Automated tools to help construction of Trait Ontologies

1. Automated tools to help construction of Trait Ontologies Chris Mungall Monarch Initiative http://monarchinitiative.org Gene Ontology Consortium http://geneontology.org Lawrence Berkeley National Laboratory PRO-PO-GO Workshop 2013

2. Trait Ontologies • What is a trait? • Working elucidation: attributes, not values • Existing Trait Ontologies: • TO – plant traits • Should really be called ‘PTO’ • VT – vertebrate traits • GO biological attribute ontology • Internal ontology used to provide logical definitions for terms like ‘regulation of blood pressure’, ‘regulation of synaptic plasticity’

3. Many terms in TOs can be trivially composed • Many follow ‘EA’ pattern • Entity (anatomical structure, chemical entity, …) • Attribute (subset of PATO) • Pre-vs-post composition? • Strictly speaking, from a logical perspective it doesn’t matter • BUT there are many practical advantages to pre-composition • Provided the right tools are used

4. Using TermGenie for traits • Scenario: • Annotator needs new trait term “cotyledon length” • Today please if possible! • Approach: • Go to termgenie.org, login • Selects • “cotyledon” as entity • “length” as attribute • TermGenie uses Elk reasoner • Checks not equivalent to existing class • Checks ‘satisfiability’ • Determines placement in hierarchy • TermGenie suggests text def and synonyms based on template

5. GO biological attribute TG instance • GO has been using TG for GO terms for >2 years • Recently created a new instance for biological attributes • To create new terms like ‘regulation of cell shape’ • TO and VT automatically pulled in • Use existing terms if available

6. Demo • http://purl.obolibrary.org/obo/to/termgenie • Examples: • ‘leaf size’ • ‘gynoecium size’ • ‘cotyledon size’

7. How does this work? • Requires OWL equivalence axioms • For plant TO, these currently live in trait_xp.obo file • Seeded using Obol, manually vetted and improved • Modeling patterns documentation: • http://obofoundry.org/wiki/index.php/PATO:XP_Best_Practice Integrating phenotype ontologies across multiple species CJ Mungall, GV Gkoutos, CL Smith, MA Haendel, SE Lewis, M Ashburner Genome Biology 11 (1), R2

8. Proposal: Combined trait ontology • Merge of existing TOs • Existing plant TO IDs can be ‘grandfathered’ in • Not taxon-restricted • Some cell component traits are shared across all kingdoms • Taxon subsets can be extracted automatically • Editors version is in OWL • Most term requests via TermGenie • Templated or freeform

9. Modeling issues • Best OWL model • Many pros and cons • Complex traits • Ratios • Integration with quantitative data

10. Integration with phenotypes ontologies • Phenotype ontologies • Terms can be thought of as ‘leaf nodes’ of TO terms (values) • Many phenotypes are complex (multiple traits) • Diverse species • FYPO – fission yeast • CPO – all species, cellular, automatically generated • MP – mouse • HP – human • WBbt – worm • FBcv – fly • Zebrafish – autogenerated from post-compositions

11. Combined Phenotype Ontologies • Examples • ‘UberPheno’ • Phenomenet combined ontology • Automatically generated using Uberon as bridging anatomy ontology

12. Summary • Automated tools can make the ontology development cycle more efficient • Problem: OWL environments hard for non-experts (and experts) • TermGenie provides a simple intuitive interface • Configurable • Merging trait efforts is a win-win