Dec 13th, 2016 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Dec 13th, 2016
  • Time: 8:15am PST (GMT-8)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/125946326
  • Attendees: LC, AM, PJ, Mal, BtSinn, DC, DWS
  • Regrets: CM,

Agenda

Fruit types in the Plant Ontology

  • achene fruit (PO:0030107): A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a dry exocarp (PO:0009085), a dry mesocarp (PO:0009087), and a dry endocarp (PO:0009086) that are connected to a seed coat (PO:0009088) by a funicle (PO:ID).
    • Include funiculus ? PO term funicle
    • Review funicle def’n?
  • Synonyms: achäne (exact, German), aquenio (exact, Spanish), akene (exact), achene (exact), indehiscent fruit (broad)
  • Comment: Plant structures commonly referred to as ‘accessory’ (such as strawberry) or multiple fruits (such as figs..) which are comprised of accrescent receptacle (PO:ID) or infructescence (PO:ID) tissue, contain as parts achene fruits.
    • strawberry: ‘glandetum’ do we need to add this? Collective plant structure? Develops from single flower with multiple carpels
    • For example, when annotating for a gene involved in strawberry development, any gene of interest that is involved in the development of the receptacle tissue would be mapped to receptacle (PO:0009064); genes involved in sepal (PO:0009031) persistence or accrescence would map to sepal (PO:0009031), and those involved in fruit characteristics would be mapped to achene (PO:0030107).
    • Examples: sunflower (Helianthus annuus), strawberry (Fragaria spp.), fig (Ficus carica), and marijuana (Cannabis sativa).
  • nut fruit (PO:0030102):

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 are not fused to a seed coat (PO:0009088).

    • Synonyms: nuez (exact, Spanish), nuß (exact, German), acorn (narrow), glans (exact), glandes (exact), nutlet (narrow), indehiscent fruit (broad)
    • Comment: The common names of some species do not accurately reflect their fruit type. For example, the fruit the peanut plant is a legume fruit (PO:ID) rather than a nut fruit.
    • Example: pecan (Carya illinoinensis), walnut (Juglans regia), pistachio (Pistacia vera), lotus (Nelumbo nucifera), and acorn (Quercus spp.).
  • caryopsis fruit (PO:0030104):

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 are fused to a seed coat (PO:0009088). Three carpels start and two abort pseudomomary?

  • Synonyms: caryopse (exact, German), cariopse (exact, Spanish), cariópside (exact, Spanish), caryopsides (exact), grain (exact), kernel (exact), indehiscent fruit (broad)
    • Add cereals as broad syn
    • brown rice- exact
    • dehulled grain/kernel- exact
    • Polished rice lacks the pericarp and the seed coat and caryopsis hull (po:id)- just endosperm
  • Comment: Examples: barley (Hordeum vulgare), rice Oryza spp. (Oryza australiensis, O. eichingeri, O. longistaminata, O. officinalis, O. rufipogon, and O. sativa), common wheat (Triticum aestivum), einkorn wheat (Triticum monococcum),

corn (Zea mays), sorghum (Sorghum bicolor), rivet wheat (Triticum turgidum), red wild einkorn (Triticum urartu), Tausch’s goatgrass (Aegilops tauschii), stiff brome (Brachypodium distachyon), cutgrass (Leersia perrieri), and foxtail millet (Setaria italica)

    • Use 'All Poaceae spp - the grass family, include oat, Miscanthus, etc. Add comment: Bamboo has caryopsis but they are not dry- need to look into...
  • samara fruit (PO:0030099): 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) that are elongated into a wing.
    • Use wing-like structure?
    • Synonyms: flügfrucht (exact, German), sámara (exact, Spanish), samara (exact), indehiscent fruit (broad)
    • Comment: The pericarp (poid) can be expanded laterally or radially.

Examples: green ash (Fraxinus pennsylvanicum) and tree of heaven (Ailanthus altissima). Add comment to look at schizocarp for Maple

  • schizocarp fruit (PO:0030098): 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 separate into carpellate units.
    • Use mericarps?- yes, unobsolete it
    • Synonyms: spalt-nußfrucht (exact, German), doppelnuß (exact, German), nutlet (exact), pyrine (exact), indehiscent fruit (broad)
  • Comment: The individual carpellate units of a schizocarp are often referred to as mericarps (PO:0020075; obsolete). Examples: maple (Acer spp.) and cassava (Manihot esculenta).

Parts of fruits:

  • Comment to be added to the parts of fruits: see example of comment added to parts of leaves
  • To be added to the parts of fruits: “If you are annotating to this term, please add an additional annotation to the specific type of fruit (PO:0009001), such as achene fruit (PO:0030107), berry fruit (PO:0030108), capsule fruit (PO:0030091), caryopsis fruit (PO:0030104), drupe fruit (PO:0030103), follicle fruit (PO:0030105), legume fruit (PO:0030100), nut fruit (PO:0030102), samara fruit (PO:0030099), schizocarp fruit (PO:0030098), silique fruit (PO:0030106), or their subclasses, depending on the species.“
  • List of fruit parts:
    • fruit abscission zone PO:0006503
    • fruit columella PO:0004540
    • fruit dehiscence zone PO:0004707
    • fruit distal end PO:0008001
    • fruit locule PO:0025270
    • fruit nucellus PO:0008005
    • fruit operculum PO:0025298
  • Shouldn’t fruit pedicel abscission zone PO:0025605 be included here? (check part_of on fruit pedicel )
  • 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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