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Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.

ABSTRACT: UniProtKB/Swiss-Prot provides expert curation with information extracted from literature and curator-evaluated computational analysis. As knowledgebases continue to play an increasingly important role in scientific research, a number of studies have evaluated their accuracy and revealed various errors. While some are curation errors, others are the result of incorrect information published in the scientific literature. By taking the example of sirtuin-5, a complex annotation case, we will describe the curation procedure of UniProtKB/Swiss-Prot and detail how we report conflicting information in the database. We will demonstrate the importance of collaboration between resources to ensure curation consistency and the value of contributions from the user community in helping maintain error-free resources. Database URL: www.uniprot.org.

SUBMITTER: Poux S

PROVIDER: S-EPMC3950660 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.

Poux Sylvain S Magrane Michele M Arighi Cecilia N CN Bridge Alan A O'Donovan Claire C Laiho Kati K

Database : the journal of biological databases and curation 20140312

UniProtKB/Swiss-Prot provides expert curation with information extracted from literature and curator-evaluated computational analysis. As knowledgebases continue to play an increasingly important role in scientific research, a number of studies have evaluated their accuracy and revealed various errors. While some are curation errors, others are the result of incorrect information published in the scientific literature. By taking the example of sirtuin-5, a complex annotation case, we will descri ...[more]

PMID: 24622611

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On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.

Project description:MotivationBiological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized and computable knowledge extracted from the literature by expert curators. While knowledgebases play an increasingly important role in the scientific community, their ability to keep up with the growth of biomedical literature is under scrutiny. Using UniProtKB/Swiss-Prot as a case study, we address this concern via multiple literature triage approaches.ResultsWith the assistance of the PubTator text-mining tool, we tagged more than 10 000 articles to assess the ratio of papers relevant for curation. We first show that curators read and evaluate many more papers than they curate, and that measuring the number of curated publications is insufficient to provide a complete picture as demonstrated by the fact that 8000-10 000 papers are curated in UniProt each year while curators evaluate 50 000-70 000 papers per year. We show that 90% of the papers in PubMed are out of the scope of UniProt, that a maximum of 2-3% of the papers indexed in PubMed each year are relevant for UniProt curation, and that, despite appearances, expert curation in UniProt is scalable.Availability and implementationUniProt is freely available at http://www.uniprot.org/.Contactsylvain.poux@sib.swiss.Supplementary informationSupplementary data are available at Bioinformatics online.

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Project description:Database URL:http://biomodels.caltech.edu.

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ClinGen Myeloid Malignancy Variant Curation Expert Panel recommendations for germline RUNX1 variants.

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ClinGen expert clinical validity curation of 164 hearing loss gene-disease pairs.

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Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

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| S-EPMC4236444 | biostudies-literature

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