Open Biomedical Ontologies

Open Biomedical Ontologies (OBO) An umbrella project for grouping different ontologies in biological/medical field –a repository for ontologies with defined set of standards Available from a single source:

Why do we need OBO? GO covers three domains of biology: –molecular function of a protein –biological function of a protein –cellular location of a protein

Why do we need OBO? Lots of other aspects could also be annotated, e.g.: –phenotype –anatomy –genomic –taxonomy

Why do we need OBO? Other groups outside of GO developed own ontologies for their own use –e.g. anatomies for specific organisms No standardisation of ontologies with respect to: –format –scope –relationships No way of knowing whether such ontologies already exist No mechanism of distribution for other groups

Why do we need OBO? Creating ontologies takes a lot of work –Makes sense to reuse existing ontologies where possible Improves data integration where small set of ontologies used Allows ontologies to be made available from a single place

Why do we need OBO? In addition, GO also contains other ‘implicit’ ontologies: –anatomies e.g. eye development –chemical e.g. silicone metabolism –cell type e.g. erythrocyte differentiation

Why do we need OBO? Useful to have the implicit ontologies –can be ‘aligned’ with GO –Helps highlight errors –For reasoning (advanced GO!)

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint

OBO requirements: open Ontologies can be used by anyone without any constraints, except: –original authors are acknowledged –cannot be edited and then released under same name

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint Be in a common shared syntax

OBO requirements: syntax Usually the OBO format, same as primary GO format –and adaptions of OBO format Also accept OWL (Web Ontology Language) format Allows the same tools to be applied, facilitating shared software implementations

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint Be in a common shared syntax Not overlap with other ontologies in OBO

OBO requirements: overlapping Ontologies can overlap partially, but large overlap should be avoided Idea is that terms from different ontologies can be combined to form new terms Striving for accepted standards rather than competition

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint Be in a common shared syntax Not overlap with other ontologies in OBO Share a unique identifier space

OBO requirements: id space So, for example, the GO identifier is GO: –No other OBO ontology could use this id space Prevents problems where ontologies are used together

OBO requirements To be part of OBO, ontologies must: Be open, can be used by all without any constraint Be in a common shared syntax Not overlap with other ontologies in OBO Share a unique identifier space Include text definitions of their terms

OBO requirements In addition, OBO includes ontology of relationships –all ontologies should use these definitions of relationships For example –part_of –develops_from –regulates

What’s available demo:

How you might use OBO Extra annotation –developmental timelines –taxonomy –pheontype Create your own ontologies and submit to OBO –e.g. anatomy of your organism