Oct 25th, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday Oct 25th, 2016
• Time: 8:15am PDT (GMT-7)
• Connection details: https://zoom.us/j/639256485
• Attendees: DWS, BtSinn, DC, LC, MAL, AM, PJ, CM

• Regrets: BS

• Recordings:
  • File:Ontology Working Group meeting-video 10-25-2016.mp4
  • File:Ontology Working Group meeting-audio 10-25-2016.m4a

spine root terms for PO

• Added two new terms to describe spines formed on roots:

• shoot-borne root spine (PO:0030089): A shoot-borne root (PO:0000042) that is sclerified, pointed, and lacks indeterminate growth and nutritive function.

• lateral root spine (PO:0030088): A lateral root (PO:0020121) that is sclerified, pointed, and lacks indeterminate growth and nutritive function.

Comments: remove "indeterminate growth" and 'nutritive function' from the def'n of 'root' term" because the root spines do not grow indeterminate manner. and Some roots don't serve this function-- eg palm tree brace roots

Revisions to lenticel (PO:0000031) and new term for lenticel like structure on root tubers

• Propose slightly revised def'n:

lenticel (PO:0000031): A portion of the shoot axis periderm (PO:0005048) characterized by the presence of intercellular spaces between the cells of the phellem (PO:0004003) and phelloderm (PO:0005050)

• put in comment: produced by the cork cambium (PO:0005599)

the "lenticels" look similar in potatoes and sweet potatoes, but they arise from a different structure. This leads to confusion. Has been moved to shoot-axis periderm (for the true stem lenticels). Roots have proto-zylem (star shape) - lateral roots arise opposite these protozylem poles.

• root lenticels will be called 'root periderm scars'
• PJ - add a comment on the lenticel term to improve the understanding of the difference in function of each. Also add broad synonym "root lenticel" to the new periderm scars

root periderm scar- new

• Proposed:
  • root periderm scar (PO:new): A portion of root periderm (PO:0005047) formed in response to a disruption of the root epidermis (PO:0006036). source: (Artschwager, 1931; Evert, 2006)

• Comment: Root periderm scars are lenticel-like structures on the tuberous roots (PO:0025523) and tuberous root tuber (PO:0025476) of sweet potato, parsnips, and carrots. Disruption of the epidermis by the emergence of a lateral roots initiates a wound response that results in the production of a root periderm scar.

Addition of fruit subclasses

• After Oct 11th meeting, we decided to add the specifc types of fruits to the PO
• Brandon and Dario have a working set- see: Provisional fruit Hierarchy

• The goal is to create a framenwork that can be easily added to. (drupe-let, and other *-lets will go in as synonyms). The community has a lot of different opinions on the names of fruits.

• Would be great to have line art/pictures of the different fruit types

• We will give DWS et al, access to modify pages on the planteome site, can put a picture of the structure on the page, with a link to the Amigo page for those terms. Will start with the fruit terms.
  • Question- how can we link from the term page?

"Ghost seeds"

• How to create a terms to annotate the seed where the embryo has been removed?
  • microdissections add novel terms (eg: remove embryo from the seed, what do you call the remaining part? "ghost")

• should we be concentrating on things that actually exist? These artificial structures might be a slippery slope
  • PJ -counter argument - plant biology is drifting towards more artificial biology (think about mutants)
  • CM - you can make a one-of term that contains the remaining terms, and that it is derived_from seed. Make sure to tag them appropriately

New Taxon constraints added to PO

• Prototype taxon constraints have been added to the Plant Ontology
• This will be an area where the botanical expertise of the NYBG group will be very helpful

• Currently:
  • whole plant (PO:0000003): only_in_taxon NCBITaxon:33090 Viridiplantae {source="cjm"}
  • plant ovary (PO:0000004): only_in_taxon NCBITaxon:3398 Magnoliophyta {source="GO:0035670"}
  • microspore (PO:0020048):

• microspores are present in at least 5 different taxa (flowering plants, gymnosperms, some of the ferns, selaginella, and isoetes). Those taxa don’t have a common ancestor.
  • DWS: Only, Marsilea, Regnellidium, Pilularia, Azolla, and Salvinia in the ferns. A monophyletic group comprised of two families, Marsiliaceae (the first three genera) and Salvinaceae (the last two genera).

How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways:

• In GO they name taxon unions (CM: but these are a real pain)
  • id: GO:0009766
  • name: primary charge separation
  • namespace: biological_process
  • def: "In the photosynthetic reaction centers, primary charge separation is initiated by the excitation of a molecule followed by the transfer of an electron to an electron acceptor molecule following energy transfer from light harvesting complexes." [ISBN:0792361431]
  • is_a: GO:0022904 ! respiratory electron transport chain
  • relationship: only_in_taxon NCBITaxon_Union:0000007 {id="GOTAX:0000169"} ! Viridiplantae or Bacteria or Euglenozoa
  • relationship: part_of GO:0019684 ! photosynthesis, light reaction

• The other was is to use "X only_in_taxon (Y OR Z)", but this needs to be tested....

• BS Suggestion from 10-11-16: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation

• Possible solutions: Use the GO union classes (see: http://purl.obolibrary.org/obo/go/extensions/go-taxon-groupings.owl)
  • http://geneontology.org/ontology/extensions/go-taxon-groupings/

• Or use weaker "present_in", or negative relations like "never_in"
  • For microspores, use a term for "heterosporous plants"- is it in NCBI? Doubtful
  • Make our own taxonomy??? Not a good alternative
  • Taxonomies change frequently

Suggest adding a new relation between the morphology trait and a quality trait

- tabled for next meeting - see notes on Oct 11th

Upcoming Meetings and Workshops

IC-FOODS Conference November 7-9, 2016 Davis, California

• http://www.ic-foods.org/conference
• Matthew Lange is organizing
• BS cannot attend, will be at ISO meeting in Europe
• MAL and PJ will attend

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 is October 28, 2016

Phenome 2017, Feb 10th to 14th, 2017

http://www.phenome2017.org/#homepage

• DWS will attend- evo devo presentation
• CM will attend and present Planteome and pheno-BLASTing
• If you would like to be considered for a talk please submit your abstract by November 1, 2016
• early bird registrations till Nov. 15th- 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/