Dec 6th, 2016 Ontology Working Group Meeting: Difference between revisions

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* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/146374357
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/146374357
   
   
* Attendees:  
* Attendees: LC, AM, PJ, BtSinn, DC, MLP, MAL
 
* Regrets:  
* Regrets:  


Revision as of 18:43, 6 December 2016

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Dec 6th, 2016
  • Time: 8:15am PST (GMT-8)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/146374357
  • Attendees: LC, AM, PJ, BtSinn, DC, MLP, MAL
  • Regrets:
  • Recordings:

Agenda

Fruit types in the Plant Ontology

  • Covered today- notes from Gdoc:
  • capsule fruit (PO:0030091): A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086), and dehisces at maturity.
    • Synonym: capsule (exact), kapsel (exact, German), cápsula (exact, Spanish)
    • Comment: Capsule fruits are divided into subclasses depending upon the location of sutures in the pericarp that the seeds are released through.
  • circumscissile capsule fruit (PO:0030096): A capsule fruit (PO:0030091) which dehisces through the release of a fruit operculum (PO:0025298).
    • Synonyms: deckelkapsel (exact, German), cápsula circuncisa (exact, Spanish), diplotegia (exact), pyxidium (exact), pyxis (exact), circumscissile capsule (exact)
    • Comment: Example: rose gum (Eucalyptus grandis).
    • Add Comment about there could be one or more seeds
  • urticle capsule fruit (PO:0030097): A circumscissile capsule fruit (PO:0030096) which contains one seed (PO:0009010), that is not attached to a pericarp (PO:0009084).
    • Synonym: hautfrucht (exact, German), utrículo (exact, Spanish), urticle (exact),
    • Comment: Example: common amaranth (Amaranthus retroflexus).
    • coccarium capsule fruit (PO:0030094): A capsule fruit (PO:0030091), which dehisces through both the fruit septa (PO:0025268), and the fruit locules (PO:0025270).
    • Synonym: coccarium (exact), lokulizide-septifrage kapsule (exact, German), cápsula bicida (exact, Spanish)
    • Comment: Examples: physic nut (Jatropha curcas) and Manihot brachyloba.

** Add a couple more examples?

  • loculicidal capsule fruit (PO:0030092): A capsule fruit (PO:0030091) which dehisces through fruit locules (PO:0025270).
    • Synonym: lokulizide kapsule (exact, German), cápsula loculicida (exact, Spanish), loculicidal capsule (exact)
    • Comment: Examples: cotton (Gossypium raimondii) and rose mallow (Hibiscus syriacus).
    • Add comment: to direct to septicidal and coocarium if needed
  • poricidal capsule fruit (PO:0030095): A capsule fruit (PO:0030091) which dehisces through pores on a pericarp (PO:0009084).
    • Synonym: porenkapsel (exact, German), cápsula porífera (exact, Spanish), poricidal capsule (exact)
    • Comment: Example: poppy (Papaver spp.).

** Do we need a term for pericarp pore? Is this really a pore? Maybe an opening? - look into...

  • septicidal capsule fruit (PO:0030093): A capsule fruit (PO:0030091) which dehisces through fruit septa (PO:0025268).
    • Synonym: septizide kapsel (exact, German), cápsula septicida (exact, Spanish), cápsula septífraga (exact, Spanish), septicidal capsule (exact), septifragal capsule (exact)
    • Comment: Examples: dutchman's pipe (Aristolochia elegans) and black cottonwood (Populus trichocarpa).


  • silique fruit (PO:0030106): A fruit (PO:0009001) which develops from a gynoecium (PO:0009062) and at maturity comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086), that dehisce along two fruit valves (PO:0000033), that separate from a persistent fruit replum (PO:0025267).
    • Synonyms: schote (exact, German), silicua (exact, Spanish), silícula (exact, Spanish), silicle (exact), siliqua (exact), silicula (exact), silique (exact)
    • Comment: Examples: members of Brassicaceae, lyrate rockcress (Arabidopsis lyrata), mouse-ear cress (Arabidopsis thaliana), wild cabbage (Brassica oleracea), field mustard (Brassica rapa), and pink shepherd's purse (Capsella rubella).

** Add comment about gynoecium being multicarpellate ...

  • follicle fruit (PO:0030105): A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity, comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) which dehisce along a single fruit valve (PO:0000033).
    • Synonyms: balgfrucht (exact, German), folículo (exact, Spanish), follicetum (exact), pod (broad)
    • Comment: Examples: milkweed (Asclepias syriaca) and Carolina larkspur (Delphinium carolinianum).
  • legume fruit (PO:0030100): A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity, comprises a dry exocarp (PO:0009085), dry mesocarp (PO:0009087), and dry endocarp (PO:0009086) which dehisce along two fruit valves (PO:0000033).
    • Synonym: hülse (exact, German), legumbre (exact, Spanish), pod (broad)
    • Comment: Examples: members of Fabaceae, including pigeon pea (Cajanus cajan), chickpea (Cicer arietinum), and lentils (Lens culinaris subsp. culinaris).

- Clarify Fabaceae vs Legumacea, expand comment…and include pulses

  • loment fruit (PO:0030101): A legume fruit (PO:0030100) which is constricted between each seed (PO:0009010).
    • Synonym: gliederhülse (exact, German), lomento (exact, Spanish), lomentum (exact)
    • Comment: Examples: some members of Fabaceae, including soybean (Glycine max).

- Clarify "some members of the Fabaceae"- vague...

  • The main categories of fruits will be (see the associated trackers for each):
    • capsule (#642)
    • schizocarp (#643)
    • samara (#644)
    • legume (#645)
    • nut (#646)
    • drupe (#647)
    • caryopsis (#648)
    • achene (#651)
    • silique (#650)
    • follicle (#649)
    • berry (#652)

Upcoming Meetings and Workshops

4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016

Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA

http://www.intlpag.org/

  • October 31 early registration deadline
  • Deadline for workshop abstract submissions is December 2, 2016.
  • Deadline for changes to program (posting speakers) is November 30, 2016
  • Poster Abstracts Submission Deadline Extension to Nov. 14, 11:59 pm EDT
    • Editing Deadline: 11/28/16

Phenome 2017, Feb 10th to 14th, 2017

http://www.phenome2017.org/#homepage

  • DWS will attend- evo devo presentation, submitted abstract with BtSinn and Dario
  • LC submitted Planteome abstract and AM submitted Samara abstract- in dropbox folder
  • To be considered for a talk you must submit your abstract by November 17, 2016
  • January 9, 2017: Final deadline for abstracts to be in the online program and conference mobile app
  • Early bird registrations till Dec. 1st- Registration Link

Biocuration 2017, March 26-29, 2017

  • Stanford University, Palo Alto, California, United States
  • http://biocuration2017.org
  • Call for Workshops:
    • Submission deadline: November 11, 2016
    • Submission email: biocuration2017@lists.stanford.edu
  • Biocuration 2017 will bring together hundreds of leading curation scientists, bioinformaticians, and developers from all over the world to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research.
  • The purpose of a workshop is to provide an opportunity for participants from academia and industry to present and discuss novel ideas on current and emerging topics relevant to biocuration. Workshops are an excellent forum for exploring emerging approaches and task areas, for bridging the gaps between the curation and technology subfields of biocuration, and for critiquing existing approaches. This is a great opportunity to discuss specific topics with so many colleagues and working scientists gathered in the same location.
  • For the best opportunity for consideration, proposals should be received by November 11, 2016. Please submit a short paragraph (or two) describing the following:
    • Proposed scope and main objective, and their relation to biocuration
    • Brief discussion of why the topic is of particular interest at this time
    • Suggested format (talks, panel discussion, etc.)
    • Potential speakers, panels, or other activities

XIX International Botanical Congress, July 23-29, 2017, Shenzhen, China

Workshop proposal accepted

ICBO 2017, Sept 12th-15th, 2017

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