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106 5 Survey of Ontologies in Bioinformatics MML The Medical Markup Language provides the XML-based standard for medi- cal data ...

5.3 Macromolecular Sequence Databases 107 5.3.1 Nucleotide Sequence Databases GenBank http://www.ncbi.nlm.nih.gov/Genbank GenBan ...

108 5 Survey of Ontologies in Bioinformatics et al. 2004). It is available in several formats, including FASTA and XML. The XML ...

5.4 Structural Databases 109 contacts, is calculated and stored in the database. Database entries are fur- ther annotated to inc ...

110 5 Survey of Ontologies in Bioinformatics tools in sequence analysis. PROSITE was developed in 1988 to systemati- cally colle ...

5.4 Structural Databases 111 formats are non-XML text formats. COG http://www.ncbi.nlm.nih.gov/COG The database of clusters of o ...

112 5 Survey of Ontologies in Bioinformatics more flexible and less stable than those in a crystal. Indeed, solution struc- ture ...

5.4 Structural Databases 113 ficient sequence search protocols and reliable thresholds. The database is available as a collectio ...

114 5 Survey of Ontologies in Bioinformatics MIPS mips.gsf.de The Munich Information Center for Protein Sequences provides prote ...

5.5 Transcription Factor Databases 115 Provide human protein interaction data precomputed from existing struc- tural and experi ...

116 5 Survey of Ontologies in Bioinformatics information on 1167 genes, 5537 transcription factor binding sites, 1714 reg- ulato ...

5.6 Species-Specific Databases 117 genes and proteins of this yeast from the scientific literature, and presents this informatio ...

118 5 Survey of Ontologies in Bioinformatics clues regarding gene location, phenotype, and function. Synteny maps are built base ...

5.8 Gene Expression Databases 119 ing, an XML-encoded file is then built that is entered into the database via an HTML submissio ...

120 5 Survey of Ontologies in Bioinformatics for transcriptional expression. These databases can be used for both hypoth- esis t ...

5.9 Pathway Databases 121 occurring in the entire organism (Villanueva et al. 2004). Proteomics data- bases address five biologi ...

122 5 Survey of Ontologies in Bioinformatics signaling, genetic regulatory, and genetic pathways. BioPAX is an OWL on- tology. K ...

5.10 Single Nucleotide Polymorphisms 123 5.10 Single Nucleotide Polymorphisms Asingle nucleotide polymorphism(SNP) is defined as ...

124 5 Survey of Ontologies in Bioinformatics HGVbase is the product of a collaboration between the Karolinska Institute (Sweden) ...

5.10 Single Nucleotide Polymorphisms 125 nent of the Cancer Genome Anatomy Project (Packer et al. 2004) of the Na- tional Cancer ...