Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Paul D Thomas; David P Hill; Huaiyu Mi; David Osumi-Sutherland; Kimberly Van Auken; Seth Carbon; James P Balhoff; Laurent-Philippe Albou; Benjamin Good; Pascale Gaudet; Suzanna E Lewis; Christopher J Mungall

doi:10.1038/s41588-019-0500-1

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Nat Genet. 2019 Oct;51(10):1429-1433. doi: 10.1038/s41588-019-0500-1.

Authors

Affiliations

¹ Department of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, CA, USA. pdthomas@usc.edu.
² The Jackson Laboratory, Bar Harbor, ME, USA.
³ Department of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, CA, USA.
⁴ European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
⁵ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
⁶ Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁷ Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁸ SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.

Abstract

To increase the utility of Gene Ontology annotations for interpretation of genome-wide experimental data, we have developed GO-CAM, a structured framework for linking multiple GO annotations into an integrated model of a biological system. We expect that GO-CAM will enable new applications in pathway and network analysis as well as improving standard GO annotations for traditional GO-based applications.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Computational Biology / methods*
Databases, Genetic
Gene Ontology*
Humans
Models, Biological*
Molecular Sequence Annotation*
Phenotype
Signal Transduction*

Grants and funding

U41 HG002273/HG/NHGRI NIH HHS/United States