290 12 Building Bioinformatics Ontologies
<!ATTLIST db_entry format NMTOKEN #REQUIRED >
<!ATTLIST db_entry name CDATA #REQUIRED ><!ELEMENT ddomain EMPTY >
<!ATTLIST ddomain end NMTOKEN #REQUIRED >
<!ATTLIST ddomain name CDATA #REQUIRED >
<!ATTLIST ddomain start NMTOKEN #REQUIRED ><!ELEMENT dna ( #PCDATA ) >
<!ATTLIST dna end NMTOKEN #REQUIRED >
<!ATTLIST dna name CDATA #REQUIRED >
<!ATTLIST dna start NMTOKEN #REQUIRED ><!ELEMENT exon EMPTY >
<!ATTLIST exon end NMTOKEN #REQUIRED >
<!ATTLIST exon name CDATA #REQUIRED >
<!ATTLIST exon start NMTOKEN #REQUIRED ><!ELEMENT gene ( dna, ddomain+, exon, intron ) >
<!ATTLIST gene name CDATA #REQUIRED >...If the DTD generated by this tool is not exactly what one had in mind, then
it is easy to modify it. The most common modification is to relax some of
the constraints. For example, one might change some of the mandatory
(#REQUIRED) attributes to optional (#IMPLIED) attributes.- XML editor.There are many XML editors, and some of them allow one
to create DTDs and XML schemas. For a survey of these tools, see (XML
2004). - RDF editor. Many RDF editors are now available. For a survey of the
RDF editors that were available as of 2002, see (Denny 2002a,b). - OWL editor. There are very few of these. The few that do exist were
originally developed for another ontology language and were adapted for
OWL. The best known OWL editor is Protégé-2000 from Stanford Medi-
cal Informatics (Noy et al. 2003). Protégé is an open source ontology and