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 Haendel (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

• SKOS vocabulary
• something that might be useful for PSO relationships and interactions; 1370 is_Pathogen_Of links
• CM has been experimenting with aligning it to our ontologies; interested to convert it to OWL version using OBO conventions
• See: https://github.com/cmungall/agrovoc-obo
• Looks like Cyril is involved, I'm aware of his work on GMOD/Chado: https://rd-alliance.org/groups/agrisemantics-wg.html

• Marie, is there a repository for GACS? Are you involved in any of the mapping work? Found this: http://tester-os-kktest.lib.helsinki.fi/gacsdemo/en/
  • Mentioned in these slides: http://www.slideshare.net/CIARD_AIMS/from-gacs-to-agrisemantics-steps-forward-towards-interoperability-of-data-for-agriculture-and-nutrition-by-caterina-caracciolo; Lots of common interest, e.g. slide 10
  • It seems agrisemantics is one step beyond GACS, but having difficulties finding anything concrete - is it at the early stages?
  • is GACS intended as an uberon or PO/TO life effort that serves as a reference unifying multiple sources?
• I'm not completely sure it's an improvement, e.g. spikelet in GACS: http://tester-os-kktest.lib.helsinki.fi/gacsdemo/agrovoc/en/page/c_7301 vs. spikelet in AGROVOC: http://aims.fao.org/skosmos/agrovoc/en/page/c_7301; As you can see the AGROVOC one is richer as it has partOf relationships, etc
• Of course, both could import PO in this particular case, but keeping their own language translations. Hopefully the PhenoHarmonIS meeting will be the first step in the OBO and FAO etc communities learning from each other

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: TO Issues: 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’

Example: leaf number (TO:0000241)

• def: "A leaf morphology trait (TO:0000748) which is the number of leaves in a plant at a particular growth stage."

is_a: TO:0000748 ! leaf morphology trait intersection_of: PATO:0001555 ! has number of intersection_of: inheres_in PO:0025034 ! leaf

• Revised def’n: A shoot system morphology trait (TO:0000077) which is the number of leaves (PO:0025034) in a shoot system (PO:0009006) of a plant.

• 'has number of' and ('inheres_in' some 'leaf') occurs_in PO:0009006 ! shoot system

Or should this be whole plant????

Comments:

• CM: prefers simpler definition, not G-D format?
• BS thinks it is OK
• Compare with OBA, use YAML
• Look at example from the Planteome workshop- ????

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: Did not get a chance to cover today

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