FlyBase:Controlled vocabularies used by FlyBase
The controlled vocabularies currently used by FlyBase are:
- Gene Ontology (GO). This provides structured controlled vocabularies for the annotation of gene products (although FlyBase at present annotates genes with GO terms, as a surrogate for their products). The GO has three domains: the molecular function of gene products, the biological process (i.e. roles) in which they are involved and their cellular component (location).
- Fly Anatomy (FBbt). A structured controlled vocabulary of the anatomy of Drosophila melanogaster, used, for example, for the description of phenotypes and where a gene is expressed.
- Fly Development (FBdv). A structured controlled vocabulary of the development of Drosophila melanogaster, used, for example, for the description of phenotypes and when a gene is expressed.
- Sequence Ontology (SO). A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases. Its use by FlyBase means that the various components of the genome are described in a consistent and rigorous manner.
- FlyBase controlled vocabulary (FBcv). A structured controlled vocabulary used for the annotation of various objects in FlyBase, including publications (by their type), alleles (for their mutagen etc) and phenotypic class. Although some of these domains will probably always remain local to FlyBase, in time, community ontologies will be available for others (e.g. chemical compounds for mutagens) and FlyBase will then use these.
- FlyBase stock ontology (FBsv). A structured controlled vocabulary used to describe the types of fly stocks listed in FlyBase.
- Biological Imaging Methods Ontology (FBbi, image ontology). A structured controlled vocabulary used to describe the types of images in FlyBase.
- Disease Ontology (DO). A structured controlled vocabulary of human diseases. Disease model annotations are made by assigning terms from this ontology to alleles shown to recapitulate an aspect of a human disease in Drosophila melanogaster.
- Molecular Interactions Ontology (MI). A structured controlled vocabulary used in FlyBase to capture assay or molecular information.
All of these structured controlled vocabularies are in the same format, that used by the Open Biomedical Ontology group. This format is called the OBO format and files using it have the suffix '.obo', e.g. gene_ontology.obo. The OBO format is designed to be used with the freely-downloadable OBO-Edit tool.
Users should be aware that controlled vocabularies undergo continual development; terms and definitions are refined, added, merged, split and obsoleted in an effort to improve the way they represent their various subjects.
Both the current 'live' versions of each controlled vocabulary and the static versions taken at the time data for this FlyBase release was frozen are available to download from the Precomputed files download page under the Files menu of the Navigation bar.
The detail of each controlled vocabulary term is displayed in a CV Term Report in FlyBase. Individual CV Term Reports can be reached either by clicking on the controlled vocabulary term where it is displayed in a report page (e.g. the GENE ONTOLOGY: Function, Process, and Cellular component section of the Gene Report), or by using the Vocabularies tool (previously known as TermLink), which allows users to search directly for controlled vocabulary terms from any of the controlled vocabularies used by FlyBase.
Controlled vocabulary terms can also be searched using the QueryBuilder tool, via their links to objects (such as genes) in FlyBase. If you wish to search using a controlled vocabulary term in QueryBuilder, you should select the GO/Anatomy CV DB dataset in the query segment box (see the QUERY BUILDER HELP section at the bottom of the QueryBuilder page for more details.