Mar 14th, 2017 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Tuesday March 14th, 2017
  • Time: 8:15am PST (GMT-8)
  • Connection details:

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/370267127

  • Attendees: LC, AM, PJ, JE, BS, DWS, BSinn, DC, MLP*
  • Regrets: GG, JD, BS, CM


Agenda

Revisions to inflorescence branch terms & axis terms

  • Proposal that inflorescence branch (PO:0009081) be renamed higher order inflorescence axis, and that each order of inflorescence branch be renamed using its corresponding inflorescence axis exact synonym; for example, third order inflorescence branch would be renamed its current synonym, fourth order inflorescence axis.
  • Link to google doc: PO Inflorescence Axis Terminology Revision
  • Link to history of these terms on GitHub: #264
  • Link to new tracker: #667

inflorescence axis (PO:0020122)

  • Current def'n: A shoot axis (PO:0025029) that is part of an inflorescence (PO:0009049).
  • Revised def’n: No revisions
  • Current comment: None
  • Current synonyms: eje de la inflorescencia (Spanish, exact), 花序軸 (Japanese, exact), first order inflorescence branch (related), inflorescence rachis (related)
  • Revised synonyms: eje de la inflorescencia (Spanish, exact), 花序軸 (Japanese, related), inflorescence branch (related), inflorescence rachis (related)
  • Revised comment: An inflorescence axis (PO:0020122) has either a determinate apex, which terminates in a flower (PO:0009046), or has an indeterminate apex, which terminates in an inflorescence apical meristem (PO:0009108). Flower pedicel (PO:0009052) serves as the simplest example of a determinate inflorescence axis.
  • Propose revised Comment: An inflorescence axis (PO:0020122) has either a determinate apex, which terminates in a flower meristem (PO:0000229), or has an indeterminate apex, which terminates in an inflorescence apical meristem (PO:0009108).

A flower pedicel (PO:0009052) is the simplest example of a determinate inflorescence axis.

  • PJ: Do we have the relationship 'flower' develops_from 'flower meristem'? Yes, but it is not visible on the browser, except in the neighborhood tab: develops_from (RO:0002202).
  • Need to add: 'inflorescence' develops_from 'inflorescence meristem'

first order inflorescence axis (PO:0025104)

  • Current def'n: An inflorescence axis (PO:0020122) that is the primary or main axis of an inflorescence (PO:0009049).
  • Revised def'n: No revisions.
  • Current comment: A first order inflorescence axis consists of either a peduncle alone or a peduncle plus its continuation, depending on the form of the inflorescence.
  • Revised comment: Monopodial inflorescences, such as a raceme, have a centrally-located main axis; this axis is a first order inflorescence axis. In contrast, sympodial inflorescences, such as the riphidium, do not have a centrally-located main axis. The basal-most portion of a first order inflorescence axis is referred to as a peduncle (PO:0009053).
  • Current synonyms: inflorescence rachis (exact), inflorescence rhachis (exact), primary inflorescence axis (exact), primer orden del eje de la inflorescencia (Spanish, exact), 第一花序軸 (Japanese, exact), ray (broad)
  • Revised synonyms: inflorescence rachis (exact), inflorescence rhachis (exact), primary inflorescence axis (exact), primer orden del eje de la inflorescencia (Spanish, exact), 第一花序軸 (Japanese, related)

higher order inflorescence axis (PO:0009081)

  • Renaming of: inflorescence branch (PO:0009081)
  • Current def'n: An inflorescence axis (PO:0020122) that is a branch (PO:0009081) arising from a first order inflorescence axis (PO:0025104) or from a higher order inflorescence branch.
  • Revised def'n: An inflorescence axis (PO:0020122) that develops from an inflorescence axillary meristem (PO:0009105) of an inflorescence axis (PO:0020122).
  • Current comment: None.
  • Revised comment: A higher order inflorescence axis is any inflorescence axis (PO:0020122) that develops from another inflorescence axis (PO:0020122), and is named according to its position in an inflorescence (PO:0009049). Tenth order inflorescence axis (PO:0025111) is the greatest specific inflorescence axis order in the PO; when mapping annotations to inflorescence axes which are of an order greater than ten, or when order is ambiguous or unknown, annotate directly to higher order inflorescence axis.
  • Current synonyms: conflorescencia (Spanish, exact), paraclade (exact), paraclado (Spanish, exact), 花序枝 (Japanese, exact), coflorescence (related)
  • Revised Synonyms: conflorescencia (Spanish, broad), 花序枝 (Japanese, related), inflorescence branch (exact), paraclade (broad), paraclado (Spanish, broad), coflorescence (related)


second order inflorescence axis (was: primary inflorescence branch) (PO:0006321)

  • Current def'n: An inflorescence branch (PO:0009081) arising from a first order inflorescence axis (PO:0025104).
    • Revised def'n: A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a first order inflorescence axis (PO:0025104).
  • Comment: None
    • Revised comment: No revisions
  • Current synonyms: first order inflorescence branch (exact), first order paraclade (exact), rama de la inflorescencia principal (Spanish, exact), second order inflorescence axis (exact), 第一（主）花序分枝 (Japanese, exact)
    • Revised synonyms: primary inflorescence branch (exact), first order inflorescence branch (exact), eje de segundo orden de la inflorescencia (Spanish, exact), 第一（主）花序分枝 (Japanese, related)



Monopodial inflorescence
Sympodial inflorescence
Revised Heirarchy

Year Three Goals

https://docs.google.com/document/d/10IsjeG8vew62apsM16J4YsoYI5IsBphPrT75CqOtDco/edit?usp=sharing

Upcoming Meetings and Workshops

Biocuration 2017, March 26-29, 2017

  • Stanford University, Palo Alto, California, United States
  • http://biocuration2017.org
  • Upcoming deadlines:
  • Abstract submission for poster ONLY February 17, 2017
  • Early conference registration February 17, 2017
  • Online conference registration March 10, 2017
    • 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.

2017 Gene Ontology Consortium Meeting, June 1-5th, 2017, Corvallis

  • Dates: June 1-5, 2017 (Details)
    • Arrive (May 31) View travel directions
    • GOC meeting (June 1-3)
    • Noctua gene annotation jamboree (June 4)
    • Reactome Pathway curation jamboree (June 5)
    • Depart (June 5 late evening / June 6 anytime)

Plant Biology 2017, June 24th-28th, Honolulu, Hawaii

  • Important deadlines:
  • April 30, 2017: Deadline for early-bird registration rates for Plant Biology 2017 and iMOSS 2017.
  • May 24, 2017: Deadline for submission of abstracts to be included in the online program book and to receive a poster number.
  • May 27, 2017: Deadline for discount hotel rates. (Please note: Our discounted room block may fill up long before this deadline.)
  • June 12, 2017: Final deadline for Plant Biology 2017 abstract submissions.
  • June 12, 2017: Deadline for standard registration rates for Plant Biology 2017 and iMOSS 2017.
  • June 24–28, 2017: Onsite registration during Plant Biology 2017!

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

  • Workshop proposal accepted-
  • T5-06:Ontologizing botanical knowledge (two sessions)
    • Organizer: Hong Cui (University of Arizona, USA)
    • James Macklin (Agriculture Agri-Food Canada, Canada)
    • Pankaj Jaiswal (Oregon State University, USA)
  • T5-18: Bioinformatics resources for comparative functional and phylogenetic analysis of plant genomes, pathways and diversity
    • Organizer: Pankaj Jaiswal (Oregon State University, USA)
    • Sushma Naithani (Oregon State University, USA)
  • Deadline for the abstract submission for oral presentations has been extended for 39 of the 212 general symposia where one or a few speaker slots are available
  • New deadline: February 15, 2017 for those 39 symposia and for posters only
  • Abstract submitted? Not yet


ICBO 2017, Sept 12th-15th, 2017

  • Newcastle, GB
  • http://icbo.buffalo.edu/
  • Important dates:
    • Mar 29, 2017: Workshops and tutorials proposals submission deadline
    • Apr 19, 2017: Notification of acceptance of workshops and tutorials
    • Jun 02, 2017: Paper and Poster Deadline
    • Jun 16, 2017: Paper Reviews Due
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