Mar 1st, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday Mar. 1st, 2016
• Time: 8:15am PST (GMT-8)
• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789

• Links to recordings:
• Attendees:

Agenda:

1. Recent updates on the TO

• revisions to equivalence axioms- occurs_in and composition
• Stem and culm
• anther morphology traits, incl. anther number
• biochemical branch

2. Changes and updates in the CO files

• rice
• cassava
• lentil

• newly mapped and added- wheat--- TBA

3. Update on AmiGO APIs- Justin Elser

• API code changes have been merged into our version of AmiGO (dev.planteome.org)
• Does not work on browser.planteome.org as it will require a reload of all data to work because of a schema change to SOLR
• Small issue with main readme page not showing up, but the API itself is working
  • ie. http://dev.planteome.org/api doesn't work
  • http://dev.planteome.org/api/entity/term/GO:0022008 works and returns JSON

• Still testing out speed and working on readme page not working

4. Visit to IRRI

• Leo, Marie-Angelique and Austin will visit IRRI Monday March 7th to Friday March 11th
• Goals: TD revision and data annotation-
  • MAL, and Leo will be working on trait dictionary
  • AM: annotate 140K+ germplasm entries with PD and TO mapping data

Discussion from email:

• EA- the need for an annotation tool: "We discussed the visit of Marie, Léo and Austin and the agenda we prepared. I indicated Mau that the team would like to see how IRRI data annotations could go on Planteome. Mau asked where Planteome stands with the annotations tools because this what IRRI is waiting for long. Would you have any points you want the team to share with IRRI on that aspect?"
• MAL/LV: "We need a simple tool that scientists will be able to use to easily annotate their data. Adhoc scripts are short term and one-shot solutions that will serve Planteome but not necessarily serve IRRI because: The GAF2 format that amiGO2 requires is not known by the breeding community and the annotated data will be published on Planteome and not in the IRRI information systems. We should take the opportunity of being at IRRI to provide some guidance on how to include the ontologies in their data model. Annotating the data at the source is beneficial for everyone. IRRI information systems will have interoperable and discoverable data. And Planteome can easily add future annotations from the IRRI systems."

5. Phenotype RCN meeting February 26-28, 2016

• PJ attended

6. Status of second year funding

• Bioversity is getting impatient, PJ will follow up with NSF and find out

Upcoming Meetings and Workshops

Biocuration 2016, April 10th-14th,2016; Geneva, Switzerland

• MAL is going
  • key dates
  • Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703

GARNet/Egenis Workshop: Integrating Large Data into Plant Science, April 21st-22nd 2016, Dartington Hall, Totnes, Devon

• Elizabeth and George are going, EA will present Planteome as part of her talk

BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida

• Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
  • Short papers, up to 4 pages (will be published in JBMS)
  • Poster abstracts, up to 1 page
  • Flash updates, up to 1 page

7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR

• Link to program: ICBO + BioCreative Program
• Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589