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
• 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)

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

• GO Meeting Corvallis
• Registration
• Travel plans

• 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