Oct 11th, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday Oct 11th, 2016
• Time: 8:15am PDT (GMT-7)
• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/620296847

• Attendees:
• Regrets: PJ, DWS, EA

Recordings:

Agenda

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....

• Suggestion: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation

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

Many of these are currently is_a children resulting in dual parentage, we also have some that are part_of, but this is technically not correct

e.g. pericarp texture (TO:0002623):

• is_a pericarp morphology trait (TO:0000945)
• is_a fruit quality trait (TO:0002728)

Harmonization between TO and PO

• The PO defines classes with sometimes a lot of synonyms (broad and narrow)
  • e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001)

• In TO, the classes 'fruit weight' and 'kernel weight' exist. How to harmonize that?

• Options:

1. Add the fruit types to the PO as separate terms
2. Keep only 'fruit weight' in the TO, and then 'kernel weight' will become a synonym of 'fruit weight'
3. Keep 'fruit weight' in the TO and move 'kernel weight' to appropriate the Crop Ontologies and then these can be imported in TO. The CO class 'kernel weight' will use the same design pattern as 'fruit weight' with a taxon constraint.
4. Use the fields: subClassOf instead of equivalentClass for the design pattern (DP) when narrow synonyms

• Related question: should all the CO classes have a taxon constraint? Or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?

CO mappings

• Eight crops have been mapped to TO so far: lentil, cassava, wheat and rice are part of the current Planteome release 1.0
• New crops added: sweet potato, maize, soybean and pigeonpea

• Statistics are available here: [[1]]

• Attempt of a visualization: CO-TO mappings image (avoid this if you have ocean sickness!). Feedback is welcome
  • Suggest removing the nodes which have no mappings to clean it up and make it simpler to view

Redirect from old Plant Ontology Site

• The old Plant Ontology PO site is not maintained anymore and is going into archive
• All traffic on http://plantontology.org to has been redirected to http://planteome.org
• The main drupal site has been renamed http://archive.plantontology.org/ including the Amigo browser, so you can still visit it
• For updates, follow http://planteome.org

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

Biocuration 2017, March 23-26, 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