ECO, the Evidence &amp; Conclusion Ontology: community standard for evidence information

Giglio, Michelle; Tauber, Rebecca; Nadendla, Suvarna; Munro, James; Olley, Dustin; Ball, Shoshannah; Mitraka, Elvira; Schriml, Lynn M.; Gaudet, Pascale; Hobbs, Elizabeth T.; Erill, Ivan; Siegele, Deborah A.; Hu, James C.; Mungall, Chris; Chibucos, Marcus C.

doi:10.1093/nar/gky1036

ECO, the Evidence & Conclusion Ontology: community standard for evidence information

Journal Article · Thu Nov 08 00:00:00 EST 2018 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gky1036· OSTI ID:1625570

Giglio, Michelle ^[1]; Tauber, Rebecca ^[2]; Nadendla, Suvarna ^[2]; Munro, James ^[2]; Olley, Dustin ^[2]; Ball, Shoshannah ^[2]; Mitraka, Elvira ^[2]; ^[2]; ^[3]; Hobbs, Elizabeth T. ^[4]; Erill, Ivan ^[5]; Siegele, Deborah A. ^[6]; Hu, James C. ^[7]; Mungall, Chris ^[8]; Chibucos, Marcus C. ^[9]

Univ. of Maryland School of Medicine, Baltimore, MD (United States). Inst. for Genome Sciences; DOE/OSTI
Univ. of Maryland School of Medicine, Baltimore, MD (United States). Inst. for Genome Sciences
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Univ. of Maryland, Baltimore, MD (United States). Dept. of Biological Sciences
Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
Department of Biology, Texas A&M University, College Station, TX 77840, USA
Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA
Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA

The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures and query of evidence. ECO contains over 1500 terms and is in use by many leading biological resources including the Gene Ontology, UniProt and several model organism databases. ECO is continually being expanded and revised based on the needs of the biocuration community.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF) Div. of Biological Infrastructure; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625570

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 47; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels Kanavy, Dona M.; McNulty, Shannon M.; Jairath, Meera K. Genome Medicine, Vol. 11, Issue 1 https://doi.org/10.1186/s13073-019-0683-1	journal	November 2019
Phenotype annotation with the ontology of microbial phenotypes (OMP) Siegele, Deborah A.; LaBonte, Sandra A.; Wu, Peter I-Fan Journal of Biomedical Semantics, Vol. 10, Issue 1 https://doi.org/10.1186/s13326-019-0205-5	journal	July 2019
Biobtree: A tool to search and map bioinformatics identifiers and special keywords Gur, Tamer F1000Research, Vol. 8 https://doi.org/10.12688/f1000research.17927.2	journal	January 2019
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research Kafkas, Şenay; Abdelhakim, Marwa; Hashish, Yasmeen Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0090-x	journal	June 2019
Curation and annotation of planarian gene expression patterns with segmented reference morphologies Roy, Joy; Cheung, Eric; Bhatti, Junaid Bioinformatics, Vol. 36, Issue 9 https://doi.org/10.1093/bioinformatics/btaa023	journal	January 2020
PhaSePro: the database of proteins driving liquid–liquid phase separation Mészáros, Bálint; Erdős, Gábor; Szabó, Beáta Nucleic Acids Research https://doi.org/10.1093/nar/gkz848	journal	October 2019
A Logical Model of Homology for Comparative Biology Mabee, Paula M.; Balhoff, James P.; Dahdul, Wasila M. Systematic Biology, Vol. 69, Issue 2 https://doi.org/10.1093/sysbio/syz067	journal	October 2019
Identifying pseudoenzymes using functional annotation: pitfalls of common practice Ribeiro, Antonio J. M.; Tyzack, Jonathan D.; Borkakoti, Neera The FEBS Journal, Vol. 287, Issue 19 https://doi.org/10.1111/febs.15142	journal	December 2019
Biobtree: A tool to search and map bioinformatics identifiers and special keywords Gur, Tamer F1000Research, Vol. 8 https://doi.org/10.12688/f1000research.17927.4	journal	January 2019
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. Kafkas, Şenay; Abdelhakim, Marwa; Hashish, Yasmeen Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43596	text	January 2019

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