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
    • 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.
  • 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)
  • 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'
  • PJ: do we need a "lateral inflorescence meristem" which will be on the branches?? The inflorescence meristem (PO:0000230) could be on any higher order inflorescence axis.
  • Children of inflorescence meristem (PO:0000230) (and all their subclasses)
    • 'ear meristem'
    • 'inflorescence apical meristem'
    • 'inflorescence branch meristem'
    • 'tassel 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 (was: 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)

third order inflorescence axis (was: second order inflorescence branch) (PO:0006322)

  • Current def'n: An inflorescence branch (PO:0009081) arising from a second order inflorescence branch (PO:0006322).
    • Revised def'n: A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a second order inflorescence axis (PO:0006322).
  • Comment: None
    • Revised comment: No revisions
  • Current synonyms: rama de segundo orden de la inflorescencia (Spanish, exact), second order paraclade (exact), secondary inflorescence branch (exact), third order inflorescence axis (exact), 第二花序分枝 (Japanese, exact)
  • Revised synonyms: second order inflorescence branch (exact), eje de tercero orden de la inflorescencia (Spanish, exact), secondary inflorescence branch (exact), 第二花序分枝 (Japanese, related)

fourth order inflorescence axis (was: third order inflorescence branch (PO:0025105)

  • Current def'n: An inflorescence branch (PO:0009081) arising from a third order inflorescence branch (PO:0025105).
    • Revised def'n: A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a third order inflorescence axis (PO:0025105).
  • Comment: None
    • Revised comment: No revisions
  • Current synonyms: fourth order inflorescence axis (exact), rama de tercer orden de la inflorescencia (Spanish, exact), tertiary inflorescence branch (exact), third order paraclade (exact), 第三花序分枝 (Japanese, exact)
    • Revised synonyms: third order inflorescence branch (exact), eje de cuarto orden de la inflorescencia (Spanish, exact), tertiary inflorescence branch (exact), 第三花序分枝 (Japanese, related)

fifth order inflorescence axis (PO:0025106) through ninth order inflorescence axis (PO:0025110)

  • All follow the same pattern

tenth order inflorescence axis (was: ninth or higher order inflorescence branch) (PO:0025111)

  • Current def'n: An inflorescence branch (PO:0009081) arising from a eighth order inflorescence branch (PO:0025110) or higher.
    • Revised def'n: A higher order inflorescence axis (PO:0009081) that develops from an inflorescence axillary meristem (PO:0009105) of a ninth order inflorescence axis (PO:0025110).
  • Current comment: None
    • Revised comment: 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 (PO:0009081).
  • Current synonyms: noveno orden o superior rama de la inflorescencia (Spanish, exact), tenth or higher order inflorescence axis (exact), 第九花序分枝 (Japanese, exact)
    • Revised synonyms: ninth order inflorescence branch (exact), eje de décimo orden de la inflorescencia (Spanish, exact), 第九花序分枝 (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:
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  • 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:
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  • May 24, 2017: Deadline for submission of abstracts to be included in the online program book and to receive a poster number.
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  • 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
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