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PaperBLAST: Text-mining papers for information about homologs

Morgan N. Price, Adam P. Arkin
doi: https://doi.org/10.1101/133041
Morgan N. Price
1Environmental Genomics & System Biology, Lawrence Berkeley National Lab
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Adam P. Arkin
1Environmental Genomics & System Biology, Lawrence Berkeley National Lab
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Abstract

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources that link protein sequences to scientific articles (Swiss-Prot, GeneRIF, and EcoCyc). PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 02, 2017.
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PaperBLAST: Text-mining papers for information about homologs
Morgan N. Price, Adam P. Arkin
bioRxiv 133041; doi: https://doi.org/10.1101/133041
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PaperBLAST: Text-mining papers for information about homologs
Morgan N. Price, Adam P. Arkin
bioRxiv 133041; doi: https://doi.org/10.1101/133041

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