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The Evidence and Conclusion Ontology (ECO) describes types of evidence relevant to biological investigations. First developed in the early 2000s, ECO now consists of over 1700 defined classes and is used by a large, and growing, list of resources. ECO imports close to 1000 classes from the Ontology for Biomedical Investigations and the Gene Ontology for use in logical definitions. Historically, ECO terms have generally been categorized by either the biological context of the evidence (e.g. gene expression) or the technique used to generate the evidence (e.g. PCR-based evidence). The result is that sometimes terms that have related biological context are found under different unrelated nodes. To address this, we have been performing a rigorous review of the structure and logic of the branches of ECO. Working with additional input from collaborators through the issue tracker on GitHub, term labels, definitions, and relationships are being evaluated and updated. The goal of these changes is to increase the logical consistency of ECO, make it easier for users to find and understand terms, and allow for ECO to continue to grow and support its users. In addition to the structural review, we have been working with CollecTF to utilize ECO for automated text mining. To generate a curated corpus for this effort, we have been annotating ECO terms to sentences which contain evidence-based assertions about gene products, taxonomic entities, and sequence features. From this effort we have developed clearly-defined annotation guidelines that have been passed on to a team of undergraduates who are continuing the curation effort.
Annotations are limited to single sentences, or to two consecutive sentences, containing the evidence instance and assertion clause. The quality of the mapping to ECO
and the strength of the author’s assertion are also captured. ECO is freely available at http://evidenceontology.org/ and https://github.com/evidenceontology.