Difference between revisions of "POC Conf. Call 6-25-13"

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POC meeting, Webex Conference Call; Date: Tuesday June 25th, 2013 10am PST/1pm EST
 
POC meeting, Webex Conference Call; Date: Tuesday June 25th, 2013 10am PST/1pm EST
  
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In attendance:
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In attendance:''Laurel Cooper (OSU), Justin Elser (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Laura Moore (OSU), Brian Atkinson (OSU)''
−
Absent:
 
  
 +
Absent:''Justin Preece (OSU)''
  
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=Update on Image analysis: AISO and the Image Annotation DB=
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Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=76067222&rKey=14a3342a493b5b36
  
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* 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.
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Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=76067222&rKey=ae02e0a9148c9c81
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* 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!
 
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* I have begun expanding AISO to allow access to multiple ontologies, and to make ontology data available offline, when desired.
 
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* 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.
 
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NOTE: All of this work will be dormant for roughly the next four weeks while I attend to another project deadline.
 
  
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=Image-Net Site=
 
  
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This is part of the WordNet family of computerized lexica. Image-Net
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=Translations for next Release=
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is a computerized lexicon with images.
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We have prepared a [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdEViNmE3bFhPalY0cmJoaW9GU0toU0E#gid=0 Google doc].  Ale has added all the new Spanish translations. We will continue to add to this list as we go along.
  
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http://www.image-net.org/synset?wnid=n00017222
 
  
 +
=[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/500/ Flower development stage (PO:0021004) and subclasses]=
 +
Link to spreadsheet: [https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdFJYQmhsUVNmU0ZmbjhpbjE2Z2QyRXc&usp=sharing gdoc]
 +
 +
 +
Current and revised definitions for flower development stages:
 +
''Propose to remove the numbers in front of all the child terms to be consistent with other parts of the PSDS that have been revised.  Could consider adding new relations such as: ''
 +
* '''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]'''
 +
 +
''Revised def'n: '''Flower development stage (PO:0021004):''' A reproductive shoot system development stage (PO:0025530) which begins with the onset of the flower meristem visible stage (PO:0007601) and ends after the post anthesis stage (PO:0007617).''
 +
 +
* '''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.
 +
** ''Revised def'n: '''flower meristem visible stage (PO:0007601):''' A flower development stage (PO:0007615) marked by the emergence of the flower meristem (PO:0000229) from a portion of meristem tissue (PO:0009013).''
 +
 +
''We agreed that it should not refer to the '''flank''' of the meristem, unless the flower is part of an inflorescence.  We should add this in a comment to cover flowers that are part of an inflorescence.  Decided to refer to the general parent term for the meristem.  Discussed examples jackfruit and cacao, which apparently form fruits on the stem, but these are actually formed on short branches. ''
  
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=Collaboration with New Phytologist=
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* '''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]
  
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We were contacted by Sarah Lennon from New Phytologist:
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''proposed that we rename the term to get rid of the 'notched' word in the term name. One way to do this would be to add a comment that states that the initiation of this stage is indicated by a slight indentation.  Discussed "demarcated" vs "separated", need to explain what "notched" means, look in PATO.  Is there still a notch if there is an individual flower determinate''
  
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"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. "
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''Decided to refer to the [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/465/  floral structure primordium (PO:0025477)]: def'n: A primordium (PO:0025127) that is committed to the development of a plant structure that is part of a flower (PO:0009046), such as a floral organ (PO:0025395), gynoecium (PO:0009062), or anther (PO:0009066) and is part of a reproductive shoot apex (PO:0025222). [source: POC:curators].  Needs to be revised to meet the new floral organ definition. Is_a ''
  
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"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."
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''Ale will send additional pictures of flower development to help with the definitions''
  
 +
''proposed new name and def'n:'''floral organ primordium stage (PO:0007602)''': A flower development stage (PO:0007615) that begins when the flower meristem (PO:0000229) transitions into a floral organ primordium (PO:0025477).''
  
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-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.
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''add a comment that the floral organ primordia are demarcated by indentations at this stage.''
  
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Sent to them:  "The latest development version will always be available from this link:
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*See [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028762 link to images in PlosOne]
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http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OWL_format/plant_ontology.owl
 
  
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''So when does it end?''  '''This is actually a later stage than what was originally intended
  
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-"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.
 
  
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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."
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**'''4 anthesis stage (PO:0007616):''' The phase of a flower when pollen is presented and/or the stigma is receptive. [source: APweb:Glossary]
  
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- Should we set up a webex meeting with them?  Dennis said he may be able to meet when in London, he knows Matt Pacey.
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''Revised def'n: '''3-anthesis stage (PO:0007616):''' A flower development stage (PO:0007615) when pollen (PO:0025281) is presented and/or the stigma (PO:0009073) is receptive.''
  
 +
*''proposed def'n: '''anthesis stage (PO:0007616):''' A flower development stage (PO:0007615) that begins when pollen (PO:0025281) is presented and/or the stigma (PO:0009073) is receptive and ends with pollination (GO:0009856).''
  
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=[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/500/ Flower development stage (PO:0021004) and subclasses]=
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''Should think about the use of the word presented. May add comment stating that this usually occurs when the flower is open.''
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- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting
+
 
 +
**'''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]
 +
 
 +
''Revised def'n: '''4-post anthesis stage (PO:0007617):''' A flower development stage (PO:0007615) that occurs after the anthesis stage (PO:0007616).''
 +
 
 +
''proposed def'n: '''post anthesis stage (PO:0007617):''' A flower development stage (PO:0007615) that occurs after the anthesis stage (PO:0007616) and lasts until flower morphogenesis is complete (GO:0048439).''
 +
 
 +
[[File: flowers_snap_shot.jpg]]
 +
 
 +
 
 +
 
 +
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/546/ floral organ development stage (PO:0007600):]==
 +
 
 +
is_a plant organ development stage (PO:0025339); part_of flower development stage (PO:0021004)
 +
 
 +
''Proposed to not use the part_of relationship and use 2 is_a relationships for the time being. The thought process behind this is that by using part_of it infers that floral organ development is a sub stage of flower development meaning that flower development is not a "whole" stage because it is made up of floral organ development.  Also it is inconsistent that some of the sub-stages are part_of and some are is_a children. ''
 +
 
 +
Current Name and def'n: '''3 flower organ development stage (PO:0007600)''': Stages of development of floral organs defined by characteristic morphological, structural, histological or other visible features.
 +
 
 +
Revised name and def'n: '''floral organ development stage (PO:0007600):''' A plant organ development stage (PO:0025339) that has as primary participant a floral organ (PO:0025395).''
 +
 
 +
''new relations, current definitions and revised definitions for subclasses of floral organ development stage (PO:0007600): these were all children of flower organ development stage (PO:0007600).''
  
 
=Upcoming meetings and Presentations 2013:=
 
=Upcoming meetings and Presentations 2013:=
  
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==MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013==
+
==MONOCOTS V Meeting at NYBG, July 7th - 13th, 2013==
 
[http://www.regonline.com/builder/site/Default.aspx?EventID=1060172 MONOCOTS V]:  
 
[http://www.regonline.com/builder/site/Default.aspx?EventID=1060172 MONOCOTS V]:  
  
 
5th International Conference on Comparative Biology of Monocotyledons
 
5th International Conference on Comparative Biology of Monocotyledons
−
Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)
+
Sunday, July 07, 2013 - Saturday, July 13, 2013
  
 
The New York Botanical Garden & Fordham University
 
The New York Botanical Garden & Fordham University
  
−
==ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013==
+
==ICBO 2013, Concordia University, Montreal, Quebec July 6th - 10th 2013==
 
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  
 
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  
  

Latest revision as of 16:31, 11 July 2013

POC meeting, Webex Conference Call; Date: Tuesday June 25th, 2013 10am PST/1pm EST

In attendance:Laurel Cooper (OSU), Justin Elser (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Laura Moore (OSU), Brian Atkinson (OSU)

Absent:Justin Preece (OSU)

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=76067222&rKey=14a3342a493b5b36

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=76067222&rKey=ae02e0a9148c9c81


Translations for next Release

We have prepared a Google doc. Ale has added all the new Spanish translations. We will continue to add to this list as we go along.


Flower development stage (PO:0021004) and subclasses

Link to spreadsheet: gdoc


Current and revised definitions for flower development stages: Propose to remove the numbers in front of all the child terms to be consistent with other parts of the PSDS that have been revised. Could consider adding new relations such as:

  • 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]

Revised def'n: Flower development stage (PO:0021004): A reproductive shoot system development stage (PO:0025530) which begins with the onset of the flower meristem visible stage (PO:0007601) and ends after the post anthesis stage (PO:0007617).

  • 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.
    • Revised def'n: flower meristem visible stage (PO:0007601): A flower development stage (PO:0007615) marked by the emergence of the flower meristem (PO:0000229) from a portion of meristem tissue (PO:0009013).

We agreed that it should not refer to the flank of the meristem, unless the flower is part of an inflorescence. We should add this in a comment to cover flowers that are part of an inflorescence. Decided to refer to the general parent term for the meristem. Discussed examples jackfruit and cacao, which apparently form fruits on the stem, but these are actually formed on short branches.

  • 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]

proposed that we rename the term to get rid of the 'notched' word in the term name. One way to do this would be to add a comment that states that the initiation of this stage is indicated by a slight indentation. Discussed "demarcated" vs "separated", need to explain what "notched" means, look in PATO. Is there still a notch if there is an individual flower determinate

Decided to refer to the floral structure primordium (PO:0025477): def'n: A primordium (PO:0025127) that is committed to the development of a plant structure that is part of a flower (PO:0009046), such as a floral organ (PO:0025395), gynoecium (PO:0009062), or anther (PO:0009066) and is part of a reproductive shoot apex (PO:0025222). [source: POC:curators]. Needs to be revised to meet the new floral organ definition. Is_a

Ale will send additional pictures of flower development to help with the definitions

proposed new name and def'n:floral organ primordium stage (PO:0007602): A flower development stage (PO:0007615) that begins when the flower meristem (PO:0000229) transitions into a floral organ primordium (PO:0025477).

add a comment that the floral organ primordia are demarcated by indentations at this stage.

So when does it end? This is actually a later stage than what was originally intended


    • 4 anthesis stage (PO:0007616): The phase of a flower when pollen is presented and/or the stigma is receptive. [source: APweb:Glossary]

Revised def'n: 3-anthesis stage (PO:0007616): A flower development stage (PO:0007615) when pollen (PO:0025281) is presented and/or the stigma (PO:0009073) is receptive.

  • proposed def'n: anthesis stage (PO:0007616): A flower development stage (PO:0007615) that begins when pollen (PO:0025281) is presented and/or the stigma (PO:0009073) is receptive and ends with pollination (GO:0009856).

Should think about the use of the word presented. May add comment stating that this usually occurs when the flower is open.

    • 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]

Revised def'n: 4-post anthesis stage (PO:0007617): A flower development stage (PO:0007615) that occurs after the anthesis stage (PO:0007616).

proposed def'n: post anthesis stage (PO:0007617): A flower development stage (PO:0007615) that occurs after the anthesis stage (PO:0007616) and lasts until flower morphogenesis is complete (GO:0048439).

Flowers snap shot.jpg


floral organ development stage (PO:0007600):

is_a plant organ development stage (PO:0025339); part_of flower development stage (PO:0021004)

Proposed to not use the part_of relationship and use 2 is_a relationships for the time being. The thought process behind this is that by using part_of it infers that floral organ development is a sub stage of flower development meaning that flower development is not a "whole" stage because it is made up of floral organ development. Also it is inconsistent that some of the sub-stages are part_of and some are is_a children.

Current Name and def'n: 3 flower organ development stage (PO:0007600): Stages of development of floral organs defined by characteristic morphological, structural, histological or other visible features.

Revised name and def'n: floral organ development stage (PO:0007600): A plant organ development stage (PO:0025339) that has as primary participant a floral organ (PO:0025395).

new relations, current definitions and revised definitions for subclasses of floral organ development stage (PO:0007600): these were all children of flower organ development stage (PO:0007600).

Upcoming meetings and Presentations 2013:

MONOCOTS V Meeting at NYBG, July 7th - 13th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Sunday, July 07, 2013 - Saturday, July 13, 2013

The New York Botanical Garden & Fordham University

ICBO 2013, Concordia University, Montreal, Quebec July 6th - 10th 2013

4th International Conference on Biomedical Ontologies 2013 (ICBO 2013), Concordia University, Montreal, Quebec, July 7th - 9th 2013

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.

The event is part of the Semantic Trilogy 2013 featuring:

  • International Conference on Biomedical Ontologies (ICBO 2013)
  • Canadian Semantic Web Symposium (CSWS 2013)
  • Data Integration in the Life Sciences (DILS 2013)

Workshop on 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)

Topics of interest include, but are not limited to:

  • ontologies & terminologies for modeling computational biology
  • ontologies & terminologies for simulation (and result data) in computational biology/medicine/neuroscience
  • semantic web technologies for description, integration, query and discovery of models, simulations and result data
  • semantic web technologies for biological data and analysis
  • semantic annotations of bio-models
  • applications of ontologies in computational systems biology/medicine/neuroscience
  • semantic platforms for undertaking and visualizing simulation results

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG will present the work she has been doing with the images and slides CUPAC- The Cornell University Plant Anatomy Collection: a web-based tool for the Plant Sciences teachers and researchers

- BA will present a poster on his work: New evidence for the radiation of basal Cupressaceae

Next meeting scheduled for Tuesday, July 2nd, 2013 at 10am Pacific/1pm Eastern

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