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86 4 The Semantic Web and Bioinformatics Applications Figure 4.8 An example in which two resources are inferred to be the same. ...

4.5 Exercises 87 Summary OWL is based on RDF and has three increasingly more general levels: OWL Lite, OWL-DL, and OWL Full. An ...

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5 Survey of Ontologies in Bioinformatics There are a large number of biomedical ontologies and databases that are cur- rently av ...

90 5 Survey of Ontologies in Bioinformatics ogy. The first one was originally focused on medical terminology but now also includ ...

5.1 Bio-Ontologies 91 of interrelated biomedical concepts that provide metadata, relationships, and semantic information for eac ...

92 5 Survey of Ontologies in Bioinformatics tions. MetaMap can also be used for constructing a list of ranking concepts by apply ...

5.1 Bio-Ontologies 93 Molecular function.The biochemical activity of a gene product. For ex- ample, a gene product could be a t ...

94 5 Survey of Ontologies in Bioinformatics Because GO supports two relationships, its ontologies are more expressive than a tax ...

5.1 Bio-Ontologies 95 and the second is a compact, dynamically interactive directed acyclic graph. Genes displayed in GoMiner ar ...

96 5 Survey of Ontologies in Bioinformatics web-based tool for rapidly listing genes in GO categories (Dennis, Jr. et al. 2003). ...

5.1 Bio-Ontologies 97 identified a total of 1559 genes that have significantly different expression patterns between the cases a ...

98 5 Survey of Ontologies in Bioinformatics ucts in a number of its databases, such as SWISS-PROT, TrEMBL, and InterPro (Camon e ...

5.2 Ontology Languages in Bioinformatics 99 $structures.goff ; ZFIN:0000000 <001_Zygote\:1-cell\,embryo ; ZFIN:0000004 <00 ...

100 5 Survey of Ontologies in Bioinformatics BSML http://www.bsml.org The Bioinformatic Sequence Markup Language (BSML) is a lan ...

5.2 Ontology Languages in Bioinformatics 101 Figure 5.5 The BSML representation for the SWISS-PROT entry P04637. BioML http://ww ...

102 5 Survey of Ontologies in Bioinformatics DNA RNA Protein <dna> <rna> <protein> <promoter> <rdomai ...

5.2 Ontology Languages in Bioinformatics 103 Rule: a mathematical expression that is added to the model equations constructed f ...

104 5 Survey of Ontologies in Bioinformatics versity of Auckland and affiliated research groups. The purpose of CellML is to sto ...

5.2 Ontology Languages in Bioinformatics 105 istry (IUPAC) lettering and PDB ATOM records. If RNAML needs to depict multiple int ...