Article Figures & Data
Figures
- 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
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.
Tables
- TABLE 1
Numbers of proteins and scientific articles and links between them in PaperBLAST’s database
Source No. of
proteinsaNo. of
papersNo. of
linksNo. of links
with a text snippet(s)EuropePMC 315,579 73,542 639,550 613,726 Swiss-Protb 79,388 27,453 38,342 GeneRIF 77,836 662,069 1,038,801 EcoCycc 3,923 11,143 22,769 Totald 400,961 748,450 1,721,795 ↵ 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.
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.
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