title: Modeling biochemical pathways in the gene ontology.
abstract: The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations. Here we present a methodology for extending and refining the classes in the GO for more comprehensive, consistent and integrated representation of pathways, leveraging knowledge embedded in current pathway representations such as those in the Reactome Knowledgebase and MetaCyc. With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis.
authors: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors: David P
authors: DP
authors: Hill
authors: Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA deustp01@med.nyu.edu.
authors: Peter
authors: P
authors: D'Eustachio
authors: Arabidopsis Information Resource, Phoenix Bioinformatics, Redwood City, CA 94063, USA.
authors: Tanya Z
authors: TZ
authors: Berardini
authors: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Christopher J
authors: CJ
authors: Mungall
authors: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors: Nikolai
authors: N
authors: Renedo
authors: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors: Judith A
authors: JA
authors: Blake
mesh_terms: D000818:Animals; D050260:Carbohydrate Metabolism / Q000502:physiology*; D030541:Databases, Genetic; D063990:Gene Ontology; D006801:Humans; D008954:Models, Biological