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Methods and Protocols | Novel Systems Biology Techniques

PaperBLAST: Text Mining Papers for Information about Homologs

Morgan N. Price, Adam P. Arkin
Morgan G. I. Langille, Editor
Morgan N. Price
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Adam P. Arkin
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Morgan G. I. Langille
Dalhousie University
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DOI: 10.1128/mSystems.00039-17
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  • FIG 1
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    FIG 1

    Example of PaperBLAST results. For each protein that is linked to the literature and is similar to the query protein, PaperBLAST shows a list of articles. For each article, PaperBLAST shows up to two snippets that mention the protein. a.a., amino acids.

  • FIG 2
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    FIG 2

    Coverage of PaperBLAST. (A) How often hypothetical proteins or other vaguely annotated proteins from different types of organisms have homologs in the PaperBLAST database with a BLAST score ratio above the given threshold. (B) How often vaguely annotated bacterial proteins have homologs in PaperBLAST, in the characterized subset of Swiss-Prot, or in any of the three curated databases that are included in PaperBLAST (the characterized subset of Swiss-Prot, GeneRIF, or EcoCyc). In both panels, only homologs with high-coverage alignments (at least 80%) were included.

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  • TABLE 1

    Numbers of proteins and scientific articles and links between them in PaperBLAST’s database

    SourceNo. of
    proteinsa
    No. of
    papers
    No. of
    links
    No. of links
    with a text snippet(s)
    EuropePMC315,57973,542639,550613,726
    Swiss-Protb79,38827,45338,342
    GeneRIF77,836662,0691,038,801
    EcoCycc3,92311,14322,769
    Totald400,961748,4501,721,795
    • ↵ a Proteins with different identifiers but with the same sequence are counted only once.

    • ↵ b The count of proteins for Swiss-Prot includes some proteins that were linked to experimental evidence but that were not linked to articles about the protein’s function (see Materials and Methods).

    • ↵ c The count of proteins for EcoCyc does not include proteins that are not linked to any scientific articles (even though these are included in PaperBLAST’s database).

    • ↵ d The total is less than the sum of the parts due to overlap of data sources.

Supplemental Material

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  • DATA SET S1

    Analysis of 40 vaguely annotated bacterial proteins that have close homologs in PaperBLAST’s database. Download DATA SET S1, XLS file, 0.04 MB.

    Copyright © 2017 Price and Arkin.

    This content is distributed under the terms of the Creative Commons Attribution 4.0 International license .

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PaperBLAST: Text Mining Papers for Information about Homologs
Morgan N. Price, Adam P. Arkin
mSystems Aug 2017, 2 (4) e00039-17; DOI: 10.1128/mSystems.00039-17

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PaperBLAST: Text Mining Papers for Information about Homologs
Morgan N. Price, Adam P. Arkin
mSystems Aug 2017, 2 (4) e00039-17; DOI: 10.1128/mSystems.00039-17
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KEYWORDS

annotation
text mining

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