Evidence map›Paper›PMID 33267792›Full record

ArticleBMC bioinformatics2020

LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata.

Bo Zhao, Luke Bryant, Rebecca Cordell, Michael Wilde, Dahlia Salman, Dorota Ruszkiewicz, Wadah Ibrahim, Amisha Singapuri, Tim Coats, Erol Gaillard and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

19 authors.

Bo ZhaoDepartment of Respiratory Sciences, University of Leicester, Leicester, UK.
Luke BryantNIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
Rebecca CordellNIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
Michael WildeNIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
Dahlia SalmanDepartment of Chemistry, Loughborough University, Loughborough, UK.
Dorota RuszkiewiczDepartment of Chemistry, Loughborough University, Loughborough, UK.
Wadah IbrahimDepartment of Respiratory Sciences, University of Leicester, Leicester, UK.
Amisha SingapuriNIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
Tim CoatsDepartment of Chemistry, University of Leicester, Leicester, UK.
Erol GaillardDepartment of Respiratory Sciences, University of Leicester, Leicester, UK.
Caroline BeardsmoreDepartment of Respiratory Sciences, University of Leicester, Leicester, UK.
Toru SuzukiNIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
Leong NgNIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
Neil GreeningNIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK.
Paul ThomasDepartment of Chemistry, Loughborough University, Loughborough, UK.
Paul MonksDepartment of Chemistry, University of Leicester, Leicester, UK.
Christopher BrightlingDepartment of Respiratory Sciences, University of Leicester, Leicester, UK.
Salman SiddiquiDepartment of Respiratory Sciences, University of Leicester, Leicester, UK.
Robert C FreeDepartment of Respiratory Sciences, University of Leicester, Leicester, UK. rob.free@leicester.ac.uk.ORCID http://orcid.org/0000-0001-8053-435X

Funding

British Lung Foundation BLFPHD17-1Department of Health PDF-2017-10-052Engineering and Physical Sciences Research Council MR/N005880/1Medical Research Council MR/N005880/1
6 · The paper itself

Abstract

backgroundData handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, flexible metadata collection and linkage of related experimental data generated locally by vendor software.

resultsTo address this problem, we created LabPipe, a flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study.

conclusionsLabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges.

Indexed as

MetadataComputational BiologyData AnalysisHumansSoftwareBiomedicalBreathomicsData managementMetadata

Identifiers

PMID33267792
PMCPMC7709404

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.