Indexing Nano Medicine Resources with caOBR

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ABSTRACT:

caOBR has been developed to provide an interface between caBIG cancer informatics resources and the NCBO ontology-based annotation tools.   In the past, caGRID resources have not been accessible for annotating and indexing data using the NCBO Annotator/resource tools.  This has posed a problem for annotating caNanoLab data using NPO or other relevant ontologies.  At the same time, the caBIG community can benefit from access to OBR annotations from data resources relevant to cancer research (eg., MICAD) but are outside of the caBIG resource. Therefore, we have developed a middleware software tool called caOBR that 1) provides BioPortal NCBO Resource Index access to caGRID resources for annotating data in caGRID resources, and 2) provides caGRID access to the OBRs to access OBR annotations.  In both cases, the caOBR offers the ability to annotate and search a wide range of biomedical data resources with a large number of ontologies. 

Our initial development work on caOBR has focused on the caNanoLab caGrid resource and the NanoParticle Ontology. caOBR uses the NCBO Annotator workflow to make caNanoLab to be accessible through the NCBO Resource Index.  This has enabled the annotation and indexing of caNanoLab data using NPO.  The caOBR has enhanced the use of caNanoLab in several ways.  First, semantic integration and searching of data is now feasible by data annotation with ontology terms.  Second, caNanoLab data is now accessible by semantically-enabled tools and for searching and analyses outside caGRID.  Finally, the problem of synonymy can be addressed through the availability of semantically-aware searching of the caNanoLab resource.  Synonymy is a problem for any interdisciplinary field, such as nanomedicine, where different terms are used by researchers from different backgrounds for the same concept.  Semantically-aware search resources such as caOBR resolves this problem by implicitly incorporating synonyms into the annotation and search of the data.


05/12/2010