POC Conf. Call 10-20-10

POC meeting, Webex Conference Call; Date: Oct 20th, 2010 10am (PDT)

In attendance:

POC members:Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Alejandra Gandolfo, (Cornell University), Justin Elser (OSU), Justin Preece (OSU), Barry Smith (University at Buffalo, NY)

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: None

Acceptance of the minutes from the 10-13-10 meeting? There were no additions, deletions or changes to the minutes of the last meeting.

Adding links to more images through PlantSystematics.org

• Goal is to add links between PO terms and images on PlantSystematics.org.

With current technology, we can add html links to specific pages on PlantSystematics.org. If we register PlantSystematics.org with the GO database directory, we could make those links automatic in Amigo (need to talk with Chris about this). Send a message about this request to the GoHelpdesk

PlantSystematics can set up a sister node for Plant Ontology on their home page. This would create a separate browser/search page using PO terms and IDs. Ideally, we would integrate the PO ontology structure so that if someone searched for images for a parent term, all of the images associated with descendant terms would also show up. This search engine would locate terms that are uploaded by PO (Ale's image collection) as well as images in the main PlantSystematics database.

We could set it up so that the search results page also has a link to the corresponding term page on PO's Amigo browser, and maybe even includes some data from the PO on the search results (e.g. definition, parent term)

Better to have PO terms attached to the images and just have an additional drop down box for direct searches. Create mappings from the keywords to PO terms, add additional PO terms if necessary.

Ale will take care of uploading the images and making sure that their labels correspond to PO terms. Will need help from PJ's lab in setting up the PO node and using HTML labels to create links to specific areas of images. Once the format and overall guidelines are decided on, they we can decide what kind of bioinformatic help is needed and how much. We will set up a separate meeting to workout these details

Image files are in series -- from lowest magnification to the highest. It would be good if we could set up the browser to allow users to scroll through multiple images of the same slide, so they wouldn't have to return to the search results each time.

Pankaj asked Alejandra and Ramona to prepare ~5 sample pages which would show the images and what other information that would be on the page, as well as a list of the type of queries a biologist might want to make. Lol has created a spot PlantSystematics.org on our collaborators page for these to be put.

Ramona and Ale met with Kevin Nixon (who created and maintains PlantSystematics.org) after the conference call. He is willing to integrate PO IDs into PS.org database, so that when people are submitting images, they will get a hierarchical pull down list of PO terms to associate with their photos. Anyone can submit images, but they have to register first. Ramona sent him the current plant_ontology.obo flat file, and he will use this to create a series of tables that have the terms and their is_a and part_of hierarchies, so that recursive searches can be done in both directions (down the tree and up the tree). He was open to the idea of having html tags associated with the images to point to specific structures on parts of the image, but we will have to figure out the best way to implement this ?Will this actually be any less work than having Ale make labeled images with arrows?

PS.org is set up so that users submit their search criteria, then this generates an SQL query, rather than having the queries generated directly. This prevents people from messing with the database. We can use Boolean operators for our queries, even though they aren't currently used on PS.org

Ramona and Ale are working on templates pages to show what the search interface and search results pages should look like. Will post them on the collaborators page when they are ready.

PO slims

GO includes reduced versions of their ontologies (Go slims) for some user groups. The slims are developed and maintained by the users, but publicly accessible as part of the GO flat file. We have one user group (TraitNet) that is interested in creating a PO slim. This is basically done by creating a subset, which can then be extracted to make a smaller file.

The problem with users creating and maintaining subsets, is that whenever the plant_ontology file changes, their file will become out of date. This problem can be overcome if we maintain the subset within the main plant_ontology file.

We need to decide if we want to include users subsets in the PO flat file, and if we want to have any other policies regarding slims. For example, GO also maintains a generic slim. PO has a 'reference plant structure' subset, but we have not been maintaining it.

We need to decide asap about whether or not to maintain Traitnet's subset, because they are beginning work on it now.

Ramona will create a subset in the dev file (plant_ontology.obo) for them. When they want to add or remove terms from the subset, they will have to contact us. Need to find out if the root terms can be included in the filtered subset through OE. If not, then we will have to select them manually and make them part of the subset. Then the slim can be extracted automatically with a filtered save.

Status and Update of Progress: PO Release

• The new release is on the live, public PO web page! Thanks to everyone for all their hard work, it has definitely been a team effort.

• The plant structure and plant developmental stages ontology file have been merged.

New merged file called plant_ontology.obo. (Don't need to use 'test' suffix any more)

Now available on the dev browser. This is the one we will work on from now till the next release.

Reminder: PO terms added by POC curators to the Plant structure namespace should be in the PO:0025001-PO:0028000 range and ones in the PGDSO namespace should be PO:0028001-PO:0030000 Not necessary to continue this. This was only done when they were two separate files, to prevent duplication of ids.

POC meeting to be held at NYBG in fall 2010. Date Nov 4-6th

Date: Thursday Nov 4th (LC and RW), all day on Friday, November 5th and Sat Morning, Nov 6th

• See Wiki page for more details.

We will be adding items to this over the next few weeks

• Invited outside experts, scientists, students and postdocs:

-Farshid Ahrestani from TraitNet has been invited

-Dan Bunker from Traitnet (both from NJIT in Newark, so could attend for only a few hours without too much travel)

-Folks from the NYBG- review the PGDSO and comment on terms from non-angiosperms. Suggestions?

Should probably invite Barbara Ambrose (fern evo-devo)

-Could also invite someone from VirtualPlant (Coruzzi lab). Maybe their bioinformatics person (Manny).

Ramona will look after contacting folks since she is the local person

Will invite outside users (Traitnet and maybe Virtual Plant) to participate from 4-6 on Friday, then join us for dinner afterwards.

Priorities for next release

The next revision with the completed is_a parents should be ready by early/mid December so release can go out before PAG in mid January. Then the longer term goal will be revision of the PGDSO upper levels to accommodate non-flowering plants

High Priority items:

*is_a parents for remaining terms

~50 terms. Link to list: list of terms without is_a parents.

The terms in question are listed on next week's agenda and Source Forge (see POC_Conf._Call_10-26-10) .

Most of the terms that still lack a parent are the difficult ones, so this may take some time. We will need to address the issue of how to categorize non-material entities and trichomes.

Ramona has been working on suggestions for is_a parents, as well as new classes where needed.

The following items were addressed this week:

Raphe, funicle and hilum

Raphe, antiraphe, and hilum

Seed raphe (PO:0006331), seed funicle (PO:0006332), hilum (PO:0020063), and hilum groove (PO:0004719) have no is_a parents. These are related to the open SF items for raphe and antiraphe.

Dealing with this will assign parents to 4 terms without and close 2 SF tracker items.

Current defintions:

raphe (PO:0020027): That part of the funicle that is adnate to the ovule.
[source: APWeb:Glossary], part_of funicle, no is_a parent

seed raphe (PO:0006331): The ridge along the body of the seed formed from the part of funiculus that was adnate to the ovule. [ISBN:047124529]

antiraphe (PO:0020028):The region on the other side of the ovule from the raphe. [source: APWeb:Glossary]

seed funicle (PO:0006332): Remnants of the funicle from the ovary where it attaches the ovule to the placenta. [GR:pj]

hilum (PO:0020063): The scar on a seed at the place where it was attached to its funicle. [APWeb:Glossary]

hilum groove (PO:0004719): Longitudinal groove in the testa through the prominent hilum of the seed.

funicle (PO:0020006): A stalk that attaches the ovule to the placenta. [source: APWeb:Glossary, GR:pj] is_a stalk, which is_a cardinal organ part (definition is okay, just here or reference)

Question: For all of these, are they better classified as portions of plant tissue (contain only one tissue type) or cardinal organ parts (contain more than one tissue type? Depending on the answer to this question, all of the following definitions will be portions of plant tissue or cardinal organ parts.

We decided it as best to keep them as cardinal organ parts. They are really grooves on the ovary or scar, which can extend several layers deep and may encompass several types of tissue.

Proposed definitions (see SF tracker items):

raphe: A cardinal organ part that is a ridge on an ovule
where a funicle is or was fused to the ovule. is_a cardinal organ part,
part_of ovule



seed raphe: A cardinal organ part that is a ridge on a seed
that develops from a raphe. is_a cardinal organ part, part_of seed,
develops_from raphe

antiraphe: A cardinal organ part that is the
part of an ovule on the opposite side from a raphe. is_a cardinal organ part,
part_of ovule



seed funicle: A stalk that is attached to a seed and is the remnants of a funicle. is_a stalk, develops_from funicle.

hilum: A cardinal organ part that is a scar on a seed at the place where it was attached to a funicle. . is_a cardinal organ part, part_of seed

hilum groove: A cardinal organ part that forms a longitudinal groove in the testa through the prominent hilum of a seed. is_a cardinal organ part, part_of seed.

These definitions were accepted and will be added to the developer's file.

stylar ridge

The following terms have no is_a parents and no definitions:

stylar ridge of lower floret of pedicellate spikelet of ear (PO:0009024)

stylar ridge of lower floret of sessile spikelet of ear (PO:0009076)

stylar ridge of upper floret of pedicellate spikelet of ear (PO:0009079)

stylar ridge of upper floret of sessile spikelet of ear (PO:0009092)

They already have part_of relationships to their corresponding spikelets

Each of them occurs in a different structure, and has slightly different development, but they are all characterized by the following description: “The gynoecium development of the lower floret begins with the
production of a ridge on the abaxial surface of the apical meristem of the
floret, distal to the third stamen (which later degenerates). This is the
stylar ridge.” (MaizeGDB:60893)

Suggest a new parent term stylar ridge, proposed definition: A portion of meristem tissue that is part of a floret meristem and is characterized as a ridge on the abaxial surface of a floret meristem.

[FYI: Floret meristem (sensu Poaceae) (PO:0006329): Meristem that gives rise to the organs of a floret of a grass plant. [source: GR:pj]. Is_a floral meristem, which is_a meristem. Perhaps floral meristem should be is_a apical meristem instead.]

Proposed definitions for children:

stylar ridge of lower floret of pedicellate spikelet of ear: A stylar ridge that is part of a gynoecium of a lower floret of pedicellate spikelet of ear. Comment: While the development of this stylar ridge is very similar to
that of the upper florets, the development does not proceed beyond the
early ridge stage.

stylar ridge of lower floret of sessile spikelet of ear: A stylar ridge that is part of a gynoecium of a lower floret of sessile spikelet of ear. Comment: Continued overgrowth of the shoot apex (which becomes the
ovule primordium) by the ring of stylar tissue leads to the formation of
the stylar canal, which is detected as a slight protruberance on the mature
ovary.

stylar ridge of upper floret of pedicellate spikelet of ear: A stylar ridge that is part of a gynoecium of a pedicellate spikelet of ear.

stylar ridge of upper floret of sessile spikelet of ear: A stylar ridge that is part of a gynoecium of a sessile spikelet of ear.

Definitions from MaizsGDB cite Cheng & Pareddy, ID#60893 but I can’t find this reference. Not sure where the descriptions came from. Can’t actually find any references to stylar ridge on WOS. There are no annotations to these terms in the PO.

Ramona will research further to see if she find a better description of these structures. PJ sent paper by LaRoux and Kellogg, 1999, that describes floret development in Poaceae. It clearly describes the gynoecial ridge, and refers to the early publication by Cheng and Pareddy (which was a book chapter). PJ suggested we could contact Kellogg with link to SF tracker item for her input on these definitions if we can't find literature on them.

AmiGO Browser Issues and Questions

• AmiGO browser: There are no icons for relations that we added (has_part, derives_from). Show up as question marks.

What about participates_in? We have also created the participates_in and derives_from relations, but they are not currently in use. Will need to create icons for them if we use them in the next release.

Might be possible to make icons in OboEdit. Justin E. said that if we can figure out how to make the icons, he can probably figure out how to get them on to Amigo.

Barry said to contact Chris Mungall to be sure whatever icons we use are consistent with Obo Foundry use.

From CM: OE should come with a set of images you can use, including all letters of the alphabet plus greek

recommended:

H - has_part

D - develops/derives from

are you sure you want participates in rather than capable of? (note from RW: participates_in relation is for structures that occur during a particular growth or development stage. This relation was recommended by Chris)

Perhaps move on to the greek for participates_in (so as not to confuse it with P for part_of)

RW: I didn't get any other responses from the OE users group re. standard icons. Guess we can pick the color and shape.

*The new species annotated by SGN are not reflected in the drop down box on the advanced search page.

Missing: Anisodus acutangulus, Atropa baetica, Coffea arabica (coffee), Nicotiana tabacum (tobacco), Physalis spp., Solanum insanum (eggplant)

We do not have Lycopersicum esculentum tomato, (but we do have Solanum lycopersicum)

Laurel posted a request a feature on [AmiGO SF tracker] for the script to pull in all synonyms based on the NCBI taxon ID and should display common names as well. Annotation files should just use NCBI id.

• The top level parent term "all" is problematic and should have a comment that states :'this is an artefact created by the AmiGO browser. Inclusion is required. All should be redefined as 'an entity that exists'."

Not sure how we do this since it does not show up in OE. It is present in GO, but does not have a definition there. May have to be done in Amigo

Comments:?

PO Web Page things that need to be fixed:

See the detailed discussion of this on [9-29-10 Conf Call]

• The PO front page, release notes, acknowledgments pages have all been revised, but still needs some minor fixes, add 'About us' tab to top of page

• Download Ontologies page: links have been updated (thanks Justin), needs minor text edits. Has a link to the page "ontology concepts and how they are organized." That page needs to be updated.

• Documentation page: the table itself is okay. Suggest mirroring this table on the PO wiki, then moving all of the links form the table to the PO wiki, so it is easier for Ramona and Lol to update. Many of the documents linked from this table need to be updated.

• There are plans to move the entire web site to a new application(?). This might make editing easier. Before this is done, we should decide what is going on the web page, and what is on the wiki. Files will have to be renamed and reorganized for this move. Some of the current names are not intuitive, and this would be a good opportunity to fix them (e.g. release notes is really release statistics, ontology_doc is really the developers guide, but links through "concepts", the file with the old announcements is called "new" ).

• need to update the related publications page on both the website and wiki. Barry sent some suggestions for new publications, and there are other that have come out in the past few years that should be on there. Consolidate to one page (now on both website and wiki)

- updates from BS have been added to the wiki page (http://wiki.plantontology.org:8080/index.php/Related_Publications)

Plans for a publication to detail the updates in the PO

-This is a priority for the fall to detail the changes in the PSO and promote its application see TIPS Fall 2010

-We have been keeping track of the changes on the 'Summary of Changes' page

FIrst manuscript will target journal: 'Trends in Plant science' or 'Current Opinions in Plant Biology' may also consider 'Trends in Ecology and Evolution'

-Laurel and Ramona will prepare a summary preproposal (300-400 words) to be sent to Trends in Plant Science for their consideration. Focus will be on the benefits and usefulness of the PO, global perspective, links between PO and GO

-two papers to consider when writing this He et al, 2009 and Vincent etal, 2003

Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions. Use info from the grant proposal. Focus will be on updates to PO, and how it is now applicable to all plants.

-Compare to previous publication Ilic et al, Plant Phys.

Laurel and Ramona- Adding Annotations

10/14/10-LC, RW and PJ had a conf call discuss.

Summary: Laurel will work on annotating rice flowering time genes using the Phenote configuration from the ASPB workshop.

Note: Check that it is properly installed and working on Laurel's computer. Beta 1.7 ver 18? Not functioning right now

Coordinate with the work going on in the lab by Mamatha, Keshvan and Gina - have list of ~270 flowering time genes and the associated references. Link those to the PO.

Ramona will focus on the gymnosperm EST datasets. Exclude plastid/ mitochodrial data sets. Can also search Pubmed for papers on gymnosperms, e.g. Wuschel gene in Picea. Will coordinate with Dennis and Manny(?) about getting EST info from GenBank - need description of libraries (description, tissues, stage, evironment, treatment, variety or germplasm name, accession number) and genbank ids that belong to them.

Note: will need a special config in order to use Phenote for EST annotation.

Also: Coordinating with Rensing and the moss ontology folks as well to add annotations from their work. Probably will need to add terms for them see: Moss_Ontology-_Stefan_Rensing,_Daniel_Lang

Can sign up on the Physcomitrella ontology website to follow.

We should follow up with them - upcoming Annotation Jamboree. Need to be sure that the PO is ready for them to use if they are going to start creating annotations.

Other Items

• Plant and Animal Genome XIX Conference- Workshop

January 15-19, 2011 PAG 2011

PAG 2011 workshop wiki page has been created: PAG_2011_Collaborators_Workshop -half day workshop

Need more details about what we want to do for this- will it be similar to the Gramene workshop? Laurel Contacted Noel Yap, the Coordinator of the Computer Room in regard to the computer Demo, but it is not clear who to talk to about organizing a workshop. Main organizer: Contact E-mail: pag@scherago.com

• Mailing lists

We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal. I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?

In mid-August the new list po-discuss@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers.

We all agreed that these need to be reviewed and we need to deal with the spam problem as well. May be able to use images instead of textual links to email addresses.

We will need to update the links to this lists on the PO web site (http://plantontology.org/mailarchs/mail_list.html)

Upcoming meetings 2010-2011:

• Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010. To qualify for reduced registration rates, must register by October 15th.

Lol and Ramona are planning on attending and setting up a PAG_2011_Collaborators_Workshop half day workshop and meeting with collaborators.

We will present a computer demonstration and poster. Alejandra cannot attend. PJ is not attending as he is teaching. DWS will attend also Justin Preece. Abstract under construction....

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open- deadline for abstracts: 31 October 2010, Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and must submit abstracts by October 31st. Three additional speakers will be chosen from abstracts that are submitted.

Ramona sent out abstract for review. Any comments?

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology.