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Resources

National Center for Biomedical Ontologies (NCBO, U.S.)

Related Metadata Standards/Initiatives

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Background

The NCBO, NCI/caBIG and NCRI all support the fundamental concept that the adoption of standards by the research community and the education of the community in their use are essential to both data sharing and interoperability. Each has come from a slightly different start point, but all agree that some consistency in the promotional approach will better serve the research community and avoid confusion in the messages sent out.

Issues

caBIG has adopted a vocabulary review process, based on published best practices (ref) to evaluate existing controlled vocabularies. caBIg wishes to promote these "Standard vocabularies" for use within software applications and services to enable "semantic interoperability": that is so users of the software services and data within can unambiguously determine what the services do and what the data is. The issue is that software developers typically do not know about the existence of these standard vocabularies (lack of advertisement) and if so, they do not know which vocabulary would be best for their particular use (lack of description of the vocabulary). Finally, if a developer wanted to use another vocabulary outside of these standards, s/he might be compelled to search thru hundreds of vocabularies to find one that fit her needs (lack of description) and was used and well received by others (lack of a rating system).

NCBO

The UK's NCRI Informatics Initiative's work focuses on the technical and cultural aspects of data sharing. One of the challenges from a technical point of view has been the vast diversity of resources in the UK and internationally. Many of these are excellent tools, but they have evolved separately and so present an incoherent fragmented landscape. To bring these resources together so they can be used effectively requires a community approach to identify a set of relevant data standards for each scientific area. The NCRI Informatics Initiative has started to address this through the development of the 'Cancer InfoMatrix' - an online tool for the visualisation and discovery of three types of data standards: vocabularies, exchange formats; and reporting guidelines as well as standards tools. These resources are categorised across a number of biomedical domains such as 'clinical trials', 'DNA', 'tissue' etc. The dilemma now facing the NCRI is how to promote a consistent set of 'core' recognised standards to the community in order to promote a coherent pattern of use of these 'core' standards. The NCRI, caBIG® and the NCBO are well placed to address this challenge. The NCRI would thus like to achieve consensus with and across caBIG® and NCBO in defining the way forward in promoting standards in order to facilitate international interoperability.

Goals - Philosophy and Purpose

From an outside perspective one could take the view that the:

Goals for the small working group would cover:

Technical -
All three organisations utilise LexEVS in some form.

Deliverables

  1. Description outlining the recommended way forward to represent metadata of the standards to users.
    1. how its done
    2. what elements are needed
      1. description (profile)?
      2. rating?
  2. Recommendation on the applicability of a Rating system, either
    1. Open Rating Systems - that is, public via the user community (for example, like amazon reviews?)
      1. Aggregation, distributed registries, shared metadata schema, rating the raters and reputation management (for example, KudoRank , Slashdot moderation system )

    2. Closed Rating Systems - that is, professional (for example, by NCRI, NCBO, caBIG?)
  3. possible "roadshow (demo) to possible end-users to test what we have so far (NCBO Bioportal and thoughts)
    1. see plan for RoadShow
    2. see feedback for Roadshow idea, questions form Domain WS facilitators (https://wiki.nci.nih.gov/x/dIIFB)

See Project plan

Results and Conclusions

Below list the accomplishments achieved:

Next Steps

Presentation

Meetings

Meeting Notes

List of caBIG Approved Terminologies

NCI Thesaurus
GO
LOINC
CTCAE 4.0
SNOMED CT
ICD 9-CM
ICD-10
RadLex
RxNorm
MedDRA

Participants

Stuart Bell, Brian Davis, Sherri De Coronado, Robert Freimuth, Alan Hogg, Richard Kiefer, Natasha Noy, Hua Min, Mark Musen, Michael Riben, Harold Solbrig, Grace Stafford, Stuart Turner, Larry Wright, Jyoti Pathak

References

  1. Open Rating Systems , R. Guha (IBM Research, Stanford University), 2001 - PDF
  2. Where to Publish and Find Ontologies: A Survey of Ontology Libraries Journal of Web Semantics (Pre-print)