Representation of roles in biomedical ontologies: a case study in functional genomics.
OBJECTIVE
Representing roles, i.e. functions of proteins, sequences and structures, is the cornerstone of knowledge representation in functional genomics. The objective of this study is to investigate representation of roles as functional categories or associative relations. We focus on GeneOntology (GO) and the UMLS and take examples from iron metabolism.


METHODS
The terms corresponding to the main proteins involved in iron metabolism were mapped to GO (including the annotations) and the UMLS. The representation of their biological roles was then analyzed.


RESULTS
Functional aspects are represented in both GO and the UMLS. However, the granularity may not be appropriate.


CONCLUSIONS
Advantages and limits of functional categories and associative relations are discussed.
Burgun
Anita
A
Laboratoire d'Informatique Medicale, Faculté de Médecine, Rennes, France.
Bodenreider
Olivier
O
Le Duff
Franck
F
Moussouni
Fouzia
F
Loreal
Olivier
O
D005796:Genes; D023281:Genomics; D006801:Humans; D007501:Iron / Q000378:metabolism*; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D017432:Unified Medical Language System; D018875:Vocabulary, Controlled
D011506:Proteins; D007501:Iron