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Open Biomedical Ontologies (OBO): Uniting Biological Sciences

Explore the OBO project, a repository with standardized ontologies for biology and medicine. Learn why OBO is essential for data integration, alignment, and error detection. Follow OBO requirements to contribute and benefit from shared ontologies.

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Open Biomedical Ontologies (OBO): Uniting Biological Sciences

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  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

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