Ontology, gene

Description logic http //www.ida.liu.se/labs/ilslab/people/patla/DL/ 

Graph http //www.nist.gov/dads/HTML/graph.html 

Gruber http //www-ksl.stanford.edu/kst/what-is-an-ontology.html 

GXD http //www.informatics.jax.oig/searches/expression form.shtml 

Ontology projects http //www.cs.utexas.edu/users/mfkb/related.html 

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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... 

Gene Ontology Consortium. Gene Ontology tool for the unification of biology. Nature Genet 2000 25 25-29. 

In one study by Hood et al., 282 of 1153 identified proteins were identified by at least 2 unique tryptic peptides from FFPE prostate cancer (PCa) tissue.9 According to the gene ontology classification of the proteins identified, -65% of proteins were predicted to be intracellular proteins, while -50% of the total human proteome is predicted to be located in the intracellular compartment. Additionally, 20% of the proteins identified in the PCa tissue were classified as membrane proteins, which is significantly less than the predicted 40% for the human proteome. This relative disparity is not unexpected, considering the Liquid Tissue sample preparation kit lacks specific protocols for membrane protein extraction. The Liquid Tissue method has also been used for proteomics studies of a variety of FFPE tissue samples, including pancreatic tumors,28 squamous cell carcinoma,4 and oral human papillomavirus lesions.27... 

Figure 11.2 Gene Ontology assignments of the M. truncatula expressed sequence tags.

Neurodegeneration, microglial activation BV-2 microglial cells Lipopolysaccharide, HIV protein TAT, dopamine quinone Gene ontology analysis of common pathway response [28]... 

Epigenetic silencing, hepatic tumors 6 Hepatoma lines 5-AzaC Comparison of gene ontology for responses suggests common modulation of cellular functions in models [31]... 

II. KEGG Pathways and Ortholog Groups A. Gene Ontology... 

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. 

YuXetal (2006) A system-based approach to interpret dose- and time-dependent microarray data quantitative integration of gene ontology analysis for risk assessment. Toxicol Sci 92 560-577. doi kfjl84 (pii)10.1093/ toxsci/kfjl84... 

The Gene Ontology Consortium. Nucleic Acids Res. 2008, 36, D440-D444. 

GO. tools The Gene Ontology Tools for analysis of microarray data (http //www.geneon-tology.org/ GO. tools.microarray.shtml)... 

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