Warwick Vesztrocy, A;
Dessimoz, C;
(2020)
Benchmarking gene ontology function predictions using negative annotations.
Bioinformatics
, 36
(S1)
i210-i218.
10.1093/bioinformatics/btaa466.
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Abstract
Motivation: With the ever-increasing number and diversity of sequenced species, the challenge to characterize genes with functional information is even more important. In most species, this characterization almost entirely relies on automated electronic methods. As such, it is critical to benchmark the various methods. The Critical Assessment of protein Function Annotation algorithms (CAFA) series of community experiments provide the most comprehensive benchmark, with a time-delayed analysis leveraging newly curated experimentally supported annotations. However, the definition of a false positive in CAFA has not fully accounted for the open world assumption (OWA), leading to a systematic underestimation of precision. The main reason for this limitation is the relative paucity of negative experimental annotations. Results: This article introduces a new, OWA-compliant, benchmark based on a balanced test set of positive and negative annotations. The negative annotations are derived from expert-curated annotations of protein families on phylogenetic trees. This approach results in a large increase in the average information content of negative annotations. The benchmark has been tested using the naïve and BLAST baseline methods, as well as two orthology-based methods. This new benchmark could complement existing ones in future CAFA experiments.
| Type: | Article |
|---|---|
| Title: | Benchmarking gene ontology function predictions using negative annotations |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/bioinformatics/btaa466 |
| Publisher version: | https://doi.org/10.1093/bioinformatics/btaa466 |
| Language: | English |
| Additional information: | This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10106670 |
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