Open Biomedical Ontologies

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Oct 22, 2013 (3 years and 11 months ago)

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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