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

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.

Figure 1.

Two annotation examples. In Annotation Event #1, the annotation is made by a curator who has read a published experimental characterization of a protein. In Annotation Event #2, the annotation is made in a transitive manor based on sequence similarity.

Figure 2.

Tree view of ECO terms. This tree view shows all of the first level children of the root node ‘evidence’, showing the variety of types of evidence. In addition, the ‘sequence alignment evidence’ node is expanded showing its parentage back to the root and its two assertion method-specific children.

Figure 3.

Growth of the ECO. The graph shows total number of terms according to dates taken at 5-month intervals.

Figure 4.

Logical definitions link ECO, OBI and GO terms together.

Figure 5.

Screen capture of ECO website homepage.

Figure 6.

Wikidata annotation for n-acetyltransferase lmo1400.