Mar 14th, 2017 Ontology Working Group Meeting

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

• Recordings:
  • File:Ontology WG meeting audio 3-14-17.m4a
  • File:Ontology WG meeting video 3-14-17.mp4

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)- all children of reproductive shoot apical meristem (PO:0008028) Note: this is to include gymnosperms.
  • ear meristem (PO:0009109)
  • inflorescence apical meristem (PO:0009108)
  • tassel meristem (PO:0009106)
  • inflorescence branch meristem (PO:0009105) [https://github.com/Planteome/plant-ontology/issues/437)- needs to be revised....probably will be a "higher order inflorescence axis apical meristem"

• • • PJ's point was that the upper branches in some mutants (eg. tfl1) do not arise in an axil and we need to distinguish between the meristem that gives rise to the higher level axes.
    • MLP: Cannot use "lateral" as that implies secondary growth.

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

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

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

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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
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