SDIWG: NCBC Scientific Ontologies

This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: Scientific Ontologies

Top page of ncbcs.org web site which is maintained by the NCBCs themselves

Top page of NCBC Working Groups web site

Contacts for this Working Group are Zak Kohane (isaac_kohane@harvard.edu), Suzi Lewis(suzi@fruitfly.org), and Mark Musen (musen@stanford.edu)

Mission Statement

The goal of the NCBC Scientific Ontologies working group has been a purposefully narrow and pragramatic one: to create a succinct categorization of ontologies and terminologies that are useful for the biomedical research community. We are cognizant that there are a multiplicity of user communities for ontologies and indeed these a growing rapidly. Many of these communities are not primarily interested in further development or refinement of ontologies but recognize the utility of such computable corpora of biomedical knowledge and wish to use them right now. This is our target audience. We are not representing this work as that of a standards organization nor of a prescriptive or authoritative body. Rather we have reviewed the ontologies that we, the members of the NCBC community, are using or intend to use shortly and have provide a rough-cut categorization. Simple as this task may seem, it has taken many telephone conference calls, a multi-hour meeting in Washington, DC and multiple emails and collective edits to arrive at this consensus. Frankly, we are pleased and even a little surprised at how successful we were in reaching a consensus view.

The current categorization of these ontologies (and note that we use this term intentionally loosely and it encompassed rather flat and unstructured terminologies as well) can be found at: courtesy of Suzi Lewis. There are three main categories:

• Category 1: Fully endorsed
• Category 2: Widely used and endorsed but there are some reservations among at least a subset of the users about the structure and/or function and/or useability of these ontologies.
• Category 3: Not quite ready for use but highly promising and efforts to develop these are strongly endorsed by the NCBC's.

Current Action Items

We are in the final processes of vetting the aforementioned categorization and we are also currently writing a manuscript describing this consensus result for submission for publication over the Summer of 2007

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Work to date

The following is history of the output from the Scientific Ontologies working group, with most recent at the top, and we welcome comments from the community

• Suzi Lewis Compilation of proposed ontologies and data standards selected for use by the NCBCs, as of February 2007. Additional information can be found in the Working Group Meeting Minutes 20070209

• Preliminary Results from Scientific Ontologies WG #1

• Proposal for common reference ontologies/vocabularies (The States 8)

• Commentary on States 8

• Need for (semi-)automated ontology mapping

• Comments from Bill Bug

• Comments_on_Imaging_and_Neuroinformatics_Ontologies

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Meetings of Relevance to Scientific Ontologies

• Past meetings

• Upcoming meetings:
  • The next meeting of the Scientific Ontologies Section of the SDIWG will take place on October 30-31, 2007 in Newark, NJ as part of a joint NCBO/MagNet workshop on Ontology and Cellular Networks.

• Highlights from Scientific Ontologies TCONs
  • Meeting Minutes 20070209
  • Meeting Minutes 20060601