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

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.

doi:10.1038/s41588-019-0500-1

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:

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^[1]; Osumi-Sutherland, David ^[3];

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Univ. of Southern California, Los Angeles, CA (United States)
The Jackson Lab., Bar Harbor, ME (United States)
European Bioinformatics Inst. (EMBL-EBI), Cambridge (United Kingdom)
California Inst. of Technology, Pasadena, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of North Carolina, Chapel Hill, NC (United States)
Swiss Inst. of Bioinformatics (SIB), Geneva (Switzerland)

Publication Date:: Mon Sep 23 00:00:00 EDT 2019

Research Org.:: Lawrence Berkeley National Laboratory (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.  doi:10.1038/s41588-019-0500-1.

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                    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

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                    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.

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@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         = {Mon Sep 23 00:00:00 EDT 2019},

  month        = {Mon Sep 23 00:00:00 EDT 2019}

}

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Works referencing / citing this record:

Incremental data integration for tracking genotype-disease associations
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Title: Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Abstract

Citation Formats

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

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

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

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

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

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

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

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

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

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

The Systems Biology Graphical Notation journal, August 2009

The Gene Ontology Resource: 20 years and still GOing strong journal, November 2018

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

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

The Gene Ontology Resource: 20 years and still GOing strong. journalarticle, January 2019

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

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

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

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

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

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

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
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PINA v2.0: mining interactome modules
journal, November 2011

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

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

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

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

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

The Systems Biology Graphical Notation
journal, August 2009

The Gene Ontology Resource: 20 years and still GOing strong
journal, November 2018

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

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

The Gene Ontology Resource: 20 years and still GOing strong.
journalarticle, January 2019

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

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