wood anatomy ontology meeting, 2012 at NYBG, agenda]] wiki pages for more information.<br />
<br />
Confirmed dates are Feb. 5th-7th, 2012 (Sun-Tues)<br />
<br />
'''Update and status:'''<br />
<br />
Attendees:<br />
<br />
*Frederic Lens: [http://www.nhn.leidenuniv.nl/index.php/nhn/institute/nlcb/ Netherlands Centre for Biodiversity Naturalis]<br />
*Barb Lachenbruch [http://woodscience.oregonstate.edu/people/faculty/lachenbruch-barb link]<br />
*Elisabeth Wheeler (paleobotanist and wood anatomist at [http://cnr.ncsu.edu/fb/about/faculty/wheeler.php NC State]<br />
*Rachel Spicer [http://www.conncoll.edu/academics/web_profiles/spicer.html Connecticut College]<br />
*John Carlson (jec16@psu.edu) [http://sfr.psu.edu/directory/jec16 link]<br />
*Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the [http://www.fagaceae.org/ Fagaceae Genomics Web] <br />
<br />
Hotel is booked and flights have been arranged for all except for Rachel spicer, who is driving<br />
<br />
Barry, please send me flight info so we can coordinate shuttle<br />
<br />
BS will give his presentation on Sunday morning (see: [[Wood anatomy ontology meeting, 2012 at NYBG, agenda]]). This will be open to the public and notices have been sent out.<br />
<br />
=Vascular tissues and cell types=<br />
<br />
These terms will need to be fixed before the Wood Ontology meeting in February.<br />
<br />
==vascular tissue types==<br />
<br />
For vascular plants, we have the class:<br />
<br />
'''portion of vascular tissue (PO:0009015):''' A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]<br />
<br />
Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.<br />
<br />
part_of vascular bundle (which is part_of vascular system)<br />
<br />
This is okay, but suggest that we change definition to include xylem '''or''' phloem, and it may not always be part_of vascular bundle.<br />
<br />
<br />
'''Proposed definition:''' A portion of plant tissue that has as parts tracheary elements or sieve elements.<br />
<br />
Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissues or cells, such as parenchyma or fibers.<br />
<br />
part_of vascular system (should add vascular system participates_in sporophytic phase)<br />
<br />
<br />
'''vascular bundle (PO:0005020) current def.:''' A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]<br />
<br />
This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.<br />
<br />
'''proposed definition:''' A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.<br />
<br />
Comment: Usually contains both xylem and phloem. May also contain other types of cells or tissue such as fibers, vascular cambium, or portions of ground tissue.<br />
<br />
part_of vascular system<br />
<br />
add vein as exact synonym -- can be in any organ<br />
<br />
===primary and secondary vascular tissue===<br />
'''primary vascular tissue:''' A portion of vascular tissue that develops from a procambium. (ref: Esau)<br />
<br />
comment: Forms as part of primary growth (GO:xxxx). <br />
<br />
'''secondary vascular tissue:''' A portion of vascular tissue that develops from a vascular cambium. (ref: Esau)<br />
<br />
comment: Forms as part of secondary growth (GO:0080117) in vascular plants. Often differentiated into the axial system and ray system.<br />
<br />
If we '''set both of these up as a cross products''', then primary and secondary xylem and phloem will be inferred children.<br />
<br />
===phloem===<br />
<br />
'''phloem (PO:0005417) current def.:''' A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]<br />
<br />
'''proposed definition:''' A portion of vascular tissue that has as parts sieve elements.<br />
<br />
Comment: Functions in the conduction of organic substances in vascular plants.<br />
<br />
''Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.''<br />
<br />
<br />
'''metaphloem (PO:0006076) current def.:''' Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.<br />
<br />
'''proposed definition:''' A portion of primary phloem that differentiates after the protophloem.<br />
<br />
Comment: Differentiates before the secondary phloem, if any is formed.<br />
<br />
<br />
'''protophloem (PO:0006077) current def.:''' The first-formed elements of the primary phloem.<br />
<br />
'''proposed definition:''' A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.<br />
<br />
<br />
'''primary phloem (PO:0006075) current def.:''' A portion of phloem tissue of the primary plant body.<br />
<br />
'''proposed definition:''' A portion of phloem tissue that develops from the procambium.<br />
<br />
Comment: Primary phloem develops as part of GO:xxxx primary growth. (''see below'')<br />
<br />
develops_from PO:0025275 procambium<br />
<br />
<br />
'''secondary phloem (PO:0005043) current def.:''' A portion of phloem tissue formed by the activity of the vascular cambium.<br />
<br />
'''proposed definition:''' A portion of phloem tissue that develops from the vascular cambium.<br />
<br />
Comment: Secondary phloem develops as part of GO:0080117 secondary growth.<br />
<br />
develops_from PO:0005598 vascular cambium<br />
<br />
===xylem===<br />
<br />
'''xylem (PO:0005352) current def.:''' A portion of vascular tissue composed of xylem elements.<br />
<br />
comment: The principal function is the upward translocation of water and solutes. See also primary xylem and secondary xylem.<br />
<br />
'''proposed definition:''' A portion of vascular tissue that has as parts tracheary elements.<br />
<br />
comment: Functions in the translocation of water and solutes from roots to the shoot system and in support.<br />
<br />
<br />
'''primary xylem (PO:0005849) current def.:''' A portion of xylem tissue of the primary plant body. [source: GR:Pankaj_Jaiswal, ISBN:0122151704, ISBN:0471245194] <br />
<br />
Comment: In stem or root it is differentiated behind the apical meristem.<br />
<br />
'''proposed definition:''' A portion of xylem tissue that differentiates from the procambium.<br />
<br />
Comment: Primary xylem develops as part of GO:xxxx primary growth.<br />
<br />
develops_from PO:0025275 procambium<br />
<br />
<br />
'''protoxylem (PO:0000272) current def.:''' A portion of xylem tissue composed of any of the first formed elements of the primary xylem. [source: ISBN:047125208] <br />
<br />
'''proposed definition:''' A portion of primary xylem that has as parts the first formed xylem elements of the primary xylem.<br />
<br />
<br />
'''metaxylem (PO:0000372) current def.:''' A portion of xylem tissue that is part of the primary xylem and differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed. [source: ISBN:047125208] <br />
<br />
'''proposed definition:''' A portion of primary xylem that differentiates after the protoxylem.<br />
<br />
Comment: Differentiates before the secondary xylem, if any is formed.<br />
<br />
<br />
'''secondary xylem (PO:0005848) current def.:''' A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators] <br />
<br />
Comment: Absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas.<br />
<br />
Existing definition is okay.<br />
<br />
New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. Secondary xylem is the "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. May be organized into axial and ray systems. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed of secondary xylem.<br />
<br />
develops_from PO:0005598 vascular cambium<br />
<br />
<br />
''Note: exarch, endarch, mesarch are descriptors for different types of xylem development.''<br />
<br />
<br />
'''tracheid bar (PO:0019026) current def.:''' A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]<br />
<br />
'''proposed definition:''' A portion of xylem tissue that is a distinct ring-like structure, composed of tracheid cells, which surrounds the hilum and forms a groove in the surface of the pericarp immediately adjacent to the hilum.<br />
<br />
Comment: Found some taxa such as Phaseolus. [ISBN:0080280293]<br />
<br />
part_of seed; adjacent_to hilum<br />
<br />
===leaf vein, midrib===<br />
<br />
*'''leaf vein (PO:0020138), current def:''' A strand of vascular tissue in the leaf blade. <br />
<br />
is_a portion of vascular tissue; part_of leaf vascular system<br />
<br />
<br />
'''proposed definition, leaf vein (PO:0020138):''' A vascular bundle that is part of a leaf lamina in a vascular leaf.<br />
<br />
part_of leaf vascular system, part_of leaf lamina<br />
<br />
synonym: leaf vascular bundle<br />
<br />
<br />
Suggest new term '''primary leaf vein''': A leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.<br />
<br />
Comment: A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139).<br />
<br />
<br />
*'''midvein (PO:0020139):''' The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary] <br />
<br />
Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ.<br />
<br />
'''proposed definition:''' A primary leaf vein that is the central vein of a vascular leaf.<br />
<br />
Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf.<br />
<br />
broad synonyms: mid rib, midrib, mid-rib, vascular leaf midvein<br />
<br />
related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128<br />
<br />
We already have terms for secondary, tertiary, quaternary, and higher order veins.<br />
<br />
===Primary and secondary growth, lateral meristems, etc.===<br />
====proposed terms for GO==== <br />
'''primary growth (new term):'''<br />
<br />
'''proposed definition:''' Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)<br />
<br />
comment: Has its inception in the apical meristems and continues in their derivative meristems - protoderm and procambium - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism. <br />
<br />
is_a growth (GO:0040007)<br />
<br />
<br />
'''secondary or lateral growth'''<br />
<br />
GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290 <br />
<br />
Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by [http://www.jstor.org/stable/10.2307/4354165 Rudall et al.] in Botanical Review. <br />
<br />
Perhaps GO should have a general term for '''lateral growth''' (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.<br />
<br />
<br />
'''lateral growth (GO:new term):''' Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).<br />
<br />
Comment: Includes thickening of plant axes due to the activity of a cambium (secondary growth, found in most gymnosperms and dicotyledons), a primary thickening meristem (found in many monocotyledons, some ferns and some cycads), or secondary thickening meristem (in some monocotyledons). <br />
<br />
<br />
'''proposed new def., secondary growth (GO:0080117):''' Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)<br />
<br />
Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium (phellogen). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism. <br />
<br />
Add synonym "cambial secondary growth", which is makes the meaning clearer.<br />
<br />
<br />
'''secondary thickening (GO:new term):''' Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:xxxx).<br />
<br />
comment: Occurs shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.<br />
<br />
References: Fahn 1990, ISBN:0080374903, Rudall 1991, JSTOR:4354165<br />
<br />
<br />
'''primary thickening (GO:new term):''' Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039) <br />
<br />
comment: Occurs in shoot axes and rarely in roots in many monocotyledons.<br />
<br />
Ref: JSTOR:4354165, Rudall 1991, and Esau ISBN:0471245208<br />
<br />
<br />
'''diffuse secondary thickening (GO:new term)''': Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fibers of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.<br />
<br />
comment: Occurs in the stems of some Arecaceae (palms).<br />
<br />
Ref.: Fahn 1990, ISBN:0080374903<br />
<br />
====PO terms for lateral meristems====<br />
<br />
The PO has a general term for lateral meristem, of which cambium is a subtype:<br />
<br />
[[File:lateral_meristem1.jpg]]<br />
<br />
'''lateral meristem (PO:0020145)'''<br />
<br />
'''current def.:''' A meristem containing cells along the stem or root that first differentiate and function as members of a mature tissue system but then again take up meristematic activity.<br />
<br />
'''proposed def.:''' A meristem located parallel to the circumference of a plant organ.<br />
<br />
comment: Participates in lateral growth (GO:xxxx) of a plant organ, primarily shoot axes and roots. Contrast with apical meristem (PO:0020144).<br />
<br />
<br />
'''root lateral meristem (PO:0006308)'''<br />
<br />
'''current def.:''' Meristem of the root located parallel to the sides of the axis.<br />
<br />
comment: Generally causes root thickening. Not to be confused with lateral root meristem, which is the meristem of the lateral root.<br />
<br />
This is just a cambium in the root, which also has vascular cambium and phellogen.<br />
<br />
'''proposed new name and def.: root cambium:''' A cambium that is part of a root.<br />
<br />
This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.<br />
<br />
If we are going to have this term, maybe we should have root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium?<br />
<br />
<br />
'''cambium (PO:0005597)'''<br />
<br />
'''current def.:''' A lateral meristem, the cells of which divide mostly periclinally. [source: ISBN:0080374913]<br />
<br />
'''proposed def.:''' A lateral meristem that has a part a single layer of cambial initial cells and their derivatives, arranged orderly in radial files. (Ref.: Esau)<br />
<br />
comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).<br />
<br />
<br />
'''vascular cambium (PO:0005598)'''<br />
<br />
'''current def.:''' A lateral meristem, the cells of which give rise to secondary xylem and phloem, leading to an increase in girth.<br />
<br />
Current definition is okay, but needs minor changes. <br />
<br />
'''proposed def.:''' A cambium that gives rise to secondary xylem and secondary phloem.<br />
<br />
comment: Vascular cambium is located between the secondary xylem and secondary phloem and gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis.<br />
<br />
<br />
'''cork cambium/phellogen (PO:0005599)'''<br />
<br />
'''current def.:''' Lateral meristem which produces the phellem (cork) and the phelloderm.<br />
<br />
'''proposed def.:''' A cambium that is part of a periderm and produces phellem (cork) and phelloderm.<br />
<br />
comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.<br />
<br />
<br />
'''primary thickening meristem (PO:0005039)'''<br />
<br />
'''current def.:''' A meristem that develops from a peripheral zone of a shoot apical meristem and is responsible for the primary increase in thickness of a shoot axis.<br />
<br />
comment: May appear as a distinct mantle like zone. Often found in monocotyledons.<br />
<br />
Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM. <br />
<br />
'''proposed def.:''' A lateral meristem that has a parts multiple layers of cells located near the shoot apical meristem.<br />
<br />
comment: Contributes to primary thickening of the stem, adventitious root formation, and formation of linkages between the stem, leaf, and root vasculature. Contiguous with the shoot apical meristem in some species, but not all. Produces more or less distinct vascular bundles surrounded by ground tissue, as opposed to the more or less continuous xylem and phloem produced by a vascular cambium. A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.<br />
<br />
<br />
'''secondary thickening meristem (new term)'''<br />
<br />
'''proposed def.:''' A lateral meristem has a parts multiple layers of cells in a shoot axis...<br />
<br />
comment: Contributes mainly to formation of the body of a stem, but may also produce adventitious roots. May be continuous or discontinuous with the primary thickening meristem. Found in some monocot species of the Liliales and Asperigales.<br />
<br />
<br />
<br />
'''Other types of lateral meristems''' <br />
<br />
PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel merristem (PO:0009107), plus their subtypes.<br />
<br />
Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches generall develop from apical meristems, not a lateral meristem.<br />
<br />
There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem. <br />
<br />
'''inflorescence lateral meristem (PO:0009105)'''<br />
<br />
'''current def.:''' The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.<br />
<br />
This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.<br />
<br />
<br />
'''ear lateral meristem (PO:0009110)'''<br />
<br />
'''current def.:''' The meristem that gives rise to the lateral structures of a maize ear.<br />
<br />
This should be called '''ear inflorescence branch meristem''', and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).<br />
<br />
'''proposed def.:''' An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.<br />
<br />
=Upcoming meetings and Presentations 2012:=<br />
<br />
==Phenotype RCN meeting, February 23rd-25th, 2012==<br />
<br />
The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting. <br />
<br />
It will be held again at NESCent (Durham, NC).<br />
<br />
RW has a friend there she can stay with and is interested in going.<br />
<br />
This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.<br />
<br />
The projects of the Plant Working Group that we started in CO will be worked on during the next meeting.<br />
<br />
Eva said that they can cover RW's plane fare from NY.<br />
<br />
==Maize Genetics Meeting, March 15-18, 2012==<br />
<br />
The maize meetings are being held in Portland, OR this year. <br />
<br />
For more info see: [http://www.maizegdb.org/maize_meeting/2012/index.php Maize Genetics Meeting 2012]<br />
<br />
Registration Link:<br />
2012 Maize Genetics Conference Registration Page will open on December 30, 2011.<br />
<br />
Deadlines:<br />
Advance meeting registration is due by January 31, 2012.<br />
<br />
The PO and Gramene will most likely be co-hosting a workshop. Details TBA....<br />
<br />
==[http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]==<br />
<br />
April 2-4, 2012, Washington DC<br />
<br />
• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.<br />
<br />
See link: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf]]<br />
<br />
• Notification date: February 3, 2012<br />
<br />
From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?<br />
<br />
==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==<br />
Annual meeting of the Society for the Preservation of Natural History Collections <br />
<br />
Yale University, New Haven Connecticut<br />
June 11-16, 2012 <br />
<br />
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).<br />
<br />
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).<br />
<br />
''From PJ: If we can show progress in the FNA work or Morphobank yes we should''<br />
<br />
==[http://www.2011.botanyconference.org/info/Botany2012.php Botany 2012]==<br />
<br />
July 7 - 11, 2012 - Columbus, Ohio<br />
<br />
Call for Symposia, Colloquia and Workshops:<br />
<br />
<br />
RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.<br />
<br />
Proposal was submitted, waiting for news.<br />
<br />
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes. <br />
<br />
===exhibitor's booth===<br />
We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' <br />
<br />
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)<br />
<br />
• 2 months of Rotating Banner Ads in the online American Journal of Botany<br />
<br />
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin<br />
<br />
• A Rotating Banner Ad on the Botany 2012 abstract submission site<br />
<br />
• A Rotating Banner Ad on the 2012 Conference Registration site.<br />
<br />
''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''<br />
<br />
===Annotation wiki===<br />
JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.<br />
<br />
==[http://my.aspb.org/?page=Meetings_PB2012 ASPB Plant Biology 2012]==<br />
<br />
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX<br />
<br />
Registration scheduled to open first week in January.<br />
<br />
Early Bird Registration: by May 11<br />
<br />
Advance Discounted: May 12-June 15<br />
<br />
==ICBO 2012==<br />
'''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012]), July 22nd-25th, Graz, Austria<br />
<br />
co-located with the 7th International Conference on [http://www.kr-med.org/icbofois2012/ Formal Ontologies in Information Systems] (FOIS 2012)<br />
<br />
'''Relevant dates'''<br />
* '''Jan. 31st, 2012: Paper submission deadline'''<br />
* Feb. 28th, 2012: Notification of paper acceptance<br />
* March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline<br />
* April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance<br />
* June 30th 2012: Deadline for all camera-ready copies for the proceedings<br />
<br />
BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.<br />
<br />
RW will circulate a draft of a manuscript for a plant disease extension of the Infectious Disease Ontology. Must be submitted by Jan. 31, 2012.<br />
<br />
RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.<br />
<br />
<br />
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts<br />
<br />
=Next meeting scheduled for Tuesday, Jan. 31st, 2012 at 10am PST/1pm EST=</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Outreach_Events&diff=13458POC Outreach Events2011-11-23T22:53:19Z<p>Preecej: /* Year 2011 */</p>
<hr />
<div>==Workshops, Presentations, Posters etc==<br />
<br />
==Year 2012==<br />
<br />
[http://www.intl-pag.org/ PAG 2012]<br />
<br />
'''[[PAG 2012 Ontology workshop]]: Saturday January 14th from 10:20am-12:30pm'''<br />
<br />
[http://pag.confex.com/pag/xx/webprogrampreliminary/Session1272.html Use of Ontologies for Organizing Plant and Animal Genomics Data]<br />
<br />
==Year 2011==<br />
<br />
* '''[http://www.swat4ls.org/workshops/london2011/ Semantic Web Applications and Tools for Life Sciences Workshop]''' Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), Dec 6-9<br />
<br />
JP will present a poster entitled "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes". (abstract: [[Media:SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf|SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf]]). He will also participate in a "hackathon" software development session meant to spur innovation in semantic web applications.<br />
<br />
<br />
* '''[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: from Genes to Networks]''' Cold Spring Harbor Laboratory, November 30 - December 3, 2011<br />
<br />
RW will present a poster entitled "Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets". (link to abstract: [[Media:PO_abstract_PGB_CSHL2011.pdf]]<br />
<br />
<br />
* '''Departmental seminar: Facultad de Ciencis Naturales y Museo , Universidad Nacional de La Plata, Argentina''', Nov. 1, 2011<br />
MAG presented: 'El valor de las fosiles para descrifar la historia evolutiva de las angiospermas y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany Laboratory- Dr. Ari Iglesias.<br />
<br />
* '''Departmental seminar: Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Argentina''', Oct. 31, 2011<br />
MAG presented: "Paleobotanica en la era de la Biologia Molecular y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany and Palynology laboratory- Dr. Maria del Carmen Zamaloa.<br />
<br />
<br />
* '''12th Genomic Standards Consortium Meeting''' ([http://gensc.org/gc_wiki/index.php/GSC_12 GSC 12]), Max Planck Institute for Marine Microbiology, Bremen, September 28-29, 2011<br />
<br />
Barry Smith addressed Plant Ontology issues in two presentations, on “An Introduction to Ontology as a Strategy for Data Integration”, and on “The Structure of the Environment Ontology”)<br />
<br />
<br />
* '''Syngenta Presentation'''. Global webinar, September 26, 2011<br />
<br />
PJ and JP presented our current work on the Planteome Annotation Wiki to the IT Research and Development Dept. at Syngenta. (presentation: [[Media:Jaiswal_Lab_-_Semantic_Wiki_Presentation_-_2011.pdf|Jaiswal Lab - Semantic Wiki Presentation - 2011.pdf]])<br />
<br />
<br />
* '''[http://conference.cgrb.oregonstate.edu/ 2011 CGRB Fall Conference]''' Oregon State University, September 18th-19th, 2011.<br />
<br />
Two posters related to the Plant Ontology were presented.<br />
<br />
LC presented the poster: "[[Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa]]".<br />
<br />
JP presented a poster: "[[Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes]]". This explains the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service and includes an initial data set built from PO GAF (.assoc) files for ''Oryza sativa''. <br />
<br />
<br />
<br />
* '''Moss 2011 PO presentation''' (Black Forest, September 11th - 15th, 2011, done via Webex) [[Moss 2011 Meeting- PO presentation]] Sept 12, 2011<br />
<br />
<br />
* '''NSF Plant Genome Awardee meeting''' Sept, 2011. Washington, DC. Submission: [[Media:2-pager_plant_ontology-2011.pdf]]<br />
<br />
<br />
* '''ASPB Plant Biology meeting 2011,''' [http://my.aspb.org/?page=Meetings_PB2011 PB2011], Minneapolis, Minn. Aug 6th-10th, 2011<br />
<br />
PO and [http://www.gramene.org/ Gramene] hosted a [http://outreach.gramene.org/gramene-outreach/index.php/Main_Page Data Curation Workshop] <br />
<br />
LC presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster] and we took part in an [[Plant Biology 2011 Outreach Booth]]<br />
<br />
<br />
* '''International Botanical Congress''' [http://www.ibc2011.com/Default.htm (IBC2011)], July 23rd – 30th 2011<br />
Symposium hosted: [[Bio-Ontologies for the Plant Sciences]] under the Genetics, Genomics and Bioinformatics theme. <br />
<br />
Please see the [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details.<br />
<br />
Press release about the PO at IBC 2011: [[Media:IBC_2011_Congress_News_Thursday_28_July_WEB.pdf]]<br />
<br />
POC presented talks:<br />
<br />
Pankaj Jaiswal, Oregon State University, [[Ontologies for Plant Biology - IBC 2011]]<br />
<br />
Dennis Stevenson, Genomics of Seed Plants and Ontologies.<br />
<br />
Ramona Walls, The New York Botanical Garden, [[The Plant Ontology: an updated tool for all plant biologists - IBC 2011]]. Link to PDF of presentation: [[Media:Walls_PO_presentation_IBC11.pdf]]<br />
<br />
<br />
<br />
* '''International Conference on Biomedical Ontologies''' [http://icbo.buffalo.edu IBCO 2011] July 26-30, 2011<br />
LC co-organized the session on [http://icbo.buffalo.edu/2011/WorkshopD_Program.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability"]<br />
and presented a flash talk "The Plant Ontology: Development of a Reference Ontology for all Plants"<br />
<br />
LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership (link to this?)<br />
<br />
<br />
<br />
'''*Plant Working Group Meeting of the Phenotype Ontology RCN''',Google Campus in Boulder, CO; June 1-3, 2011 <br />
<br />
All four (Plants, Arthropoda, Vertebrates and Bioinformatics) Working Group sessions ran concurrently to maximize the benefits of emerging results, group experiences and collective synergy.<br />
<br />
<br />
<br />
'''*Semantic Web Workshop''', June 6-7, 2011, Santa Fe, NM.<br />
<br />
The Plant Ontology was represented at the 2011 [http://www.iplantcollaborative.org/learn/events/2011/04/22/2011-semantic-web-workshop Semantic Web Workshop]. Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop focused on biological applications for semantic web services. JP and JE attended. <br />
<br />
<br />
'''* Presentation to Physcomitrella Collaborators''' May 2011 [[Plant Ontology Webinar- May 2011 release]]<br />
<br />
<br />
*'''Phenotype RCN Meeting Durham, NC''', February 25-27, 2011 [http://www.phenotypercn.org/?page_id=289]<br />
The Plant Ontology attended the inaugural meeting of the newly-funded [http://phenotypercn.org Phenotype Ontology RCN] at the National Evolutionary Synthesis Center in Durham, NC. <br />
<br />
<br />
<br />
<br />
===Plant and Animal Genome XIX Conference===<br />
[http://intl-pag.org/ PAG 2011], San Diego, CA. January 15-19, 2011<br />
<br />
LC, RW, JP and DWS presented a [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_887.html PO poster and a computer demo].<br />
<br />
LC took part in the [http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes workshop] and panel discussion<br />
<br />
We also hosted a [http://wiki.plantontology.org:8080/index.php/PAG_2011_Collaborators_Workshop PO Collaborators workshop] on Sunday, Jan 16th, 2011.<br />
<br />
==Year 2010==<br />
<br />
* [http://www.nettab.org/2010/ NETTAB 2010 conference on Biological Wikis], Nov 29-Dec 1, 2010, Naples, Italy<br />
Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" [[File:NETTAB 2010 poster proposal.pdf]]<br />
<br />
* Seminar, Department of Botany and Plant Pathology, Oregon State University <br />
Laurel presented a seminar: Bridging Plant Anatomy and Genomics in the Digital Era: Recent Advances at The Plant Ontology<br />
[[File:Cooper_BPP_final_(LC_10-14-10).pdf]]<br />
<br />
*Seminar, New York Botanical Garden. October 6, 2010. Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'<br />
<br />
*[http://www.aspb.org/pb-2010/ American Society of Plant Biologists], Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010<br />
Laurel Cooper and Pankaj Jaiswal attended. Laurel presented a poster:[http://abstracts.aspb.org/pb2010/public/P14/P14010.html The Plant Ontology: A Database for Plant Genomics].<br />
<br />
''Cooper, L., Elser, J., Walls, R., Stevenson, Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Database for Plant Genomics. American Society of Plant Biologists, Quebec, Montreal, Canada''<br />
<br />
<br />
We also organized a Plant Biology 2010 Outreach Booth: [[Plant Genome Resources Outreach Booth]].<br />
<br />
*PO-Gramene Annotation Workshop at Plant Biology 2010 [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop PO-Gramene Annotation Workshop]<br />
A workshop to demonstrate the Phenote Annotation Tool was held at the ASPB Plant Biology Meeting in Montreal, Quebec, Canada. <br />
<br />
You can find a link to the workshop page at: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop Phenote Workshop] <br />
<br />
*[http://www.botanyconference.org/ Botany 2010], Providence, RI. Jul. 31 - Aug. 4, 2010. Dennis Stevenson, Alejandra Gandolfo, and Ramona Walls attended.<br />
Ramona Walls gave a presentation for the Developmental and Structural Section [[Abstract-BSA2010]] [[File:Presentation-BSA2010.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Stevenson Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: a tool for structural, developmental, and molecular plant biologists. Providence, RI.''<br />
<br />
<br />
*[http://sites.google.com/site/bioontologiessig2010/ Bio-Ontologies 2010: Semantic Applications in Life Sciences] July 9th-10th, 2010<br />
Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk' <br />
<br />
[[File:PO_Poster_BioOntologies2010.pdf]]<br />
<br />
[[File:PO_FlashTalk_BioOntologies2010.pdf]]<br />
<br />
[[File:Walls_Cooper_BioOntologies29.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Dennis W. Stevenson, Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Common Reference Ontology for Plants. Boston, MA.''<br />
<br />
<br />
*[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology Workshop],Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010 <br />
Laurel Cooper and Ramona Walls attended and Laurel presented a talk [http://obofoundry.org/wiki/images/9/95/Plant_Ontology_CL_Workshop.ppt "Introduction to the Plant Ontology™"]<br />
<br />
*[http://intl-pag.org/ Plant and Animal Genome XVIII Conference], San Diego, CA. Jan. 9-13, 2010<br />
Laurel Cooper and Justin Elser [[Poster and Computer Demonstration]]<br />
<br />
''Elser, J., Cooper, L., and Jaiswal, P. (2010). Plant Ontology: Databases And Applications. San Diego, CA.''<br />
<br />
==Year 2009==<br />
* [http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=582&Itemid=283/ GCP Ontology Workshop] Rome, Italy, April 20-22, 2009<br />
** Chih-Wei Tung, Gave a talk on "Plant and Trait Ontology"<br />
<br />
* [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html/ 3rd International Biocuration Conference] Berlin, Germany, April 16-19, 2009<br />
** Chih-Wei Tung, POC poster presentation<br />
<br />
* [http://www.intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 10-14, 2009<br />
** Chih-Wei Tung, [http://www.intl-pag.org/17/abstracts/P08a_PAGXVII_807.html/ POC poster presentation]<br />
<br />
==Year 2008==<br />
* [http://bti.cornell.edu/ MetaCyc database workshop] Ithaca, Oct 21, 2008<br />
** Chih-Wei Tung, present a talk "An Introduction to the Plant Ontology Database "<br />
* [http://intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 12, 2008<br />
** Chih-Wei Tung, [http://intl-pag.org/16/abstracts/PAG16_C01_931.html POC poster presentation]<br />
<br />
==Year 2007==<br />
<br />
* [http://www.aspb.org/plantbiology/events.cfm ASPB 2007] Chicago, July 7-11, 2007<br />
** Chih-Wei Tung, [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/ASPB2007_PO_cw.ppt presentation], [http://2007.botanyconference.org/engine/search/index.php?func=detail&aid=2127 poster abstract]<br /><br />
<br />
* [http://www.gramene.org/workshop/rcn/ontology/rcn_onto-cshl07.html RCN Plant and Trait Ontology Workshop], CSHL, NY, June 10-11<br />
** Doreen Ware, Pankaj Jaiswal, Shuly Avraham, Chih-Wei Tung<br /><br />
<br />
* AGRONOMICS workshop " Ontologies, Standards and Best Practices", Gent, Belgium, May 21-23<br />
** Chih-Wei Tung, [http://www.agron-omics.eu/index.php/resource_center/workshops presentation]<br />
<br />
* [http://itmi.haifa.ac.il/06.html ITMI] Israel, April 16-20, 2007<br />
** Shuly Avraham, poster<br />
<br />
* [http://www.intl-pag.org/15/15-pag.html PAG XV] CA, January 13-17, 2007<br />
** Chih-Wei Tung, poster [http://www.intl-pag.org/pag/15/abstracts/PAG15_P08a_841.html abstract]<br />
<br />
==Year 2006==<br />
<br />
* [http://www.intl-pag.org/14/ PAG XIV] Ontology Workshop (2006): Ontologies for Databases<br />
** Anuradha Pujar: [http://www.intl-pag.org/14/abstracts/PAG14_W406.html Development of a generic plant growth stage ontology]<br />
** Katica Ilic: [http://www.intl-pag.org/14/abstracts/PAG14_P871.html Application of plant ontologies]<br />
<br />
==Year 2005==<br />
<br />
* [http://www.intl-pag.org/13/ PAG XIII] Ontology Workshop (2005): Development and Implementation of Ontologies in the Database<br />
** Leonore Reiser: [http://www.intl-pag.org/13/abstracts/PAG13_W244.html Using the Plant Ontologies]<br />
** Katica Ilic: [http://www.intl-pag.org/13/abstracts/PAG13_W242.html Controlled vocabularies for describing and cmparing phenotypes and gene expression]<br /><br />
** Pankaj: [http://www.intl-pag.org/cgi-bin/swish-bin/SwishPAGXIII.pl posters]<br />
<br />
* The 16th International Conference on Arabidopsis Research, Madison, WI, June 18, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_ki2005.ppt Katica Ilic] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_lr2005.ppt Leonore] presentations<br />
** [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_arabfnl_2005ki.ppt Poster]<br />
<br />
* The [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0010077 8th Annual Bio-Ontologies Meeting] at the [http://www.iscb.org/ismb2005/index.html ISMB], June 24, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/poc-ismb_pj2005.ppt Pankaj Jaiswal], presentation<br />
<br />
* The [http://www.maizegdb.org/maize_meeting/2005/ 47th Maize Genetic Conference], WI, March 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocpostermaizegenetics2005_mp.ppt Poster]<br />
<br />
* Frontiers in Plant Biology, MO, April 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_missouri2005ki.ppt Poster]<br />
<br />
* [http://www.ibc2005.ac.at The XVII International Botanical Congress], Vienna, Austria, July, 2005. Felipe, poster<br />
<br />
==Year 2004==<br />
<br />
* [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/annotationdemo_april2004.ppt Annotation Demo, 04/07/2004]<br />
* [http://www.botanyconference.org/ Botany 2004], Abstract #347 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_tk2004.ppt Toby.ppt]) and #351 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_fz2004.ppt Felipe.ppt])<br />
* [https://www.aspb.org/meetings/ ASPB 2004], FL, July, Abstract #864, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/aspbposter_ki23072004.ppt KI]), Workshop ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_pj2004.ppt PJ] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_lr2004.ppt LR])<br />
* [http://www.intl-pag.org/12/ PAG XII 2004], CA, January, Abstract # 927, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/pag_poster_pj2004.ppt Pankaj]), [http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html abstract]<br />
<br />
==Year 2002==<br />
<br />
* PAG X Bioinformatics: Database<br />
** Leszek Vincent: The POC and Plant ontologies ([http://www.intl-pag.org/pag/10/abstracts/PAGX_P815.html poster])<br />
** Leszek Vincent: The POC and Plant ontologies - silk purpose from a maize ear ([http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html workshop: ontology])<br />
<br />
[[Category:Documents]]<br />
[[Category:Outreach]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:Jaiswal_Lab_-_Semantic_Wiki_Presentation_-_2011.pdf&diff=13457File:Jaiswal Lab - Semantic Wiki Presentation - 2011.pdf2011-11-23T22:45:51Z<p>Preecej: Presentation of our current work on the Planteome Annotation Wiki to the IT Research and Development Dept. at Syngenta (PDF format).</p>
<hr />
<div>Presentation of our current work on the Planteome Annotation Wiki to the IT Research and Development Dept. at Syngenta (PDF format).</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Outreach_Events&diff=13456POC Outreach Events2011-11-23T22:43:50Z<p>Preecej: /* Year 2011 */</p>
<hr />
<div>==Workshops, Presentations, Posters etc==<br />
<br />
==Year 2012==<br />
<br />
[http://www.intl-pag.org/ PAG 2012]<br />
<br />
'''[[PAG 2012 Ontology workshop]]: Saturday January 14th from 10:20am-12:30pm'''<br />
<br />
[http://pag.confex.com/pag/xx/webprogrampreliminary/Session1272.html Use of Ontologies for Organizing Plant and Animal Genomics Data]<br />
<br />
==Year 2011==<br />
<br />
* '''[http://www.swat4ls.org/workshops/london2011/ Semantic Web Applications and Tools for Life Sciences Workshop]''' Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), Dec 6-9<br />
<br />
JP will present a poster entitled "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes". (link to abstract: [[Media:SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf]]). He will also participate in a "hackathon" software development session meant to spur innovation in semantic web applications.<br />
<br />
<br />
* '''[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: from Genes to Networks]''' Cold Spring Harbor Laboratory, November 30 - December 3, 2011<br />
<br />
RW will present a poster entitled "Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets". (link to abstract: [[Media:PO_abstract_PGB_CSHL2011.pdf]]<br />
<br />
<br />
* '''Departmental seminar: Facultad de Ciencis Naturales y Museo , Universidad Nacional de La Plata, Argentina''', Nov. 1, 2011<br />
MAG presented: 'El valor de las fosiles para descrifar la historia evolutiva de las angiospermas y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany Laboratory- Dr. Ari Iglesias.<br />
<br />
* '''Departmental seminar: Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Argentina''', Oct. 31, 2011<br />
MAG presented: "Paleobotanica en la era de la Biologia Molecular y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany and Palynology laboratory- Dr. Maria del Carmen Zamaloa.<br />
<br />
<br />
* '''12th Genomic Standards Consortium Meeting''' ([http://gensc.org/gc_wiki/index.php/GSC_12 GSC 12]), Max Planck Institute for Marine Microbiology, Bremen, September 28-29, 2011<br />
<br />
Barry Smith addressed Plant Ontology issues in two presentations, on “An Introduction to Ontology as a Strategy for Data Integration”, and on “The Structure of the Environment Ontology”)<br />
<br />
<br />
* '''[http://conference.cgrb.oregonstate.edu/ 2011 CGRB Fall Conference]''' Oregon State University, September 18th-19th, 2011.<br />
<br />
Two posters related to the Plant Ontology were presented.<br />
<br />
LC presented the poster: "[[Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa]]".<br />
<br />
JP presented a poster: "[[Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes]]". This explains the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service and includes an initial data set built from PO GAF (.assoc) files for ''Oryza sativa''. <br />
<br />
<br />
<br />
* '''Moss 2011 PO presentation''' (Black Forest, September 11th - 15th, 2011, done via Webex) [[Moss 2011 Meeting- PO presentation]] Sept 12, 2011<br />
<br />
<br />
* '''NSF Plant Genome Awardee meeting''' Sept, 2011. Washington, DC. Submission: [[Media:2-pager_plant_ontology-2011.pdf]]<br />
<br />
<br />
* '''ASPB Plant Biology meeting 2011,''' [http://my.aspb.org/?page=Meetings_PB2011 PB2011], Minneapolis, Minn. Aug 6th-10th, 2011<br />
<br />
PO and [http://www.gramene.org/ Gramene] hosted a [http://outreach.gramene.org/gramene-outreach/index.php/Main_Page Data Curation Workshop] <br />
<br />
LC presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster] and we took part in an [[Plant Biology 2011 Outreach Booth]]<br />
<br />
<br />
* '''International Botanical Congress''' [http://www.ibc2011.com/Default.htm (IBC2011)], July 23rd – 30th 2011<br />
Symposium hosted: [[Bio-Ontologies for the Plant Sciences]] under the Genetics, Genomics and Bioinformatics theme. <br />
<br />
Please see the [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details.<br />
<br />
Press release about the PO at IBC 2011: [[Media:IBC_2011_Congress_News_Thursday_28_July_WEB.pdf]]<br />
<br />
POC presented talks:<br />
<br />
Pankaj Jaiswal, Oregon State University, [[Ontologies for Plant Biology - IBC 2011]]<br />
<br />
Dennis Stevenson, Genomics of Seed Plants and Ontologies.<br />
<br />
Ramona Walls, The New York Botanical Garden, [[The Plant Ontology: an updated tool for all plant biologists - IBC 2011]]. Link to PDF of presentation: [[Media:Walls_PO_presentation_IBC11.pdf]]<br />
<br />
<br />
<br />
* '''International Conference on Biomedical Ontologies''' [http://icbo.buffalo.edu IBCO 2011] July 26-30, 2011<br />
LC co-organized the session on [http://icbo.buffalo.edu/2011/WorkshopD_Program.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability"]<br />
and presented a flash talk "The Plant Ontology: Development of a Reference Ontology for all Plants"<br />
<br />
LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership (link to this?)<br />
<br />
<br />
<br />
'''*Plant Working Group Meeting of the Phenotype Ontology RCN''',Google Campus in Boulder, CO; June 1-3, 2011 <br />
<br />
All four (Plants, Arthropoda, Vertebrates and Bioinformatics) Working Group sessions ran concurrently to maximize the benefits of emerging results, group experiences and collective synergy.<br />
<br />
<br />
<br />
'''*Semantic Web Workshop''', June 6-7, 2011, Santa Fe, NM.<br />
<br />
The Plant Ontology was represented at the 2011 [http://www.iplantcollaborative.org/learn/events/2011/04/22/2011-semantic-web-workshop Semantic Web Workshop]. Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop focused on biological applications for semantic web services. JP and JE attended. <br />
<br />
<br />
'''* Presentation to Physcomitrella Collaborators''' May 2011 [[Plant Ontology Webinar- May 2011 release]]<br />
<br />
<br />
*'''Phenotype RCN Meeting Durham, NC''', February 25-27, 2011 [http://www.phenotypercn.org/?page_id=289]<br />
The Plant Ontology attended the inaugural meeting of the newly-funded [http://phenotypercn.org Phenotype Ontology RCN] at the National Evolutionary Synthesis Center in Durham, NC. <br />
<br />
<br />
<br />
<br />
===Plant and Animal Genome XIX Conference===<br />
[http://intl-pag.org/ PAG 2011], San Diego, CA. January 15-19, 2011<br />
<br />
LC, RW, JP and DWS presented a [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_887.html PO poster and a computer demo].<br />
<br />
LC took part in the [http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes workshop] and panel discussion<br />
<br />
We also hosted a [http://wiki.plantontology.org:8080/index.php/PAG_2011_Collaborators_Workshop PO Collaborators workshop] on Sunday, Jan 16th, 2011.<br />
<br />
==Year 2010==<br />
<br />
* [http://www.nettab.org/2010/ NETTAB 2010 conference on Biological Wikis], Nov 29-Dec 1, 2010, Naples, Italy<br />
Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" [[File:NETTAB 2010 poster proposal.pdf]]<br />
<br />
* Seminar, Department of Botany and Plant Pathology, Oregon State University <br />
Laurel presented a seminar: Bridging Plant Anatomy and Genomics in the Digital Era: Recent Advances at The Plant Ontology<br />
[[File:Cooper_BPP_final_(LC_10-14-10).pdf]]<br />
<br />
*Seminar, New York Botanical Garden. October 6, 2010. Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'<br />
<br />
*[http://www.aspb.org/pb-2010/ American Society of Plant Biologists], Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010<br />
Laurel Cooper and Pankaj Jaiswal attended. Laurel presented a poster:[http://abstracts.aspb.org/pb2010/public/P14/P14010.html The Plant Ontology: A Database for Plant Genomics].<br />
<br />
''Cooper, L., Elser, J., Walls, R., Stevenson, Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Database for Plant Genomics. American Society of Plant Biologists, Quebec, Montreal, Canada''<br />
<br />
<br />
We also organized a Plant Biology 2010 Outreach Booth: [[Plant Genome Resources Outreach Booth]].<br />
<br />
*PO-Gramene Annotation Workshop at Plant Biology 2010 [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop PO-Gramene Annotation Workshop]<br />
A workshop to demonstrate the Phenote Annotation Tool was held at the ASPB Plant Biology Meeting in Montreal, Quebec, Canada. <br />
<br />
You can find a link to the workshop page at: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop Phenote Workshop] <br />
<br />
*[http://www.botanyconference.org/ Botany 2010], Providence, RI. Jul. 31 - Aug. 4, 2010. Dennis Stevenson, Alejandra Gandolfo, and Ramona Walls attended.<br />
Ramona Walls gave a presentation for the Developmental and Structural Section [[Abstract-BSA2010]] [[File:Presentation-BSA2010.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Stevenson Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: a tool for structural, developmental, and molecular plant biologists. Providence, RI.''<br />
<br />
<br />
*[http://sites.google.com/site/bioontologiessig2010/ Bio-Ontologies 2010: Semantic Applications in Life Sciences] July 9th-10th, 2010<br />
Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk' <br />
<br />
[[File:PO_Poster_BioOntologies2010.pdf]]<br />
<br />
[[File:PO_FlashTalk_BioOntologies2010.pdf]]<br />
<br />
[[File:Walls_Cooper_BioOntologies29.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Dennis W. Stevenson, Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Common Reference Ontology for Plants. Boston, MA.''<br />
<br />
<br />
*[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology Workshop],Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010 <br />
Laurel Cooper and Ramona Walls attended and Laurel presented a talk [http://obofoundry.org/wiki/images/9/95/Plant_Ontology_CL_Workshop.ppt "Introduction to the Plant Ontology™"]<br />
<br />
*[http://intl-pag.org/ Plant and Animal Genome XVIII Conference], San Diego, CA. Jan. 9-13, 2010<br />
Laurel Cooper and Justin Elser [[Poster and Computer Demonstration]]<br />
<br />
''Elser, J., Cooper, L., and Jaiswal, P. (2010). Plant Ontology: Databases And Applications. San Diego, CA.''<br />
<br />
==Year 2009==<br />
* [http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=582&Itemid=283/ GCP Ontology Workshop] Rome, Italy, April 20-22, 2009<br />
** Chih-Wei Tung, Gave a talk on "Plant and Trait Ontology"<br />
<br />
* [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html/ 3rd International Biocuration Conference] Berlin, Germany, April 16-19, 2009<br />
** Chih-Wei Tung, POC poster presentation<br />
<br />
* [http://www.intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 10-14, 2009<br />
** Chih-Wei Tung, [http://www.intl-pag.org/17/abstracts/P08a_PAGXVII_807.html/ POC poster presentation]<br />
<br />
==Year 2008==<br />
* [http://bti.cornell.edu/ MetaCyc database workshop] Ithaca, Oct 21, 2008<br />
** Chih-Wei Tung, present a talk "An Introduction to the Plant Ontology Database "<br />
* [http://intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 12, 2008<br />
** Chih-Wei Tung, [http://intl-pag.org/16/abstracts/PAG16_C01_931.html POC poster presentation]<br />
<br />
==Year 2007==<br />
<br />
* [http://www.aspb.org/plantbiology/events.cfm ASPB 2007] Chicago, July 7-11, 2007<br />
** Chih-Wei Tung, [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/ASPB2007_PO_cw.ppt presentation], [http://2007.botanyconference.org/engine/search/index.php?func=detail&aid=2127 poster abstract]<br /><br />
<br />
* [http://www.gramene.org/workshop/rcn/ontology/rcn_onto-cshl07.html RCN Plant and Trait Ontology Workshop], CSHL, NY, June 10-11<br />
** Doreen Ware, Pankaj Jaiswal, Shuly Avraham, Chih-Wei Tung<br /><br />
<br />
* AGRONOMICS workshop " Ontologies, Standards and Best Practices", Gent, Belgium, May 21-23<br />
** Chih-Wei Tung, [http://www.agron-omics.eu/index.php/resource_center/workshops presentation]<br />
<br />
* [http://itmi.haifa.ac.il/06.html ITMI] Israel, April 16-20, 2007<br />
** Shuly Avraham, poster<br />
<br />
* [http://www.intl-pag.org/15/15-pag.html PAG XV] CA, January 13-17, 2007<br />
** Chih-Wei Tung, poster [http://www.intl-pag.org/pag/15/abstracts/PAG15_P08a_841.html abstract]<br />
<br />
==Year 2006==<br />
<br />
* [http://www.intl-pag.org/14/ PAG XIV] Ontology Workshop (2006): Ontologies for Databases<br />
** Anuradha Pujar: [http://www.intl-pag.org/14/abstracts/PAG14_W406.html Development of a generic plant growth stage ontology]<br />
** Katica Ilic: [http://www.intl-pag.org/14/abstracts/PAG14_P871.html Application of plant ontologies]<br />
<br />
==Year 2005==<br />
<br />
* [http://www.intl-pag.org/13/ PAG XIII] Ontology Workshop (2005): Development and Implementation of Ontologies in the Database<br />
** Leonore Reiser: [http://www.intl-pag.org/13/abstracts/PAG13_W244.html Using the Plant Ontologies]<br />
** Katica Ilic: [http://www.intl-pag.org/13/abstracts/PAG13_W242.html Controlled vocabularies for describing and cmparing phenotypes and gene expression]<br /><br />
** Pankaj: [http://www.intl-pag.org/cgi-bin/swish-bin/SwishPAGXIII.pl posters]<br />
<br />
* The 16th International Conference on Arabidopsis Research, Madison, WI, June 18, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_ki2005.ppt Katica Ilic] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_lr2005.ppt Leonore] presentations<br />
** [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_arabfnl_2005ki.ppt Poster]<br />
<br />
* The [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0010077 8th Annual Bio-Ontologies Meeting] at the [http://www.iscb.org/ismb2005/index.html ISMB], June 24, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/poc-ismb_pj2005.ppt Pankaj Jaiswal], presentation<br />
<br />
* The [http://www.maizegdb.org/maize_meeting/2005/ 47th Maize Genetic Conference], WI, March 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocpostermaizegenetics2005_mp.ppt Poster]<br />
<br />
* Frontiers in Plant Biology, MO, April 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_missouri2005ki.ppt Poster]<br />
<br />
* [http://www.ibc2005.ac.at The XVII International Botanical Congress], Vienna, Austria, July, 2005. Felipe, poster<br />
<br />
==Year 2004==<br />
<br />
* [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/annotationdemo_april2004.ppt Annotation Demo, 04/07/2004]<br />
* [http://www.botanyconference.org/ Botany 2004], Abstract #347 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_tk2004.ppt Toby.ppt]) and #351 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_fz2004.ppt Felipe.ppt])<br />
* [https://www.aspb.org/meetings/ ASPB 2004], FL, July, Abstract #864, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/aspbposter_ki23072004.ppt KI]), Workshop ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_pj2004.ppt PJ] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_lr2004.ppt LR])<br />
* [http://www.intl-pag.org/12/ PAG XII 2004], CA, January, Abstract # 927, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/pag_poster_pj2004.ppt Pankaj]), [http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html abstract]<br />
<br />
==Year 2002==<br />
<br />
* PAG X Bioinformatics: Database<br />
** Leszek Vincent: The POC and Plant ontologies ([http://www.intl-pag.org/pag/10/abstracts/PAGX_P815.html poster])<br />
** Leszek Vincent: The POC and Plant ontologies - silk purpose from a maize ear ([http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html workshop: ontology])<br />
<br />
[[Category:Documents]]<br />
[[Category:Outreach]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Outreach_Events&diff=13455POC Outreach Events2011-11-23T22:35:50Z<p>Preecej: /* Year 2011 */</p>
<hr />
<div>==Workshops, Presentations, Posters etc==<br />
<br />
==Year 2012==<br />
<br />
[http://www.intl-pag.org/ PAG 2012]<br />
<br />
'''[[PAG 2012 Ontology workshop]]: Saturday January 14th from 10:20am-12:30pm'''<br />
<br />
[http://pag.confex.com/pag/xx/webprogrampreliminary/Session1272.html Use of Ontologies for Organizing Plant and Animal Genomics Data]<br />
<br />
==Year 2011==<br />
<br />
* '''[http://www.swat4ls.org/workshops/london2011/ Semantic Web Applications and Tools for Life Sciences Workshop]''' Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), Dec 6-9<br />
<br />
JP will present a poster entitled "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes". (link to abstract: [[Media:SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf]]). He will also participate in a "hackathon" software development session meant to spur innovation in semantic web applications.<br />
<br />
* '''[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: from Genes to Networks]''' Cold Spring Harbor Laboratory, November 30 - December 3, 2011<br />
<br />
RW will present a poster entitled "Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets". (link to abstract: [[Media:PO_abstract_PGB_CSHL2011.pdf]]<br />
<br />
<br />
* '''Departmental seminar: Facultad de Ciencis Naturales y Museo , Universidad Nacional de La Plata, Argentina''', Nov. 1, 2011<br />
MAG presented: 'El valor de las fosiles para descrifar la historia evolutiva de las angiospermas y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany Laboratory- Dr. Ari Iglesias.<br />
<br />
* '''Departmental seminar: Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Argentina''', Oct. 31, 2011<br />
MAG presented: "Paleobotanica en la era de la Biologia Molecular y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany and Palynology laboratory- Dr. Maria del Carmen Zamaloa.<br />
<br />
<br />
* '''12th Genomic Standards Consortium Meeting''' ([http://gensc.org/gc_wiki/index.php/GSC_12 GSC 12]), Max Planck Institute for Marine Microbiology, Bremen, September 28-29, 2011<br />
<br />
Barry Smith addressed Plant Ontology issues in two presentations, on “An Introduction to Ontology as a Strategy for Data Integration”, and on “The Structure of the Environment Ontology”)<br />
<br />
<br />
* '''[http://conference.cgrb.oregonstate.edu/ 2011 CGRB Fall Conference]''' Oregon State University, September 18th-19th, 2011.<br />
<br />
Two posters related to the Plant Ontology were presented.<br />
<br />
LC presented the poster: "[[Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa]]".<br />
<br />
JP presented a poster: "[[Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes]]". This explains the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service and includes an initial data set built from PO GAF (.assoc) files for ''Oryza sativa''. <br />
<br />
<br />
<br />
* '''Moss 2011 PO presentation''' (Black Forest, September 11th - 15th, 2011, done via Webex) [[Moss 2011 Meeting- PO presentation]] Sept 12, 2011<br />
<br />
<br />
* '''NSF Plant Genome Awardee meeting''' Sept, 2011. Washington, DC. Submission: [[Media:2-pager_plant_ontology-2011.pdf]]<br />
<br />
<br />
* '''ASPB Plant Biology meeting 2011,''' [http://my.aspb.org/?page=Meetings_PB2011 PB2011], Minneapolis, Minn. Aug 6th-10th, 2011<br />
<br />
PO and [http://www.gramene.org/ Gramene] hosted a [http://outreach.gramene.org/gramene-outreach/index.php/Main_Page Data Curation Workshop] <br />
<br />
LC presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster] and we took part in an [[Plant Biology 2011 Outreach Booth]]<br />
<br />
<br />
* '''International Botanical Congress''' [http://www.ibc2011.com/Default.htm (IBC2011)], July 23rd – 30th 2011<br />
Symposium hosted: [[Bio-Ontologies for the Plant Sciences]] under the Genetics, Genomics and Bioinformatics theme. <br />
<br />
Please see the [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details.<br />
<br />
Press release about the PO at IBC 2011: [[Media:IBC_2011_Congress_News_Thursday_28_July_WEB.pdf]]<br />
<br />
POC presented talks:<br />
<br />
Pankaj Jaiswal, Oregon State University, [[Ontologies for Plant Biology - IBC 2011]]<br />
<br />
Dennis Stevenson, Genomics of Seed Plants and Ontologies.<br />
<br />
Ramona Walls, The New York Botanical Garden, [[The Plant Ontology: an updated tool for all plant biologists - IBC 2011]]. Link to PDF of presentation: [[Media:Walls_PO_presentation_IBC11.pdf]]<br />
<br />
<br />
<br />
* '''International Conference on Biomedical Ontologies''' [http://icbo.buffalo.edu IBCO 2011] July 26-30, 2011<br />
LC co-organized the session on [http://icbo.buffalo.edu/2011/WorkshopD_Program.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability"]<br />
and presented a flash talk "The Plant Ontology: Development of a Reference Ontology for all Plants"<br />
<br />
LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership (link to this?)<br />
<br />
<br />
<br />
'''*Plant Working Group Meeting of the Phenotype Ontology RCN''',Google Campus in Boulder, CO; June 1-3, 2011 <br />
<br />
All four (Plants, Arthropoda, Vertebrates and Bioinformatics) Working Group sessions ran concurrently to maximize the benefits of emerging results, group experiences and collective synergy.<br />
<br />
<br />
<br />
'''*Semantic Web Workshop''', June 6-7, 2011, Santa Fe, NM.<br />
<br />
The Plant Ontology was represented at the 2011 [http://www.iplantcollaborative.org/learn/events/2011/04/22/2011-semantic-web-workshop Semantic Web Workshop]. Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop focused on biological applications for semantic web services. JP and JE attended. <br />
<br />
<br />
'''* Presentation to Physcomitrella Collaborators''' May 2011 [[Plant Ontology Webinar- May 2011 release]]<br />
<br />
<br />
*'''Phenotype RCN Meeting Durham, NC''', February 25-27, 2011 [http://www.phenotypercn.org/?page_id=289]<br />
The Plant Ontology attended the inaugural meeting of the newly-funded [http://phenotypercn.org Phenotype Ontology RCN] at the National Evolutionary Synthesis Center in Durham, NC. <br />
<br />
<br />
<br />
<br />
===Plant and Animal Genome XIX Conference===<br />
[http://intl-pag.org/ PAG 2011], San Diego, CA. January 15-19, 2011<br />
<br />
LC, RW, JP and DWS presented a [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_887.html PO poster and a computer demo].<br />
<br />
LC took part in the [http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes workshop] and panel discussion<br />
<br />
We also hosted a [http://wiki.plantontology.org:8080/index.php/PAG_2011_Collaborators_Workshop PO Collaborators workshop] on Sunday, Jan 16th, 2011.<br />
<br />
==Year 2010==<br />
<br />
* [http://www.nettab.org/2010/ NETTAB 2010 conference on Biological Wikis], Nov 29-Dec 1, 2010, Naples, Italy<br />
Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" [[File:NETTAB 2010 poster proposal.pdf]]<br />
<br />
* Seminar, Department of Botany and Plant Pathology, Oregon State University <br />
Laurel presented a seminar: Bridging Plant Anatomy and Genomics in the Digital Era: Recent Advances at The Plant Ontology<br />
[[File:Cooper_BPP_final_(LC_10-14-10).pdf]]<br />
<br />
*Seminar, New York Botanical Garden. October 6, 2010. Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'<br />
<br />
*[http://www.aspb.org/pb-2010/ American Society of Plant Biologists], Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010<br />
Laurel Cooper and Pankaj Jaiswal attended. Laurel presented a poster:[http://abstracts.aspb.org/pb2010/public/P14/P14010.html The Plant Ontology: A Database for Plant Genomics].<br />
<br />
''Cooper, L., Elser, J., Walls, R., Stevenson, Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Database for Plant Genomics. American Society of Plant Biologists, Quebec, Montreal, Canada''<br />
<br />
<br />
We also organized a Plant Biology 2010 Outreach Booth: [[Plant Genome Resources Outreach Booth]].<br />
<br />
*PO-Gramene Annotation Workshop at Plant Biology 2010 [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop PO-Gramene Annotation Workshop]<br />
A workshop to demonstrate the Phenote Annotation Tool was held at the ASPB Plant Biology Meeting in Montreal, Quebec, Canada. <br />
<br />
You can find a link to the workshop page at: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop Phenote Workshop] <br />
<br />
*[http://www.botanyconference.org/ Botany 2010], Providence, RI. Jul. 31 - Aug. 4, 2010. Dennis Stevenson, Alejandra Gandolfo, and Ramona Walls attended.<br />
Ramona Walls gave a presentation for the Developmental and Structural Section [[Abstract-BSA2010]] [[File:Presentation-BSA2010.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Stevenson Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: a tool for structural, developmental, and molecular plant biologists. Providence, RI.''<br />
<br />
<br />
*[http://sites.google.com/site/bioontologiessig2010/ Bio-Ontologies 2010: Semantic Applications in Life Sciences] July 9th-10th, 2010<br />
Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk' <br />
<br />
[[File:PO_Poster_BioOntologies2010.pdf]]<br />
<br />
[[File:PO_FlashTalk_BioOntologies2010.pdf]]<br />
<br />
[[File:Walls_Cooper_BioOntologies29.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Dennis W. Stevenson, Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Common Reference Ontology for Plants. Boston, MA.''<br />
<br />
<br />
*[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology Workshop],Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010 <br />
Laurel Cooper and Ramona Walls attended and Laurel presented a talk [http://obofoundry.org/wiki/images/9/95/Plant_Ontology_CL_Workshop.ppt "Introduction to the Plant Ontology™"]<br />
<br />
*[http://intl-pag.org/ Plant and Animal Genome XVIII Conference], San Diego, CA. Jan. 9-13, 2010<br />
Laurel Cooper and Justin Elser [[Poster and Computer Demonstration]]<br />
<br />
''Elser, J., Cooper, L., and Jaiswal, P. (2010). Plant Ontology: Databases And Applications. San Diego, CA.''<br />
<br />
==Year 2009==<br />
* [http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=582&Itemid=283/ GCP Ontology Workshop] Rome, Italy, April 20-22, 2009<br />
** Chih-Wei Tung, Gave a talk on "Plant and Trait Ontology"<br />
<br />
* [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html/ 3rd International Biocuration Conference] Berlin, Germany, April 16-19, 2009<br />
** Chih-Wei Tung, POC poster presentation<br />
<br />
* [http://www.intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 10-14, 2009<br />
** Chih-Wei Tung, [http://www.intl-pag.org/17/abstracts/P08a_PAGXVII_807.html/ POC poster presentation]<br />
<br />
==Year 2008==<br />
* [http://bti.cornell.edu/ MetaCyc database workshop] Ithaca, Oct 21, 2008<br />
** Chih-Wei Tung, present a talk "An Introduction to the Plant Ontology Database "<br />
* [http://intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 12, 2008<br />
** Chih-Wei Tung, [http://intl-pag.org/16/abstracts/PAG16_C01_931.html POC poster presentation]<br />
<br />
==Year 2007==<br />
<br />
* [http://www.aspb.org/plantbiology/events.cfm ASPB 2007] Chicago, July 7-11, 2007<br />
** Chih-Wei Tung, [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/ASPB2007_PO_cw.ppt presentation], [http://2007.botanyconference.org/engine/search/index.php?func=detail&aid=2127 poster abstract]<br /><br />
<br />
* [http://www.gramene.org/workshop/rcn/ontology/rcn_onto-cshl07.html RCN Plant and Trait Ontology Workshop], CSHL, NY, June 10-11<br />
** Doreen Ware, Pankaj Jaiswal, Shuly Avraham, Chih-Wei Tung<br /><br />
<br />
* AGRONOMICS workshop " Ontologies, Standards and Best Practices", Gent, Belgium, May 21-23<br />
** Chih-Wei Tung, [http://www.agron-omics.eu/index.php/resource_center/workshops presentation]<br />
<br />
* [http://itmi.haifa.ac.il/06.html ITMI] Israel, April 16-20, 2007<br />
** Shuly Avraham, poster<br />
<br />
* [http://www.intl-pag.org/15/15-pag.html PAG XV] CA, January 13-17, 2007<br />
** Chih-Wei Tung, poster [http://www.intl-pag.org/pag/15/abstracts/PAG15_P08a_841.html abstract]<br />
<br />
==Year 2006==<br />
<br />
* [http://www.intl-pag.org/14/ PAG XIV] Ontology Workshop (2006): Ontologies for Databases<br />
** Anuradha Pujar: [http://www.intl-pag.org/14/abstracts/PAG14_W406.html Development of a generic plant growth stage ontology]<br />
** Katica Ilic: [http://www.intl-pag.org/14/abstracts/PAG14_P871.html Application of plant ontologies]<br />
<br />
==Year 2005==<br />
<br />
* [http://www.intl-pag.org/13/ PAG XIII] Ontology Workshop (2005): Development and Implementation of Ontologies in the Database<br />
** Leonore Reiser: [http://www.intl-pag.org/13/abstracts/PAG13_W244.html Using the Plant Ontologies]<br />
** Katica Ilic: [http://www.intl-pag.org/13/abstracts/PAG13_W242.html Controlled vocabularies for describing and cmparing phenotypes and gene expression]<br /><br />
** Pankaj: [http://www.intl-pag.org/cgi-bin/swish-bin/SwishPAGXIII.pl posters]<br />
<br />
* The 16th International Conference on Arabidopsis Research, Madison, WI, June 18, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_ki2005.ppt Katica Ilic] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_lr2005.ppt Leonore] presentations<br />
** [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_arabfnl_2005ki.ppt Poster]<br />
<br />
* The [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0010077 8th Annual Bio-Ontologies Meeting] at the [http://www.iscb.org/ismb2005/index.html ISMB], June 24, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/poc-ismb_pj2005.ppt Pankaj Jaiswal], presentation<br />
<br />
* The [http://www.maizegdb.org/maize_meeting/2005/ 47th Maize Genetic Conference], WI, March 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocpostermaizegenetics2005_mp.ppt Poster]<br />
<br />
* Frontiers in Plant Biology, MO, April 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_missouri2005ki.ppt Poster]<br />
<br />
* [http://www.ibc2005.ac.at The XVII International Botanical Congress], Vienna, Austria, July, 2005. Felipe, poster<br />
<br />
==Year 2004==<br />
<br />
* [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/annotationdemo_april2004.ppt Annotation Demo, 04/07/2004]<br />
* [http://www.botanyconference.org/ Botany 2004], Abstract #347 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_tk2004.ppt Toby.ppt]) and #351 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_fz2004.ppt Felipe.ppt])<br />
* [https://www.aspb.org/meetings/ ASPB 2004], FL, July, Abstract #864, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/aspbposter_ki23072004.ppt KI]), Workshop ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_pj2004.ppt PJ] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_lr2004.ppt LR])<br />
* [http://www.intl-pag.org/12/ PAG XII 2004], CA, January, Abstract # 927, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/pag_poster_pj2004.ppt Pankaj]), [http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html abstract]<br />
<br />
==Year 2002==<br />
<br />
* PAG X Bioinformatics: Database<br />
** Leszek Vincent: The POC and Plant ontologies ([http://www.intl-pag.org/pag/10/abstracts/PAGX_P815.html poster])<br />
** Leszek Vincent: The POC and Plant ontologies - silk purpose from a maize ear ([http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html workshop: ontology])<br />
<br />
[[Category:Documents]]<br />
[[Category:Outreach]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=POC_Outreach_Events&diff=13454POC Outreach Events2011-11-23T22:24:39Z<p>Preecej: /* Year 2011 */</p>
<hr />
<div>==Workshops, Presentations, Posters etc==<br />
<br />
==Year 2012==<br />
<br />
[http://www.intl-pag.org/ PAG 2012]<br />
<br />
'''[[PAG 2012 Ontology workshop]]: Saturday January 14th from 10:20am-12:30pm'''<br />
<br />
[http://pag.confex.com/pag/xx/webprogrampreliminary/Session1272.html Use of Ontologies for Organizing Plant and Animal Genomics Data]<br />
<br />
==Year 2011==<br />
<br />
* '''[http://www.swat4ls.org/workshops/london2011/ <br />
<br />
* '''[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: from Genes to Networks]''' Cold Spring Harbor Laboratory, November 30 - December 3, 2011<br />
<br />
RW will present a poster entitled "Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets". (link to abstract: [[Media:PO_abstract_PGB_CSHL2011.pdf]]<br />
<br />
<br />
* '''Departmental seminar: Facultad de Ciencis Naturales y Museo , Universidad Nacional de La Plata, Argentina''', Nov. 1, 2011<br />
MAG presented: 'El valor de las fosiles para descrifar la historia evolutiva de las angiospermas y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany Laboratory- Dr. Ari Iglesias.<br />
<br />
* '''Departmental seminar: Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Argentina''', Oct. 31, 2011<br />
MAG presented: "Paleobotanica en la era de la Biologia Molecular y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany and Palynology laboratory- Dr. Maria del Carmen Zamaloa.<br />
<br />
<br />
* '''12th Genomic Standards Consortium Meeting''' ([http://gensc.org/gc_wiki/index.php/GSC_12 GSC 12]), Max Planck Institute for Marine Microbiology, Bremen, September 28-29, 2011<br />
<br />
Barry Smith addressed Plant Ontology issues in two presentations, on “An Introduction to Ontology as a Strategy for Data Integration”, and on “The Structure of the Environment Ontology”)<br />
<br />
<br />
* '''[http://conference.cgrb.oregonstate.edu/ 2011 CGRB Fall Conference]''' Oregon State University, September 18th-19th, 2011.<br />
<br />
Two posters related to the Plant Ontology were presented.<br />
<br />
LC presented the poster: "[[Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa]]".<br />
<br />
JP presented a poster: "[[Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes]]". This explains the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service and includes an initial data set built from PO GAF (.assoc) files for ''Oryza sativa''. <br />
<br />
<br />
<br />
* '''Moss 2011 PO presentation''' (Black Forest, September 11th - 15th, 2011, done via Webex) [[Moss 2011 Meeting- PO presentation]] Sept 12, 2011<br />
<br />
<br />
* '''NSF Plant Genome Awardee meeting''' Sept, 2011. Washington, DC. Submission: [[Media:2-pager_plant_ontology-2011.pdf]]<br />
<br />
<br />
* '''ASPB Plant Biology meeting 2011,''' [http://my.aspb.org/?page=Meetings_PB2011 PB2011], Minneapolis, Minn. Aug 6th-10th, 2011<br />
<br />
PO and [http://www.gramene.org/ Gramene] hosted a [http://outreach.gramene.org/gramene-outreach/index.php/Main_Page Data Curation Workshop] <br />
<br />
LC presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster] and we took part in an [[Plant Biology 2011 Outreach Booth]]<br />
<br />
<br />
* '''International Botanical Congress''' [http://www.ibc2011.com/Default.htm (IBC2011)], July 23rd – 30th 2011<br />
Symposium hosted: [[Bio-Ontologies for the Plant Sciences]] under the Genetics, Genomics and Bioinformatics theme. <br />
<br />
Please see the [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details.<br />
<br />
Press release about the PO at IBC 2011: [[Media:IBC_2011_Congress_News_Thursday_28_July_WEB.pdf]]<br />
<br />
POC presented talks:<br />
<br />
Pankaj Jaiswal, Oregon State University, [[Ontologies for Plant Biology - IBC 2011]]<br />
<br />
Dennis Stevenson, Genomics of Seed Plants and Ontologies.<br />
<br />
Ramona Walls, The New York Botanical Garden, [[The Plant Ontology: an updated tool for all plant biologists - IBC 2011]]. Link to PDF of presentation: [[Media:Walls_PO_presentation_IBC11.pdf]]<br />
<br />
<br />
<br />
* '''International Conference on Biomedical Ontologies''' [http://icbo.buffalo.edu IBCO 2011] July 26-30, 2011<br />
LC co-organized the session on [http://icbo.buffalo.edu/2011/WorkshopD_Program.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability"]<br />
and presented a flash talk "The Plant Ontology: Development of a Reference Ontology for all Plants"<br />
<br />
LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership (link to this?)<br />
<br />
<br />
<br />
'''*Plant Working Group Meeting of the Phenotype Ontology RCN''',Google Campus in Boulder, CO; June 1-3, 2011 <br />
<br />
All four (Plants, Arthropoda, Vertebrates and Bioinformatics) Working Group sessions ran concurrently to maximize the benefits of emerging results, group experiences and collective synergy.<br />
<br />
<br />
<br />
'''*Semantic Web Workshop''', June 6-7, 2011, Santa Fe, NM.<br />
<br />
The Plant Ontology was represented at the 2011 [http://www.iplantcollaborative.org/learn/events/2011/04/22/2011-semantic-web-workshop Semantic Web Workshop]. Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop focused on biological applications for semantic web services. JP and JE attended. <br />
<br />
<br />
'''* Presentation to Physcomitrella Collaborators''' May 2011 [[Plant Ontology Webinar- May 2011 release]]<br />
<br />
<br />
*'''Phenotype RCN Meeting Durham, NC''', February 25-27, 2011 [http://www.phenotypercn.org/?page_id=289]<br />
The Plant Ontology attended the inaugural meeting of the newly-funded [http://phenotypercn.org Phenotype Ontology RCN] at the National Evolutionary Synthesis Center in Durham, NC. <br />
<br />
<br />
<br />
<br />
===Plant and Animal Genome XIX Conference===<br />
[http://intl-pag.org/ PAG 2011], San Diego, CA. January 15-19, 2011<br />
<br />
LC, RW, JP and DWS presented a [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_887.html PO poster and a computer demo].<br />
<br />
LC took part in the [http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes workshop] and panel discussion<br />
<br />
We also hosted a [http://wiki.plantontology.org:8080/index.php/PAG_2011_Collaborators_Workshop PO Collaborators workshop] on Sunday, Jan 16th, 2011.<br />
<br />
==Year 2010==<br />
<br />
* [http://www.nettab.org/2010/ NETTAB 2010 conference on Biological Wikis], Nov 29-Dec 1, 2010, Naples, Italy<br />
Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" [[File:NETTAB 2010 poster proposal.pdf]]<br />
<br />
* Seminar, Department of Botany and Plant Pathology, Oregon State University <br />
Laurel presented a seminar: Bridging Plant Anatomy and Genomics in the Digital Era: Recent Advances at The Plant Ontology<br />
[[File:Cooper_BPP_final_(LC_10-14-10).pdf]]<br />
<br />
*Seminar, New York Botanical Garden. October 6, 2010. Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'<br />
<br />
*[http://www.aspb.org/pb-2010/ American Society of Plant Biologists], Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010<br />
Laurel Cooper and Pankaj Jaiswal attended. Laurel presented a poster:[http://abstracts.aspb.org/pb2010/public/P14/P14010.html The Plant Ontology: A Database for Plant Genomics].<br />
<br />
''Cooper, L., Elser, J., Walls, R., Stevenson, Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Database for Plant Genomics. American Society of Plant Biologists, Quebec, Montreal, Canada''<br />
<br />
<br />
We also organized a Plant Biology 2010 Outreach Booth: [[Plant Genome Resources Outreach Booth]].<br />
<br />
*PO-Gramene Annotation Workshop at Plant Biology 2010 [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop PO-Gramene Annotation Workshop]<br />
A workshop to demonstrate the Phenote Annotation Tool was held at the ASPB Plant Biology Meeting in Montreal, Quebec, Canada. <br />
<br />
You can find a link to the workshop page at: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop Phenote Workshop] <br />
<br />
*[http://www.botanyconference.org/ Botany 2010], Providence, RI. Jul. 31 - Aug. 4, 2010. Dennis Stevenson, Alejandra Gandolfo, and Ramona Walls attended.<br />
Ramona Walls gave a presentation for the Developmental and Structural Section [[Abstract-BSA2010]] [[File:Presentation-BSA2010.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Stevenson Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: a tool for structural, developmental, and molecular plant biologists. Providence, RI.''<br />
<br />
<br />
*[http://sites.google.com/site/bioontologiessig2010/ Bio-Ontologies 2010: Semantic Applications in Life Sciences] July 9th-10th, 2010<br />
Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk' <br />
<br />
[[File:PO_Poster_BioOntologies2010.pdf]]<br />
<br />
[[File:PO_FlashTalk_BioOntologies2010.pdf]]<br />
<br />
[[File:Walls_Cooper_BioOntologies29.pdf]]<br />
<br />
''Walls, R., Cooper, L., Elser, J., Dennis W. Stevenson, Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Common Reference Ontology for Plants. Boston, MA.''<br />
<br />
<br />
*[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology Workshop],Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010 <br />
Laurel Cooper and Ramona Walls attended and Laurel presented a talk [http://obofoundry.org/wiki/images/9/95/Plant_Ontology_CL_Workshop.ppt "Introduction to the Plant Ontology™"]<br />
<br />
*[http://intl-pag.org/ Plant and Animal Genome XVIII Conference], San Diego, CA. Jan. 9-13, 2010<br />
Laurel Cooper and Justin Elser [[Poster and Computer Demonstration]]<br />
<br />
''Elser, J., Cooper, L., and Jaiswal, P. (2010). Plant Ontology: Databases And Applications. San Diego, CA.''<br />
<br />
==Year 2009==<br />
* [http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=582&Itemid=283/ GCP Ontology Workshop] Rome, Italy, April 20-22, 2009<br />
** Chih-Wei Tung, Gave a talk on "Plant and Trait Ontology"<br />
<br />
* [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html/ 3rd International Biocuration Conference] Berlin, Germany, April 16-19, 2009<br />
** Chih-Wei Tung, POC poster presentation<br />
<br />
* [http://www.intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 10-14, 2009<br />
** Chih-Wei Tung, [http://www.intl-pag.org/17/abstracts/P08a_PAGXVII_807.html/ POC poster presentation]<br />
<br />
==Year 2008==<br />
* [http://bti.cornell.edu/ MetaCyc database workshop] Ithaca, Oct 21, 2008<br />
** Chih-Wei Tung, present a talk "An Introduction to the Plant Ontology Database "<br />
* [http://intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 12, 2008<br />
** Chih-Wei Tung, [http://intl-pag.org/16/abstracts/PAG16_C01_931.html POC poster presentation]<br />
<br />
==Year 2007==<br />
<br />
* [http://www.aspb.org/plantbiology/events.cfm ASPB 2007] Chicago, July 7-11, 2007<br />
** Chih-Wei Tung, [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/ASPB2007_PO_cw.ppt presentation], [http://2007.botanyconference.org/engine/search/index.php?func=detail&aid=2127 poster abstract]<br /><br />
<br />
* [http://www.gramene.org/workshop/rcn/ontology/rcn_onto-cshl07.html RCN Plant and Trait Ontology Workshop], CSHL, NY, June 10-11<br />
** Doreen Ware, Pankaj Jaiswal, Shuly Avraham, Chih-Wei Tung<br /><br />
<br />
* AGRONOMICS workshop " Ontologies, Standards and Best Practices", Gent, Belgium, May 21-23<br />
** Chih-Wei Tung, [http://www.agron-omics.eu/index.php/resource_center/workshops presentation]<br />
<br />
* [http://itmi.haifa.ac.il/06.html ITMI] Israel, April 16-20, 2007<br />
** Shuly Avraham, poster<br />
<br />
* [http://www.intl-pag.org/15/15-pag.html PAG XV] CA, January 13-17, 2007<br />
** Chih-Wei Tung, poster [http://www.intl-pag.org/pag/15/abstracts/PAG15_P08a_841.html abstract]<br />
<br />
==Year 2006==<br />
<br />
* [http://www.intl-pag.org/14/ PAG XIV] Ontology Workshop (2006): Ontologies for Databases<br />
** Anuradha Pujar: [http://www.intl-pag.org/14/abstracts/PAG14_W406.html Development of a generic plant growth stage ontology]<br />
** Katica Ilic: [http://www.intl-pag.org/14/abstracts/PAG14_P871.html Application of plant ontologies]<br />
<br />
==Year 2005==<br />
<br />
* [http://www.intl-pag.org/13/ PAG XIII] Ontology Workshop (2005): Development and Implementation of Ontologies in the Database<br />
** Leonore Reiser: [http://www.intl-pag.org/13/abstracts/PAG13_W244.html Using the Plant Ontologies]<br />
** Katica Ilic: [http://www.intl-pag.org/13/abstracts/PAG13_W242.html Controlled vocabularies for describing and cmparing phenotypes and gene expression]<br /><br />
** Pankaj: [http://www.intl-pag.org/cgi-bin/swish-bin/SwishPAGXIII.pl posters]<br />
<br />
* The 16th International Conference on Arabidopsis Research, Madison, WI, June 18, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_ki2005.ppt Katica Ilic] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/pocarab_lr2005.ppt Leonore] presentations<br />
** [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_arabfnl_2005ki.ppt Poster]<br />
<br />
* The [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0010077 8th Annual Bio-Ontologies Meeting] at the [http://www.iscb.org/ismb2005/index.html ISMB], June 24, 2005<br />
** [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/poc-ismb_pj2005.ppt Pankaj Jaiswal], presentation<br />
<br />
* The [http://www.maizegdb.org/maize_meeting/2005/ 47th Maize Genetic Conference], WI, March 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocpostermaizegenetics2005_mp.ppt Poster]<br />
<br />
* Frontiers in Plant Biology, MO, April 2005 [http://dev.plantontology.org/internal/docs/presentations/posters/pocposter_missouri2005ki.ppt Poster]<br />
<br />
* [http://www.ibc2005.ac.at The XVII International Botanical Congress], Vienna, Austria, July, 2005. Felipe, poster<br />
<br />
==Year 2004==<br />
<br />
* [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/annotationdemo_april2004.ppt Annotation Demo, 04/07/2004]<br />
* [http://www.botanyconference.org/ Botany 2004], Abstract #347 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_tk2004.ppt Toby.ppt]) and #351 ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/botpoc_fz2004.ppt Felipe.ppt])<br />
* [https://www.aspb.org/meetings/ ASPB 2004], FL, July, Abstract #864, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/aspbposter_ki23072004.ppt KI]), Workshop ([http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_pj2004.ppt PJ] and [http://dev.plantontology.org/internal/docs/presentations/pocpresentations/aspbpoc_lr2004.ppt LR])<br />
* [http://www.intl-pag.org/12/ PAG XII 2004], CA, January, Abstract # 927, Poster ([http://dev.plantontology.org/internal/docs/presentations/posters/pag_poster_pj2004.ppt Pankaj]), [http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html abstract]<br />
<br />
==Year 2002==<br />
<br />
* PAG X Bioinformatics: Database<br />
** Leszek Vincent: The POC and Plant ontologies ([http://www.intl-pag.org/pag/10/abstracts/PAGX_P815.html poster])<br />
** Leszek Vincent: The POC and Plant ontologies - silk purpose from a maize ear ([http://www.intl-pag.org/pag/10/abstracts/PAGX_W79.html workshop: ontology])<br />
<br />
[[Category:Documents]]<br />
[[Category:Outreach]]</div>Preecejhttps://wiki.plantontology.org/index.php?title=File:SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf&diff=13453File:SWAT4LS 2011 Proceedings-Planteome Annotation Wiki.pdf2011-11-23T22:23:06Z<p>Preecej: Proceedings for the Semantic Web Application and Tools for Life Sciences Workshop 2011: Planteome Annotation Wiki</p>
<hr />
<div>Proceedings for the Semantic Web Application and Tools for Life Sciences Workshop 2011: Planteome Annotation Wiki</div>Preecejhttps://wiki.plantontology.org/index.php?title=Main_Page&diff=12069Main Page2011-10-06T21:13:38Z<p>Preecej: /* Plant Ontology Development Guidelines */</p>
<hr />
<div><big>'''Welcome to the Plant Ontology Wiki'''</big><br />
<br />
<br />
== Plant Ontology Consortium Resources == <br />
* [http://www.plantontology.org Plant Ontology Home]<br />
* [http://plantontology.org/amigo/go.cgi Search or browse the Plant Ontology]<br />
* [http://plantontology.org/docs/release_notes/index.html Release notes] the most recent information on the database and website changes.<br />
* [http://plantontology.org/download/download.html Downloads]<br />
<br />
== About the Plant Ontology project == <br />
* [[ PO_Project_Overview|Overview of the PO project ]]<br />
* [[ POC_Charter|POC charter]] Describes the Consortium's responsibilities and how can you participate in its activities.<br />
* [[Citing POC]] How to cite POC in your article<br />
* [[File:PO_brochure_final_(LC_7-21-11).pdf]]<br />
<br />
==PO Updates==<br />
<br />
October 2010 release: [[2010 Release Page]]<br />
<br />
[[Jan 2011 Release Page]]<br />
<br />
[[May 2011 Release Page]]<br />
<br />
[[October 2011 Release Page]]<br />
<br />
== POC Meetings ==<br />
=== POC weekly meetings ===<br />
[[POC_Meetings_Minutes|Minutes of the Plant Ontology Consortium meetings ]]<br />
<br />
=== POC workshops and other meetings ===<br />
[[POC_Meeting and Workshop June 29th and 30th, 2010 Corvallis, OR]]<br />
<br />
[[POC Meeting and Workshop Nov 4th to 6th, 2010; NYBG, Bronx, NY]]<br />
<br />
[[POC Meeting at NYBG; Sept 10th-11th, 2011]]<br />
<br />
<br />
[[POC Technical Issues Page]]<br />
<br />
== POC Collaborators == <br />
[[Angiosperm Phylogeny Web Glossary]]<br />
<br />
[[Cell Ontology]]<br />
<br />
[[Cosmoss-_Physcomitrella]]<br />
<br />
[[CRIBI- Grape Genomics]]<br />
<br />
[[Cycad Pages]]<br />
<br />
European Arabidopsis Stock Centre [[NASC]]<br />
<br />
[[Flora of North America- FNA]]<br />
<br />
[[Gene Ontology]]<br />
<br />
[[Gramene]]<br />
<br />
[[GCP Crop Ontology]]<br />
<br />
[[Live Plant Image Group]]<br />
<br />
[[MaizeGDB]]<br />
<br />
[[MorphoBank]]<br />
<br />
[[OBO Foundry]]<br />
<br />
[[Ontology for Biomedical Investigations]]<br />
<br />
[[Oryzabase]]<br />
<br />
[[PlantSystematics.org]]<br />
<br />
[[PLEXdb]]<br />
<br />
[[SoyBase]]<br />
<br />
[[SSWAP]]<br />
<br />
[[TraitNet]]<br />
<br />
'''* New *'''<br />
<br />
[[Wheat Gene Catalog]]<br />
<br />
[[JSTOR Herbarium Annotations]]<br />
<br />
Potential new collaborator: [[eMonocot]]<br />
<br />
[[List of user group contacts]]<br />
<br />
'''[[Links to sites using the PO]]'''<br />
<br />
== Outreach ==<br />
* [[POC_Outreach_Events|POC outreach activities and presentations]] by year<br />
<br />
* [[Plant Ontology Tutorials]]<br />
* [http://plantontology.org/docs/presentations/demo/poc-demo-1.html Introduction to the project] (slide show)<br />
<br />
== Publications and Other Resources==<br />
<br />
* [[Related Publications]] References and citations of interest on ontology, published by the PO consortium and collaborators.<br />
<br />
* [[Plant Ontology Citations]] Publications from outside the consortium that discuss the PO or use it in their analyses. <br />
<br />
If you are aware of a publication that is not on this list, please send us the citation and we will add it.<br />
<br />
* [[Ontology Resources]] Links to other projects working on ontologies<br />
<br />
== Plant Ontology Development Guidelines ==<br />
''' Developers style guide '''<br />
* [[PO_Developers_Guide]]<br />
'''Descriptions of relations in the PO'''<br />
*[[Relations in the Plant Ontology]]<br />
*[http://www.obofoundry.org/ro/ OBO relation ontology]<br />
*[http://wiki.geneontology.org/index.php/Reasoner_Overview Reasoner Overview]<br />
<br />
'''Principles, Rationales and Key Organizing Rules of the PO'''<br />
<br />
''The first three pages listed below are not up to date.''<br />
* [[Plant_Structure_Principles_Rules|Plant Structure Ontology]] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure. <br />
* [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked questions]]<br />
* [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]]<br />
<br />
* Protocols page for Plant Ontology Releases: [[PO Release SOP Page]]<br />
<br />
''' Ontology accessions '''<br />
* [[Accession_IDS_Guide|Guide to unique accessions/ids associated to each PO term]]<br />
<br />
''' DBXrefs '''<br />
* [http://plantontology.org/docs/dbxref/PO_DBXref.txt Database cross reference abbreviations used in the ontology files and the database] <br />
* [http://palea.cgrb.oregonstate.edu/viewsvn/plantontology/html/docs/dbxref/PO_DBXref.txt?view=markup Database cross reference file on the SVN- current]<br />
* Custom references maintained by PO, for items without a url. See [[PO references]]<br />
<br />
'''Adding "Associated to" links to GO (final table column in the association view):'''<br />
* The "GO" links in the right-hand column of the association view page popup a window on geneontology.org pointing to the GO entry for each association (generally via their unique gene id). These links are exclusively generated by db entries in the dbxref table. To create GO links in the "Associated to" column for any particular association, look up that association's individual dbxref entry and set cols '''exist_in_go''' = 1 and '''go_id''' = (the value of the xref_key).<br />
* This data is not loaded manually, however. There are perl and shell scripts (written by Shuly) in /data/www/plantontology/*_amigo/database/'''link2go''' for the purpose of downloading GO associations from DB2GO, creating a mapped list of GO and PO associations, and populating this data into the dbxref tbl as described above. We just have to add the appropriate data source entries in the shell scripts once the folks at GO have verified that they have associations for the data in question.<br />
<br />
''' Formats for the Ontology and Annotation Files '''<br />
* [http://www.geneontology.org/GO.format.obo-1_2.shtml Ontology file format]<br />
* If your database/project would like to submit annotations to the PO database, please consult the suggested file format: [[Annotation Association File Format]]<br />
* For more information about how to use column 16: [[PO_Annotation_Extensions_(column_16)#Specific_suggestions_for_column_16]]<br />
* See also [https://docs.google.com/spreadsheet/ccc?key=0AhrY0qRdO4budHRqaklJcmJxRjlaVnV6UGlyd0xWbHc&hl=en_US Google docs spread sheet] with specific suggestions of what terms and relations to put in column 16.<br />
<br />
== Other ==<br />
[[Calendar]] (POC outreach schedule)<br />
<br />
== Wiki meta links ==<br />
* [http://meta.wikimedia.org/wiki/Help:Contents User's Guide]<br />
* [http://www.mediawiki.org/wiki/Help:Formatting Wiki syntax]<br />
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</div>Preecej