The Gene Ontology Project

Aligning with and leveraging external ontologiesThe Gene Ontology ProjectJane LomaxGO terms can be defined using terms from other ontologiesglycol metabolic process'metabolic process' and ('has participant' some glycol)

'metabolic process' and ('has participant' some glycol)

ChEBI'metabolic process' and ('has participant' some glycol)

GOchemicalscell typesanatomical structures DateTotal classesTerms with logical definitions%Mar 2012 346911048630%Mar 2013374581414438%Increase in the number of classes with logical definitions:

TermGenieOne of the bottlenecks we have is that all terms need to be added by a small group of ontology developers

To help ameliorate this, we have developed a system for adding new terms that conform to specific templates.

Called TermGenie because the prototype versions used to say your request has been granted9

http://go.termgenie.org/Users are given a login and choose a specific template.

They build the term they need based on existing terms. The term is placed in the ontology based on its logical constraints.

Users are given an id for their new term immediately.

Terms are given a final review by an expert curator and then deployed directly in to the ontology.

If its a bad term (unusual if it conforms to a template) its obsoleted in the usual way.10reasoninglessons from working with other ontologies 1. communicationRegular meetings, 132. differences can be very difficult to reconcilecf BioCHEBI143. both ontologies need to be responsiveor allow external editing e.g. CL15plants in GOAnatomy Tanya to comment16anatomy, cell types -> GO logical definitions?plant developmental stages -> happens_during?Wont be used in GO directly, but could make bridging axioms using happens_during, or possibly better captured at annotation stage.18growth and development in GOThese terms currently do not have logical definitions in GOWere hoping to work on these this year (meeting planned, but no funding), Virtual meeting?Once these are in place, will be much easier to make species-generic statements, identify common processes across animals/plants.19currently no logical defs in GOhigh-level terms species genericlogical definitions with anatomy ontologies