Automatic functional annotation of predicted active sites - European ...

Clearly, the annotation for a whole protein cannot be transferred to residue site annotation,
because different groups of residues in the protein structure have different function.
In this respect, the biological community is missing an information extraction system for
the annotation of proteins at residue level.
2.1.3 Gene Ontology
The Gene Ontology (GO) [AL02] [GOC06] is one of the most widely used functional
classification scheme including all of the most important criteria for annotations of biological
data [PKS06]. Currently, the ontology lists a total of 26,302 terms with 15,643
biological process terms, 2,233 cellular component terms, and 8,426 molecular function
terms (version November 2008). The UniProtKB/InterPro group at the European Bioinformatics
Institute (EBI) belongs to the Gene Ontology Consortium, and use its standard
vocabulary to the annotation of protein function. The vocabulary is meant to describe
biological phenomenology of genes and gene products (proteins). This is the reason why
terminologies in GO are not suitable to describe the function and property of a protein
residue. Figure 2.4 lists some examples where the identification of GO terms [GJYLRS08]
did not find the more relevant keywords for the annotation of residues. At the moment,
an ontology dedicated solely for the functional annotation of protein residues has not been
developed. However, terminologies can be in general collected from other considerable resources,
such as the Open Biomedical Ontologies [SAR + 07] which contains, for example,
REX (an ontology of physico-chemical processes), and PSI-MOD (an ontology describing
protein chemical modifications).
2.1.4 Biomedical literature
Biomedical research tackles biological questions from a number of perspectives and the
published experimental data are always heterogeneous. The sum of description of biological
phenomenon enables scientists to understand mechanisms in biology within various
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