Evidence map›Paper›PMID 35380605›Full record

ArticleBioinformatics (Oxford, England)2022

ELIXIR biovalidator for semantic validation of life science metadata.

Isuru Liyanage, Tony Burdett, Bert Droesbeke, Karoly Erdos, Rolando Fernandez, Alasdair Gray, Muhammad Haseeb, Simon Jupp, Flavia Penim, Cyril Pommier and 3 more

Erratum issuedOpen access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.2field-weighted citation impact, top 53% of its field
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, 2 citations in OpenAlex.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors at 6 institutions in 4 countries.

Isuru LiyanageEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0002-4839-5158
Tony BurdettEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0002-2513-5396
Bert DroesbekeDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.ORCID 0000-0003-0522-5674
Karoly ErdosEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0003-3063-8745
Rolando FernandezEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0002-6186-1133
Alasdair GrayDepartment of Computer Science, Heriot-Watt University, Edinburgh EH14 4AS, UK.ORCID 0000-0002-5711-4872
Muhammad HaseebEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0003-4427-4700
Simon JuppEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0002-0643-3144
Flavia PenimEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0001-7192-5279
Cyril PommierINRAE, BioinfOmics, Plant Bioinformatics Facility, Université Paris-Saclay, 78026 Versailles, France.ORCID 0000-0002-9040-8733
Philippe Rocca-SerraDepartment of Engineering Science, University of Oxford e-Research Centre, University of Oxford, Oxford OX1 3QG, UK.ORCID 0000-0001-9853-5668
Mélanie CourtotEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.ORCID 0000-0002-9551-6370
Frederik CoppensDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.ORCID 0000-0001-6565-5145
European Bioinformatics Institute · GBGhent University · BEHeriot-Watt University · GBOntario Institute for Cancer Research · CAUniversité Paris-Saclay · FRUniversity of Oxford · GB

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

summaryTo advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents. AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Biological Science DisciplinesMetadataSemanticsSoftware

Identifiers

PMID35380605
PMCPMC9154242
OpenAlexW4226329328

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.