skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

To increase the utility of Gene Ontology (GO) 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. Here, we expect that GO-CAM will enable new applications in pathway and network analysis, as well as improve standard GO annotations for traditional GO-based applications.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1];  [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6]; ORCiD logo [1]; ORCiD logo [5]; ORCiD logo [7]; ORCiD logo [5]; ORCiD logo [5]
  1. Univ. of Southern California, Los Angeles, CA (United States)
  2. The Jackson Lab., Bar Harbor, ME (United States)
  3. European Bioinformatics Inst. (EMBL-EBI), Cambridge (United Kingdom)
  4. California Inst. of Technology, Pasadena, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. Univ. of North Carolina, Chapel Hill, NC (United States)
  7. Swiss Inst. of Bioinformatics (SIB), Geneva (Switzerland)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
1581368
Grant/Contract Number:  
AC02-05CH11231; U41 HG002273
Resource Type:
Accepted Manuscript
Journal Name:
Nature Genetics
Additional Journal Information:
Journal Volume: 51; Journal Issue: 10; Journal ID: ISSN 1061-4036
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; computational biology and bioinformatics; genomic analysis

Citation Formats

Thomas, Paul D., Hill, David P., Mi, Huaiyu, Osumi-Sutherland, David, Van Auken, Kimberly, Carbon, Seth, Balhoff, James P., Albou, Laurent-Philippe, Good, Benjamin, Gaudet, Pascale, Lewis, Suzanna E., and Mungall, Christopher J. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. United States: N. p., 2019. Web. https://doi.org/10.1038/s41588-019-0500-1.
Thomas, Paul D., Hill, David P., Mi, Huaiyu, Osumi-Sutherland, David, Van Auken, Kimberly, Carbon, Seth, Balhoff, James P., Albou, Laurent-Philippe, Good, Benjamin, Gaudet, Pascale, Lewis, Suzanna E., & Mungall, Christopher J. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. United States. https://doi.org/10.1038/s41588-019-0500-1
Thomas, Paul D., Hill, David P., Mi, Huaiyu, Osumi-Sutherland, David, Van Auken, Kimberly, Carbon, Seth, Balhoff, James P., Albou, Laurent-Philippe, Good, Benjamin, Gaudet, Pascale, Lewis, Suzanna E., and Mungall, Christopher J. Mon . "Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems". United States. https://doi.org/10.1038/s41588-019-0500-1. https://www.osti.gov/servlets/purl/1581368.
@article{osti_1581368,
title = {Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems},
author = {Thomas, Paul D. and Hill, David P. and Mi, Huaiyu and Osumi-Sutherland, David and Van Auken, Kimberly and Carbon, Seth and Balhoff, James P. and Albou, Laurent-Philippe and Good, Benjamin and Gaudet, Pascale and Lewis, Suzanna E. and Mungall, Christopher J.},
abstractNote = {To increase the utility of Gene Ontology (GO) 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. Here, we expect that GO-CAM will enable new applications in pathway and network analysis, as well as improve standard GO annotations for traditional GO-based applications.},
doi = {10.1038/s41588-019-0500-1},
journal = {Nature Genetics},
number = 10,
volume = 51,
place = {United States},
year = {2019},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 2 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Uberon, an integrative multi-species anatomy ontology
journal, January 2012

  • Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V.
  • Genome Biology, Vol. 13, Issue 1
  • DOI: 10.1186/gb-2012-13-1-r5

Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data
journal, July 2015

  • Hayamizu, Terry F.; Baldock, Richard A.; Ringwald, Martin
  • Mammalian Genome, Vol. 26, Issue 9-10
  • DOI: 10.1007/s00335-015-9584-9

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Cooperative development of logical modelling standards and tools with CoLoMoTo
journal, January 2015


ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
journal, May 2009

  • Chen, J.; Bardes, E. E.; Aronow, B. J.
  • Nucleic Acids Research, Vol. 37, Issue Web Server
  • DOI: 10.1093/nar/gkp427

PINA v2.0: mining interactome modules
journal, November 2011

  • Cowley, Mark J.; Pinese, Mark; Kassahn, Karin S.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr967

NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration
journal, May 2014

  • Xia, Jianguo; Benner, Maia J.; Hancock, Robert E. W.
  • Nucleic Acids Research, Vol. 42, Issue W1
  • DOI: 10.1093/nar/gku443

SAMNetWeb: identifying condition-specific networks linking signaling and transcription
journal, November 2014


The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
journal, July 2016

  • Diehl, Alexander D.; Meehan, Terrence F.; Bradford, Yvonne M.
  • Journal of Biomedical Semantics, Vol. 7, Issue 1
  • DOI: 10.1186/s13326-016-0088-7

ChEBI in 2016: Improved services and an expanding collection of metabolites
journal, October 2015

  • Hastings, Janna; Owen, Gareth; Dekker, Adriano
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1031

SANTA: Quantifying the Functional Content of Molecular Networks
journal, September 2014


Building a Cell and Anatomy Ontology of Caenorhabditis elegans
journal, January 2003

  • Lee, Raymond Y. N.; Sternberg, Paul W.
  • Comparative and Functional Genomics, Vol. 4, Issue 1
  • DOI: 10.1002/cfg.248

The Systems Biology Graphical Notation
journal, August 2009

  • Novère, Nicolas Le; Hucka, Michael; Mi, Huaiyu
  • Nature Biotechnology, Vol. 27, Issue 8
  • DOI: 10.1038/nbt.1558

Path2Models: large-scale generation of computational models from biochemical pathway maps
journal, January 2013

  • Büchel, Finja; Rodriguez, Nicolas; Swainston, Neil
  • BMC Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1752-0509-7-116

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003


Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
journal, January 2013


Damage-Induced Ubiquitylation of Human RNA Polymerase II by the Ubiquitin Ligase Nedd4, but Not Cockayne Syndrome Proteins or BRCA1
journal, November 2007


Using VisANT to Analyze Networks
journal, March 2014


    Works referencing / citing this record:

    Incremental data integration for tracking genotype-disease associations
    journal, January 2020