Standardized description of scientific evidence using the Evidence Ontology (ECO)

Chibucos, Marcus C.; Mungall, Christopher J.; Balakrishnan, Rama; Christie, Karen R.; Huntley, Rachael P.; White, Owen; Blake, Judith A.; Lewis, Suzanna E.; Giglio, Michelle

doi:10.1093/database/bau075

Standardized description of scientific evidence using the Evidence Ontology (ECO)

Journal Article · Mon Jul 21 00:00:00 EDT 2014 · Database

DOI:https://doi.org/10.1093/database/bau075· OSTI ID:1625305

Chibucos, Marcus C. ^[1]; Mungall, Christopher J. ^[2]; Balakrishnan, Rama ^[3]; Christie, Karen R. ^[4]; Huntley, Rachael P. ^[5]; White, Owen ^[6]; Blake, Judith A. ^[4]; Lewis, Suzanna E. ^[2]; Giglio, Michelle ^[7]

Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Inst. for Genome Sciences; Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Dept. of Microbiology and Immunology; DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
Stanford Univ., CA (United States). Dept. of Genetics. Saccharomyces Genome Database
The Jackson Laboratory, Bar Harbor, ME (United States). Computational Biology and Bioinformatics
Wellcome Trust Genome Campus, Hinxton, Cambridge (United Kingdom). European Molecular Biology Lab.- European Bioinformatics Inst. (EMBL-EBI)
Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Inst. for Genome Sciences; Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Dept. of Epidemiology
Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Inst. for Genome Sciences; Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Dept. of Medicine

The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625305

Journal Information:: Database, Journal Name: Database Journal Issue: 0 Vol. 2014; ISSN 1758-0463

Publisher:: Oxford University Press - International Society for BiocurationCopyright Statement

Country of Publication:: United States

Language:: English

References (24)

Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/s0022-2836(05)80360-2	journal	October 1990
OBO-Edit an ontology editor for biologists Day-Richter, J.; Harris, M. A.; Haendel, M. Bioinformatics, Vol. 23, Issue 16 https://doi.org/10.1093/bioinformatics/btm112	journal	June 2007
AmiGO: online access to ontology and annotation data Carbon, Seth; Ireland, Amelia; Mungall, Christopher J. Bioinformatics, Vol. 25, Issue 2 https://doi.org/10.1093/bioinformatics/btn615	journal	November 2008
The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant Huala, E. Nucleic Acids Research, Vol. 29, Issue 1 https://doi.org/10.1093/nar/29.1.102	journal	January 2001
The UniProt-GO Annotation database in 2011 Dimmer, E. C.; Huntley, R. P.; Alam-Faruque, Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1048	journal	November 2011
InterPro in 2011: new developments in the family and domain prediction database Hunter, S.; Jones, P.; Mitchell, A. Nucleic Acids Research, Vol. 40, Issue 10 https://doi.org/10.1093/nar/gks456	journal	May 2012
Logical Development of the Cell Ontology Meehan, Terrence F.; Masci, Anna Maria; Abdulla, Amina BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-6	journal	January 2011
Modeling biomedical experimental processes with OBI Brinkman, Ryan R.; Courtot, Mélanie; Derom, Dirk Journal of Biomedical Semantics, Vol. 1, Issue Suppl 1 https://doi.org/10.1186/2041-1480-1-s1-s7	journal	January 2010
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery Dumontier, Michel; Baker, Christopher JO; Baran, Joachim Journal of Biomedical Semantics, Vol. 5, Issue 1 https://doi.org/10.1186/2041-1480-5-14	journal	January 2014
Integrating phenotype ontologies across multiple species Mungall, Christopher J.; Gkoutos, Georgios V.; Smith, Cynthia L. Genome Biology, Vol. 11, Issue 1 https://doi.org/10.1186/gb-2010-11-1-r2	journal	January 2010
Uberon, an integrative multi-species anatomy ontology Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V. Genome Biology, Vol. 13, Issue 1 https://doi.org/10.1186/gb-2012-13-1-r5	journal	January 2012
The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species No authors listed PLoS Computational Biology, Vol. 5, Issue 7 https://doi.org/10.1371/journal.pcbi.1000431	journal	July 2009
Basic Local Alignment Search Tool Altschul, S. Journal of Molecular Biology, Vol. 215, Issue 3 https://doi.org/10.1006/jmbi.1990.9999	journal	October 1990
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration Smith, Barry; Ashburner, Michael; Rosse, Cornelius Nature Biotechnology, Vol. 25, Issue 11 https://doi.org/10.1038/nbt1346	journal	November 2007
The Gene Ontology's Reference Genome Project: *A Unified Framework for Functional Annotation across Species Gaudet, Pascale Nature Precedings https://doi.org/10.1038/npre.2009.3150.1	journal	April 2009
A guide to best practices for Gene Ontology (GO) manual annotation Balakrishnan, R.; Harris, M. A.; Huntley, R. Database, Vol. 2013, Issue 0 https://doi.org/10.1093/database/bat054	journal	January 2013
The FlyBase Database of the Drosophila Genome Projects and community literature Consortium, FlyBase Nucleic Acids Research, Vol. 27, Issue 1, p. 85-88 https://doi.org/10.1093/nar/27.1.85	journal	January 1999
The FlyBase database of the Drosophila genome projects and community literature Consortium, FlyBase Nucleic Acids Research, Vol. 30, Issue 1, p. 106-108 https://doi.org/10.1093/nar/30.1.106	journal	January 2002
The FlyBase database of the Drosophila genome projects and community literature Consortium, FlyBase Nucleic Acids Research, Vol. 31, Issue 1, p. 172-175 https://doi.org/10.1093/nar/gkg094	journal	January 2003
InterPro in 2011: new developments in the family and domain prediction database Hunter, S.; Jones, P.; Mitchell, A. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr948	journal	November 2011
Modeling biomedical experimental processes with OBI Brinkman, Ryan R.; Courtot, Mélanie; Derom, Dirk Journal of Biomedical Semantics, Vol. 1, Issue Suppl 1 https://doi.org/10.1186/2041-1480-1-S1-S7	journal	January 2010
Relations in biomedical ontologies Smith, Barry; Ceusters, Werner; Klagges, Bert Genome Biology, Vol. 6, Issue 5, p. R46 https://doi.org/10.1186/gb-2005-6-5-r46	journal	January 2005
A guide to best practices for Gene Ontology (GO) manual annotation. Balakrishnan, Rama; Harris, Midori A.; Huntley, Rachael Oxford University Press (OUP) https://doi.org/10.17863/cam.30729	journalarticle	January 2013
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. Consortium, Gene Ontology PLoS https://doi.org/10.17863/cam.52150	text	July 2009

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The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics Cooper, Laurel; Meier, Austin; Laporte, Marie-Angélique Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1152	journal	November 2017
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The Gene Ontology Resource: 20 years and still GOing strong No authors listed Nucleic Acids Research, Vol. 47, Issue D1, p. D330-D338 https://doi.org/10.1093/nar/gky1055	journal	November 2018
Open Targets Platform: new developments and updates two years on Carvalho-Silva, Denise; Pierleoni, Andrea; Pignatelli, Miguel Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1133	journal	November 2018
An ontology for microbial phenotypes Chibucos, Marcus C.; Zweifel, Adrienne E.; Herrera, Jonathan C. BMC Microbiology, Vol. 14, Issue 1 https://doi.org/10.1186/s12866-014-0294-3	journal	November 2014
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation Sarntivijai, Sirarat; Vasant, Drashtti; Jupp, Simon Journal of Biomedical Semantics, Vol. 7, Issue 1 https://doi.org/10.1186/s13326-016-0051-7	journal	March 2016
A community-driven reconstruction of the Aspergillus niger metabolic network Brandl, Julian; Aguilar-Pontes, Maria Victoria; Schäpe, Paul Fungal Biology and Biotechnology, Vol. 5, Issue 1 https://doi.org/10.1186/s40694-018-0060-7	journal	September 2018
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The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations Bastian, Frederic B.; Chibucos, Marcus C.; Gaudet, Pascale ETH Zurich https://doi.org/10.3929/ethz-b-000104527	text	January 2015
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The SwissLipids knowledgebase for lipid biology Aimo, Lucila; Liechti, Robin; Hyka-Nouspikel, Nevila Bioinformatics, Vol. 31, Issue 17 https://doi.org/10.1093/bioinformatics/btv285	journal	May 2015
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UniProt: the Universal Protein knowledgebase Apweiler, R. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh131	journal	January 2004
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