5.2 Ontology Languages in Bioinformatics 99
$structures.goff ; ZFIN:0000000
<001_Zygote\:1-cell\,embryo ; ZFIN:0000004
<001_Zygote\:1-cell\,blastomere ; ZFIN:0000001
<001_Zygote\:1-cell\,yolk ; ZFIN:0000012
<001_Zygote\:1-cell\,extraembryonic ; ZFIN:0000005
<001_Zygote\:1-cell\,chorion ; ZFIN:0000002
<002_Cleavage\:2-cell\,embryo ; ZFIN:0000017
<002_Cleavage\:2-cell\,blastomeres ; ZFIN:0000013
<002_Cleavage\:2-cell\,yolk ; ZFIN:0000025
<002_Cleavage\:2-cell\,extraembryonic ; ZFIN:0000018
<002_Cleavage\:2-cell\,chorion ; ZFIN:0000014
<003_Cleavage\:4-cell\,embryo ; ZFIN:0000030
<003_Cleavage\:4-cell\,blastomeres ; ZFIN:0000026
<003_Cleavage\:4-cell\,yolk ; ZFIN:0000038
<003_Cleavage\:4-cell\,extraembryonic ; ZFIN:0000031
<003_Cleavage\:4-cell\,chorion ; ZFIN:0000027
<004_Cleavage\:8-cell\,embryo ; ZFIN:0000043
<004_Cleavage\:8-cell\,blastomeres ; ZFIN:0000039
<004_Cleavage\:8-cell\,yolk ; ZFIN:0000051
<004_Cleavage\:8-cell\,extraembryonic ; ZFIN:0000044
Figure 5.4 An excerpt fromzebrafish_anatomy.ontologyin OBO.
and bioinformatics. This ontology was originally written in a description
logic called GRAIL (Baker et al. 1998), but was later changed to OWL. The
ontology acts as a universal model to help users form queries that will be
understood by the various sources. The wrappers create the illusion of a
common query language for all information resources. The latest version
of TAMBIS has been translated to to OWL atimgproj.cs.man.ac.uk/
tambis/BabyTao-new.owl.
5.2 Ontology Languages in Bioinformatics
In this section we survey the main XML-based ontologies that have been de-
veloped for bioinformatics. The number of such ontologies is large, and con-
tinually increasing, so some of the ontologies will be mentioned only briefly.
