Evidence map›Paper›PMID 31702580›Full record

ArticleActa crystallographica. Section F, Structural biology communications2019

Automatic annotation of protein residues in published papers.

Robert Firth, Francesco Talo, Aravind Venkatesan, Abhik Mukhopadhyay, Johanna McEntyre, Sameer Velankar, Chris Morris

Abstract read
In one paragraph

Article in Acta crystallographica. Section F, Structural biology communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Associating protein residues in the literature with structural data.Acta crystallographica. Section D, Structural biology · 2026
    Article
  2. Taking biological structure communications into the third dimension.Acta crystallographica. Section F, Structural biology communications · 2019
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Robert FirthSTFC, Daresbury Laboratory, Warrington WA4 4AD, England.ORCID 0000-0002-9427-1850
Francesco TaloEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England.
Aravind VenkatesanEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England.
Abhik MukhopadhyayEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England.ORCID 0000-0002-9808-7620
Johanna McEntyreEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England.
Sameer VelankarEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England.ORCID 0000-0002-8439-5964
Chris MorrisSTFC, Daresbury Laboratory, Warrington WA4 4AD, England.ORCID 0000-0002-9533-5684

Funding

European Commission H2020-EINFRA-2015-1-675858European Commission H2020-INFRADEV-1-2015-1-676559Wellcome TrustWellcome Trust 108758
6 · The paper itself

Abstract

This work presents an annotation tool that automatically locates mentions of particular amino-acid residues in published papers and identifies the protein concerned. These matches can be provided in context or in a searchable format in order for researchers to better use the existing and future literature.

Indexed as

Molecular Sequence AnnotationPublicationsAmino AcidsAutomationMutationProteinsSoftwareAmino AcidsProteinsnamed entity recognizernatural language processingNLPresidue

Identifiers

PMID31702580
PMCPMC6839820

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.