Apr. 26th, 2016 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Apr. 26th, 2016
  • Time: 8:15am PDT (GMT-7)
  • attendees: LC, AM, PJ, BS, LS, JE, CM

Agenda

1. Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland

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:

  • Why the world needs phenopacketeers, and how to be one Melissa Haendel- see below
  • LEGO: expressing complex biological models using the Gene Ontology
  • 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

2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016

  • LC, AM will go from OSU
  • 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

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:

  • 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?
  • 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

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