Nov 29th, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday Nov 29th, 2016
• Time: 8:15am PST (GMT-8)
• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/418727698

• Attendees: BtSinn, DC, DWS, LC, PJ, AM, JE, GG,
• Regrets: CM, BS

• Recordings:
  • File:Ontology WG Meeting 11-29-2016 audio.m4a
  • File:Ontology WG Meeting 11-29-2016 video.mp4

Agenda

Updates:

• MAL:
  • Report from meeting: International Conference on Statistics & Big Data Bioinformatics in Agricultural Research, ICRISAT, India, Nov 20-23rd, 2016
  • International Crops Research Institute for the Semi-Arid Tropics- ICRISAT http://www.icrisat.org/
• MAL will be in Montpellier Dec 5th-16th. Breeding API meeting there week of Dec 12th

Fruit types in the Plant Ontology

• A number of Fruit types have recently been added to the PO.
  • Background: At the Oct. 11, 2016 conference call, we decided to add the various the fruit types to the PO as separate terms. This will improve the coordination between Plant Ontology and the Trait Ontology Oct_11th,_2016_Ontology_Working_Group_Meeting
  • The fruit types that are currently listed as synonyms will be added as stand alone terms in the PO.

• Revisions to fruit (PO:0009001) and new child terms for fruit types:
• Current Def’n: fruit (PO:0009001): A multi-tissue plant structure (PO:0025496) which develops from a gynoecium (PO:0009062) and may have as parts one or more seeds (PO:0009010).
  • Current Comment: A fruit may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds. Fruits only occur in angiosperms.

• Revised Def’n: fruit (PO:0009001): A multi-tissue plant structure (PO:0025496) which develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and may have as parts one or more seeds (PO:0009010).
  • Revised Comment: A fruit may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds. When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms.

• 

• Link to Google docs:
  • PO Fruit Revisions
  • Fruit images

• drupe fruit (PO:0030103): A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and a stony endocarp (PO:0009086).
  • Synonym: steinfrucht (exact, German), drupa (exact, Spanish), stone fruit (exact), drupe (exact), indehiscent fruit (broad)
  • Comment: May develop from an inferior or superior carpel (PO:0009030) and may contain one or more seeds (PO:0009010). Examples: Amborella trichopoda (basal angiosperm), coffee (Coffea canephora), Cornaceae (Davidia spp.), cashew (Anacardium occidentale), coconut (Cocos nucifera), and almond, peach and plum (Prunus spp.).

• berry fruit (PO:0030108): A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085).
  • Synonym: beere (exact, German), baya (exact, Spanish), bacca (exact), berry (exact), indehiscent fruit (broad)
  • Comment:
  • Examples: pepper (Capsicum annuum), papaya (Carica papaya), apple (Malus domestica), banana (Musa acuminata), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera).

• pepo fruit (PO:0030111): A berry fruit (PO:0030108) which develops from an inferior carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and fleshy endocarp (PO:0009086), and has as a part a hard receptacle (PO:0009064) which surrounds, and is indistinct from, the exocarp (PO:0009085).
  • Synonym: kürbisfrucht (exact, German), panzerbeere (broad, German), pepónide (exact, Spanish), pepo (exact), indehiscent fruit (broad)
  • Comment: A pepo fruit (PO:0030111) is specialized type of berry fruit (PO:0030108) which is encapsuled by persistent, accrescent receptacle (PO:0009064) tissue. The rind, or tough outer covering, of pepo fruits comprises receptacle tissue and at least the exocarp (PO:0009085) layer of the pericarp (PO:0009084).
  • Examples: pumpkin (Cucurbita pepo), cucumber (Cucumis sativus), and watermelon (Citrullus lanatus).

• pome fruit (PO:0030110): A berry fruit (PO:0030108) which develops from an inferior gynoecium (PO:0009062) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and hardened endocarp (PO:0009086) and has as a part a fleshy hypanthium (PO:0009065) which is indistinct from the exocarp (PO:0009085).
  • Synonym: pome (exact), kernfrucht (exact, German), kernobst (exact, German), apfelfrucht (exact, German), pomo (exact, Spanish), indehiscent fruit (broad)
  • Comment: A pome fruit (PO:0030110) is a specialized type of berry fruit (PO:0030108) which is encapsuled in persistent, accrescent receptacle (PO:0009064) and/or hypanthium (PO:0009065) tissue.
  • Examples: Apple, crab apple, and pear (Malus spp. and Pyrus spp.)

• hesperidium fruit (PO:0030109): A berry fruit (PO:0030108) which develops from a superior gynoecium (PO:0009062) and at maturity comprises a thickened exocarp (PO:0009085), thickened mesocarp (PO:0009087), and endocarp (PO:0009086), and has as parts juice sacs (PO:0006013) on a carpel adaxial epidermis (PO:0025618).
  • Synonyms: panzerbeere (broad, German), hesperidio (exact, Spanish), citrus fruit (exact), hesperidium (exact), indehiscent fruit (broad)
  • Comment: A hesperidium fruit (PO:0030109) develops from a superior gynoecium (PO:0009062), and therefore is not surrounded by receptacle (PO:0009064) tissue.
  • Examples: orange, grapefruit, lemon, and lime (Citrus spp.).

• 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)

• Thanks so much to @btsinn and @DarioJCavaliere for all the hard work on this!

Upcoming Meetings and Workshops

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

• International Maize and Wheat Improvement Center (CIMMYT)
• El Batan, Texcoco, México (Near Mexico City)
• Early bird registration deadline: October 16, 2016
• http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

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

• Newcastle, GB
• http://icbo.buffalo.edu/