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:
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 5 different taxa (flowering plants, gymnosperms, some of the ferns, selaginella, and isoetes). Those taxa don’t have a common ancestor.
- 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....
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
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
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 'grain weight' exist. How to harmonise that?
- use subClassOf instead of equivalentClass for the DP when narrow synonyms
- keep only 'fruit weight'. 'grain weight' will then become a synonym of 'fruit weight'
- keep 'fruit weight' in TO. 'grain weight' will then be in CO and imported in TO. The CO class 'grain weight' will use the same DP than 'fruit weight' + a taxon constraint. Related question: should all the CO class 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: [[2]] (avoid this if you have ocean sickness!). Feedback is welcome
Redirect from old Plant Ontology Site
- The old Plant Ontology PO site is not maintained anymore and is going into archive
- All AmiGO traffic on http://plantontology.org to has been redirected to http://browser.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
- 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
XIX International Botanical Congress, July 23-29, 2017, Shenzhen, China
Workshop proposal accepted