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
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’
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
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
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
Demo
• http://purl.obolibrary.org/obo/to/termgenie
• Examples:
– ‘leaf size’
– ‘gynoecium size’
– ‘cotyledon size’
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
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
Modeling issues
• Best OWL model
– Many pros and cons
• Complex traits
– Ratios
• Integration with quantitative data
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
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FYPO – fission yeast
CPO – all species, cellular, automatically generated
MP – mouse
HP – human
WBbt – worm
FBcv – fly
Zebrafish – autogenerated from post-compositions
Combined Phenotype
Ontologies
• Examples
– ‘UberPheno’
– Phenomenet combined ontology
• Automatically generated using Uberon
as bridging anatomy ontology
Summary
• Automated tools can make the
ontology development cycle more
efficient
– Problem: OWL environments hard for nonexperts (and experts)
– TermGenie provides a simple intuitive
interface
• Configurable
• Merging trait efforts is a win-win