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

By Marcus C. Chibucos, C. Mungall, R. Balakrishnan, Karen R. Christie, Rachael P. Huntley, Owen White, Judith A. Blake, Suzanna Lewis, Michelle G. Giglio. 2014

107 citations recorded by the source corpus.

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. Database URL: Evidence Ontology Web site: http://evidenceontology.org

Subfields: Artificial Intelligence, Molecular Biology

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Citations in the corpus

The Gene Ontology Resource: 20 years and still GOing strong (2018, methodology): “Each annotation includes the evidence it is based upon, such as a peer-reviewed publication, using evidence codes from the Evidence and Conclusion Ontology (ECO) (2).”
UniProt: the universal protein knowledgebase (2016, methodology): “Every new piece of knowledge is associated with the original source of the information and the type of supporting evidence, using the Evidence and Conclusion Ontology (14).”
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database (2015, background): “The degree of granularity for evidence describing the experiments that GO terms are based on was also enhanced by assigning Evidence Ontology (ECO) codes (8).”
Open Targets: a platform for therapeutic target identification and validation (2016, methodology): “The evidence is described in the Open Biomedical AssociatioN (OBAN) representation (18) and makes use of the Evidence Code Ontology (ECO) (19) (Figure 2) that in turn is part of EFO.”
The UniProtKB guide to the human proteome (2016, methodology): “Every piece of knowledge is associated with the source of the information and the type of supporting evidence, using the evidence ontology (ECO) (20).”
The GOA database: Gene Ontology annotation updates for 2015 (2014, background): “The desire for the GO Consortium to capture more detailed types of supporting evidence within an annotation has seen the gradual adoption of Evidence Ontology (ECO) terms (18).”
Open Targets Platform: new developments and updates two years on (2018, background): “This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. uk), and continue to adh”
The Ontology for Biomedical Investigations (2016, background): “Another driver of upcoming changes in OBI is the collaborative work with the Evidence Ontology (ECO) [52] which aims to utilize OBI to explicitly define how its widely used ‘ evidence codes ’ are related to specific experiments.”