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286 12 Building Bioinformatics Ontologies Graph-based languages.These include semantic networks and conceptual graphs. Knowledg ...

12.2 Selecting an Ontology Language 287 OWL Lite. This limited form of OWL was intended more for develop- ers than for serious ...

288 12 Building Bioinformatics Ontologies The choice of ontology language will be highly dependent on the purpose of the ontolog ...

12.3 Ontology Development Tools 289 selves as “ontology development tools.” They are more commonly called “ontology editors.” Th ...

290 12 Building Bioinformatics Ontologies <!ATTLIST db_entry format NMTOKEN #REQUIRED > <!ATTLIST db_entry name CDATA # ...

12.4 Acquiring Domain Knowledge 291 knowledge-base editor available atprotege.stanford.edu. It is writ- ten in Java, and can be ...

292 12 Building Bioinformatics Ontologies intended to be used by a larger community than just a local group of people. If inform ...

12.5 Reusing Existing Ontologies 293 Definitions of nouns are usually expressed by comparing them with more general nouns. While ...

294 12 Building Bioinformatics Ontologies anew. However, there are risks involved that must be balanced against the advantages. ...

12.5 Reusing Existing Ontologies 295 merged to form a single XML document. The merger occurs each time the main XML document is ...

296 12 Building Bioinformatics Ontologies We have already seen examples of including one XML file in another in section 1.4. SBM ...

12.6 Designing the Concept Hierarchy 297 and one can attach notes to events. Notes are made by medical personnel. The following ...

298 12 Building Bioinformatics Ontologies There are a number of ways to help distinguish subclass relationships from other hiera ...

12.6 Designing the Concept Hierarchy 299 <rdfs:Class rdf:ID="Prescription"> <rdfs:subClassOf rdf:resource="#Event"/> ...

300 12 Building Bioinformatics Ontologies 12.6.1 Uniform Hierarchy To help understand large hierarchies one should try to make t ...

12.6 Designing the Concept Hierarchy 301 12.6.2 Classes vs. Instances One important design issue is whether a concept should be ...

302 12 Building Bioinformatics Ontologies how the measurement was performed (e.g., orally, rectally, etc.). But one might not st ...

12.7 Designing the Properties 303 As more was learned about them, the taxonomy continued to change, but the disjointness conditi ...

304 12 Building Bioinformatics Ontologies muscles, organs, skin, and so on. While one can have an ontology consisting of just a ...

12.7 Designing the Properties 305 moment, one can only state this in the informal description of the prop- erty. However, it is ...