Gene Ontology annotations

Research into so-called ontologies is also currently very active. Ontologies can be used to characterize the principal concepts in a particular discipline and how they relate one to another. Many people believe they are necessary if database annotation is to be made accessible to both people and software, but also in facilitating more effective and efficient data retrieval. The well-known Gene Ontology consortium, or GO, defines the term ontology as ... specifications of a relational vocabulary . In other words they are sets of defined terms like the sort that you would find in a dictionary, but the terms are networked. The terms in a given vocabulary are likely to be restricted to... 

The GO (Gene Ontology) project provides a controlled vocabulary to describe gene and gene product attributes in any organism. Annotated are the biological process, the molecular function, and the cellular component of gene products. 

Dwight, S.S., Harris, M.A., Dolinski, K., Bell, C.A., Binkley, G., Christie, K.R., Fisk, D.G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., et al. 2002. Saccharomyces genome database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30, 69-72. 

The data are collected daily from a number of sources, including the National Center for Biotechnology Information (NCBI) and Gene Ontology (GO) Consortium. The warehouse includes sequences, structures, and complete genomes from Gen-Bank as well as annotation links such as NCBI taxon database terms, redundant sequences, sequence neighbors, conserved domains, Online Mendehan Inheritance in Man identifiers, GO terms, LocusLink identifiers, and PubMed links. 

Fig. 4.8 Protein family/disease ortholog view of the Drosophila protein-interaction map. Proteins are color-coded according to protein family as annotated by the Gene Ontology hierarchy. Proteins orthologous to human disease proteins have a jagged, starry border. Interactions were sorted ac-...

To estimate the number of genes expressing products that could be accessible to antibody therapeutics, we assume that proteins are required to be located in the extracellular matrix. We also assume that the extracellular location is the union of secreted and transmembrane sets of proteins. Where the extracellular location is known, this is often included in Swiss-Prot and gene ontology (GO) [37] database annotation for the protein. Secreted proteins can be predicted by the presence of a signal peptide whilst transmembrane... 

Modular analysis integrates the primary microarray analysis results and their functional annotations based on precompiled databases of pathways derived from large-scale literature analysis or computer-assisted annotation, such as Gene Ontology [39], KEGG [40], Biocarta (http //www.biocarta.com/), and GenMAPP [41]. 

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