Open Biomedical Ontologies

1. Open Biomedical Ontologies

2. 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/

3. 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

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

5. 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

6. 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

7. 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

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

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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

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

19. What’s available • demo: http://obo.sourceforge.net/

20. 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