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Organization Challenges for Building Biomedical Ontologies

Join Jennifer Clark as she discusses the challenges faced in building biomedical ontologies with insightful tips from Michael Ashburner and Suzanna Lewis in this talk. Discover steps to evaluate, improve, collaborate, and distribute ontologies effectively. Learn from experiences of established communities and committees in ontology development. Embrace the iterative process from proposal to public release, engaging in constructive criticism and feedback sessions. Embark on the journey to develop robust and user-centric ontologies for the scientific community.

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Organization Challenges for Building Biomedical Ontologies

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  1. Organization Challenges for Building Biomedical Ontologies Talk by Jennifer Clark, Slides by Michael Ashburner and Suzanna Lewis http://obo.sourceforge.net

  2. Due diligence & background research • Step 1: Learn what is out there • The most comprehensive list is on the OBO site. http://obo.sourceforge.net • Assess ontologies critically and realistically.

  3. Evaluating ontologies • What domain does it cover? • Is it active? • Is it applied?

  4. Ontologies must be shared • Proprietary ontologies • Belief that ownership of the terminology gives the owners a competitive edge • For example, Incyte or Monsanto in the past

  5. Pragmatic assessment of an ontology • Is there access to help, e.g.: help-me@weird.ontology.net ? • Does a warm body answer help mail within a ‘reasonable’ time—say 2 working days ?

  6. Where the rubber meets the road • Annotated data? • Publication of research that has used the ontology?

  7. Work with that community • To improve (if you found one) • To develop (if you did not) • How? Improve Collaborate and Learn

  8. A little sociology Experience from building the GO

  9. Community vs. Committee ? • Members of a committee represent themselves. • Committees design camels • Members of a community represent their community. • Communities design race horses

  10. Design for purpose - not in abstract • Who will use it? • If no one is interested, then go back to bed • What will they use it for? • Define the domain • Who will maintain it? • Be pragmatic and modest

  11. Start with a concrete proposal —not a blank slate. • But do not commit your ego to it. • Distribute to a small group you respect: • With a shared commitment. • With broad domain knowledge. • Who will engage in vigorous debate without engaging their egos (or, at least not too much). • Who will do concrete work.

  12. Step 1: • Alpha0: the first proposal - broad in breadth but shallow in depth. By one person with broad domain knowledge. • Distribute to a small group (<6). • Get together for two days and engage in vigorous discussion. Be open and frank. Argue, but do not be dogmatic. • Reiterate over a period of months. Do as much as possible face-to-face, rather than by phone/email. Meet for 2 days every 3 months or so.

  13. Step 2: • Distribute Alpha1 to your group. • All now test this Alpha1 in real life. • Do not worry that (at this stage) you do not have tools - hack it.

  14. GO flat file format <oocyte development ; GO:0048599 <oocyte construction ; GO:0007308 <oocyte axis determination ; GO:0007309 <oocyte anterior/posterior axis determination ; GO:0007314 %oocyte anterior/posterior axis determination (sensu <bicoid mRNA localization ; GO:0045450 <regulation of bicoid mRNA localization ; GO:0008359 %negative regulation of bicoid mRNA localization ; %positive regulation of bicoid mRNA localization ;

  15. Step 3: • Reconvene as a group for two days. • Share experiences from implementation: • Can your Alpha1 be implemented in a useful way ? • What are the conceptual problems ? • What are the structural problems ?

  16. Step 4: • Establish a mechanism for change. • Use CVS or Subversion. • Limit the number of editors with write permission (ideally to one person). • Release a Beta1. • Seriously implement Beta1 in real life. • Build the ontology in depth.

  17. Step 5: • After about 6 months reconvene and evaluate. • Is the ontology suited to its purpose ? • Is it, in practice, usable ? • Are we happy about its broad structure and content ?

  18. Step 6: • Go public. • Release ontology to community. • Release the products of its instantiation. • Invite broad community input and establish a mechanism for this (e.g. SourceForge).

  19. Step 7: • Proselytize. • Publish in a high profile journal. • Engage new user groups. • Emphasize openness. • Write a grant.

  20. The Jackson Labs, Bar Harbor, Maine, Oct 8, 1999

  21. Lawrence Berkeley National Laboratory, November 5, 2000

  22. The Jackson Labs, Bar Harbor, Maine, July 15, 2001

  23. Cold Spring Harbor Laboratory, New York, May 13, 2002

  24. The Institute for Genomic Research, Rockville, MD, June 3, 2003

  25. Atlantic Oaks, Bar Harbor, Maine, September 26, 2003

  26. Arrillaga Alumni Center, Stanford University, California, January 17, 2004

  27. Stanford University, Palo Alto, California, USA, June 1-4, 2005

  28. Step 8: Have fun!

  29. Contributors FlyBase Rat Genome Database DictyBase  WormBase GeneDB S. pombe Compugen Mouse Genome Database GeneDB for protozoa Genome Knowledge Base EBI GOA project TIGR Gramene The Arabidopsis Information Resource The Zebrafish Information Network Berkeley Drosophila Genome Project Saccharomyces Genome Database The Institute for Genomic Research The GO Editorial Office

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