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

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

doi:10.1093/nar/gky1036

Abstract

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. The ontology is freely available for download from GitHub (https://github.com/evidenceontology/) or the project’s website (http://evidenceontology.org/). Users can request new terms or changes to existing terms through the project’s GitHub site. ECO is released into the public domain under CC0 1.0 Universal.

Highlights

Biocuration is the process whereby information about biological entities is collected and stored
We provide an update on a previously described [2] collaboratively maintained table that maps the three-letter mnemonic Gene Ontology (GO) evidence codes (e.g. “IDA” or “Inferred from Direct Assay”) to equivalent Evidence and Conclusion Ontology (ECO) classes (e.g. ECO:0000314 ‘direct assay evidence used in manual assertion’)
While Ontology for Biomedical Investigations (OBI) is well-suited to describe instrumentation and research protocols, we have found that users of ECO desire simple representations of evidence that are organized around biological context

Summary

Introduction

Biocuration is the process whereby information about biological entities is collected and stored. During the course of its development, ECO terms have been categorized primarily in one of two ways: the biological context of the evidence (e.g. gene expression or sequence similarity) or the technique or assay used to generate the evidence (e.g. polymerase chain reaction-based evidence). Linking GO evidence codes to ECO terms facilitates interoperability with other resources that use ECO natively, such as UniProt [7], which contributed to development of the mapping file.

Results

Conclusion