CaBIG

The National Cancer Institute of the U.S. National Institutes of Health has undertaken construction of comprehensive cancer informatics infrastructure, the cancer Biomedical Informatics Grid (caBIG). caBIG includes data, vocabulary, standards, software infrastructure, and applications. Although the intial focus of this effort is on cancer, much of the infrastructure is generally useful in the biomedical sciences.

caBIG data currently include the Gene Expression Data Portal (GEDP34), Cancer Gene Anatomy Project (CGAP35-38), the Cancer Molecular Anatomy Project (CMAP39), and the cancer Model Organisms Databases (caMOD40). These resources integrate data describing the molecular anatomic changes that accompany tranformation of a cell from normal to cancerous. Users can approach these data from the perspective of microarray experiments, genes, tissues, pathways, chromosomes, cancer targets, targeted agents, trials, or cancer models.

The NCI Enterprise Vocabulary Service (EVS41) provides cancer-specific vocabulary in the context of mature vocabulary resources such as National Library of Medicine's Unified Medical Language System (UMLS42-46). EVS includes the NCI Thesaurus47 and the NCI Metathesaurus.48 The NCI Thesaurus provides a graph that can be browsed to find NCI Thesaurus concepts. Concept pages contain technical definitions, synonyms, more general concepts that include the current concept, and relationships to other concepts. For example, browsing from the top level to "Gene," to "DNA Repair Gene," and finally to "OGG1" yields the OGG1 concept entry. Browsing the entry reveals that OGG1 is a gene that encodes a protein that incises DNA at 8-oxoguanine residues, that it is also known as "8-Oxoguanine DNA Glycosylase," that it is included within the concept "DNA Repair Gene," and that it exhibits the "Gene_Found_In_Organism" relationship with the concept "Human." The power of such a vocabulary is not in such manual browsing, however, but in computer inference. A cancer researcher might be interested in finding human genes involved in DNA repair. The NCI Thesaurus would allow a computer to infer, for example, that something pertaining to OGG1, such as a gene expression level, also pertains to "DNA Repair Enzymes," or to include "OGG1" in a response to the question "Which DNA repair genes are found in humans?"

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