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
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