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:

http://obo.sourceforge.net/

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:

http://obo.sourceforge.net/

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