Resource Index

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Indexing biomedical resources with ontology concepts


Presentation & Demonstration

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval.

Using the annotation workflow of the Annotator Web Service NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The NCBO Resource Index is directly queriable in the BioPortal ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.

In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: ArrayExpress, Clinical, GoldMiner, Gene Expression Omnibus (GEO) and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations.

NCBO Resource Index workflow
NCBO Resource Index creation

Please try the NCBO Resource Index in BioPortal.


  • For questions or feature requests, contact Support


  • Resource index design and underlying data model (see the bottom image on the right)
    NCBO Resource Index data model
  • Populating_OBS_database - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.


  • Clement Jonquet, Mark A. Musen and Nigam H. Shah, A System for Ontology-Based Annotation of Biomedical Data, In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08, Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. conference's web site pdf - 431Kb
  • Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, Ontology-driven Indexing of Public Datasets for Translational Bioinformatics, BMC Bioinformatics, Vol. 10, February 2009. journal's web site pdf - 651 Kb

Versions (prototypes & releases)

  • December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.

Collaboration & Acknowledgment

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