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: LC, AM, PJ, BS, LS, JE, CM

• File:Ontology Zoom Meeting 4-26-15 audio only.m4a
• File:Ontology Zoom Meeting 4-26-15 video.mp4

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.
  • works with Helen Parkinson and Paul kersey

• 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. (see below)

• Follow ups:
  • Everything should be under Creative Commons licensing, so all that's required for use is a 'thank you' on the web page where Planteome data is used
  • PJ would like to set up a meeting with some of the possible collaborators

Talks of Interest:

• Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

• Why the world needs phenopacketeers, and how to be one Melissa Haendel- see below

• 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

PhenoPackets:

• https://github.com/phenopackets - Chris Mungall
  • A 'glorified GAF' that will allow for more complex capture of information
  • Generic format to describe phenotypes
  • Jasn/YAML format; uses a phenotype ontology ID, can be combined with other ontology terms to specify other aspects
  • API's available for Java and Python
• Integrates environmental aspects

• AgroVoc - something that might be useful for PSO relationships and interactions
• GACS - AgroVoc plus NATL and CABT
  • less complex
  • includes AgroVoc

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:
  • PhenoHarmonIS_List-of-participants

• Link to the agenda:
  • PhenoHarmonIS Agenda
  • agenda still in flux, should be more final by end of the week.

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

Link to Google doc: Number_of Traits

Number_of Traits

General format: (OBO file stanza)

• intersection_of: PATO:0001555 ! has number of
• intersection_of: inheres_in PO:0000XYZ ! plant part being counted
• intersection_of: occurs_in PO:0025025 ! root system- this is for the part of the plant which has the multiple parts, could also be ‘whole plant’

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
• Currently only relationships that pass annotations are displayed:
  • is_a, part_of
  • occurs_in
  • regulates- for the GO terms- why would annotation pass through these?

• Compare to GO version: http://tomodachi.berkeleybop.org/amigo/landing

• Issues of the relations and some things showing up in weird places
  • need to check if they are coming from an inference- look at the planteome.owl file

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:

http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

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