Apr. 26th, 2016 Ontology Working Group Meeting
Planteome Ontology WG Zoom Meeting
- Date: Tuesday Apr. 26th, 2016
- Time: 8:15am PDT (GMT-7)
- Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950
- attendees:
Agenda
1. Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL attended and presented a talk
- Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
- Feedback on the presentation?
- question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
- Potential collaborators
- Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
- KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
- Sebastien Briois (Syngenta): was interested in using Planteome data.
- Melissa Haedel (OHSU): phenopackets to annotate the breeders data.
- Feedback on the presentation?
Talks of Interest:
- Why the world needs phenopacketeers, and how to be one Melissa Haendel
- PhenoPackets: https://github.com/phenopackets- Chris Mungall
- Noctua: http://noctua.berkeleybop.org/
- LEGO: expressing complex biological models using the Gene Ontology
- Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full
- Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine
2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016
- Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
- http://tinyurl.com/hzsho6v
- LC, AM will go from OSU
- About 70+ Participants are signed up:
- Link to the agenda:
Planteome Presentations:
- Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
- Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
- Monday Poster presentation: (~5pm to 7pm)
- Tuesday morning: Austin (10 min + questions): Detailed 10-mn presentations on systems using selected tools for annotations and understanding of the opportunities and bottlenecks Followed by questions
- Tuesday afternoon : Hands on Trait Dictionaries: includes validation of mappings CO -TO MAL. Groups: Tree species, CWR, Barley, Cacao, Wheat, Rice, Potato, Sweet Potato
- Wednesday morning: FOCUS ON TRAIT - Intra and interspecies Trait Harmonization Mapping techniques MAL (10 min)
- Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL
3. ICBO 2016 Call for Papers is open
- ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission
http://icbo.cgrb.oregonstate.edu/ICBO_submission
Deadline is May 5th
Proposed Topics, with suggested lead:
- Planteome paper- LC
- Mappings- MAL
- Annotations project on rice, cassava and lentil, etc - AM
Formats:
- Extended Abstract- up to 2 pages
- Short Papers- up to 4 pages
- Full Papers- up to 6 pages
https://easychair.org/conferences/?conf=icbo2016
Papers will be published in a book of proceedings, not in a journal
4. Plant Trait Ontology updates
- Recent revisions and changes to the equivalence axioms etc
- Plans to do release
More details TBA:
5. AmiGO2 Update:
- New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org
- You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse
- GO version: http://tomodachi.berkeleybop.org/amigo/landing
- Issues of the relations and some things showing up in weird places
- Significant changes:
- Actual browser functionality
- Neighborhood tab (was ancestors and children)
- All relations will be displayed..?????
- annotations by species
Other Items
Tabled from previous meetings:
OBA development- Chris Mungall
- CM: If there is time I would like to walk through the procedure we use to develop OBA.
- Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples
- For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules
- The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns
- Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
Upcoming Meetings and Workshops
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
Meeting in Montpellier, 9-13 May 2016
Link to tentative agenda/website: [1]
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