Evidence map›Paper›PMID 38249839›Full record

ArticleLearning health systems2024

Toward a common standard for data and specimen provenance in life sciences.

Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio and 26 more

Abstract read
In one paragraph

Article in Learning health systems, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images.IEEE/ACM transactions on computational biology and bioinformatics
    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

36 authors.

Rudolf WittnerBBMRI-ERIC Graz Austria.ORCID https://orcid.org/0000-0002-0003-2024
Petr HolubBBMRI-ERIC Graz Austria.ORCID https://orcid.org/0000-0002-5358-616X
Cecilia MasciaCRS4-Center for Advanced Studies Research and Development in Sardinia Pula Italy.ORCID https://orcid.org/0000-0002-8952-725X
Francesca FrexiaCRS4-Center for Advanced Studies Research and Development in Sardinia Pula Italy.ORCID https://orcid.org/0000-0003-1007-1286
Heimo MüllerMedical University Graz Graz Austria.ORCID https://orcid.org/0000-0002-9691-4872
Markus PlassMedical University Graz Graz Austria.ORCID https://orcid.org/0000-0003-2718-7648
Clare AlloccaNational Institute of Standards and Technology Gaithersburg Maryland USA.ORCID https://orcid.org/0000-0003-4132-0396
Fay BetsouBiological Resource Center of Institut Pasteur (CRBIP) Paris France.ORCID https://orcid.org/0000-0002-0558-4653
Tony BurdettEMBL's European Bioinformatics Institute (EMBL-EBI) Cambridge UK.
Ibon CancioPlentzia Marine Station (PiE-UPV/EHU) University of the Basque Country, EMBRC-Spain Bilbao Spain.ORCID https://orcid.org/0000-0003-4841-0079
Adriane ChapmanUniversity of Southampton Southampton UK.
Martin ChapmanKing's College London London UK.ORCID https://orcid.org/0000-0002-5242-9701
Mélanie CourtotOntario Institute for Cancer Research Toronto Ontario Canada.ORCID https://orcid.org/0000-0002-9551-6370
Vasa CurcinKing's College London London UK.ORCID https://orcid.org/0000-0002-8308-2886
Johann EderUniversity of Klagenfurt Klagenfurt Austria.ORCID https://orcid.org/0000-0001-6050-468X
Mark ElliotDepartment of Social Statistics, School of Social Sciences University of Manchester Manchester UK.ORCID https://orcid.org/0000-0002-3142-4493
Katrina ExterFlanders Marine Institute (VLIZ), EMBRC-Belgium Ostend Belgium.ORCID https://orcid.org/0000-0002-5911-1536
Carole GobleDepartment of Computer Science University of Manchester Manchester UK.ORCID https://orcid.org/0000-0003-1219-2137
Martin GolebiewskiHeidelberg Institute for Theoretical Studies (HITS gGmbH) Heidelberg Germany.ORCID https://orcid.org/0000-0002-8683-7084
Bron KislerIndependent consultant.
Andreas KremerITTM S.A. Esch-sur-Alzette Luxembourg.ORCID https://orcid.org/0000-0003-1466-0600
Simone LeoCRS4-Center for Advanced Studies Research and Development in Sardinia Pula Italy.ORCID https://orcid.org/0000-0001-8271-5429
Sheng Lin-GibsonBiosystems and Biomaterials Division NIST Gaithersburg Maryland USA.ORCID https://orcid.org/0000-0001-5092-1519
Anna MarsanoDepartment of Biomedicine University of Basel Basel Switzerland.ORCID https://orcid.org/0000-0002-3084-0823
Marco MattavelliSCI-STI-MM École Politechnique Fédérale de Lausanne Lausanne Switzerland.ORCID https://orcid.org/0000-0002-7742-0332
Josh MooreCentre for Gene Regulation and Expression and Division of Computational Biology, School of Life Sciences University of Dundee Dundee UK.ORCID https://orcid.org/0000-0003-4028-811X
Hiroki NakaeJapan bio-Measurement and Analysis Consortium Tokyo Japan.ORCID https://orcid.org/0000-0002-5064-8468
Isabelle PerseilINSERM-Institut National de la Sante et de la Recherche Medicale Paris France.ORCID https://orcid.org/0000-0001-9058-9290
Ayat SalmanStandards Council of Canada Ottawa Ontario Canada.ORCID https://orcid.org/0000-0002-7747-2757
James SlukaBiocomplexity Institute Indiana University Bloomington Indiana USA.ORCID https://orcid.org/0000-0002-5901-1404
Stian Soiland-ReyesDepartment of Computer Science University of Manchester Manchester UK.ORCID https://orcid.org/0000-0001-9842-9718
Caterina Strambio-De-CastilliaProgram in Molecular Medicine University of Massachusetts Chan Medical School Worcester Massachusetts USA.ORCID https://orcid.org/0000-0002-1069-1816
Michael SussmanUS Department of Agriculture Washington District of Columbia USA.ORCID https://orcid.org/0000-0002-8432-0487
Jason R SwedlowCentre for Gene Regulation and Expression and Division of Computational Biology, School of Life Sciences University of Dundee Dundee UK.ORCID https://orcid.org/0000-0002-2198-1958
Kurt ZatloukalMedical University Graz Graz Austria.ORCID https://orcid.org/0000-0001-5299-7218
Jörg GeigerInterdisciplinary Bank of Biomaterials and Data Würzburg (ibdw) Würzburg Germany.ORCID https://orcid.org/0000-0002-7689-531X

Funding

4D Nucleome Network Data Coordination and Integration CenterU01CA200059 · NCI · HARVARD MEDICAL SCHOOL · PI PARK, PETER J · 2015 to 2024
$24.4M
The Human Body Atlas: High-Resolution, Functional Mapping of Voxel, Vector, and Meta DatasetsOT2OD026671 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2018 to 2021
$3.5M
Competitive Renewal of Development, Improvement and Extension of the Tissue Simulation Environment - CompuCell3DR01GM122424 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI GLAZIER, JAMES ALEXANDER · 2017 to 2020
$1.7M
Dissemination of libRoadRunner and CompuCell3DU24EB028887 · NIBIB · UNIVERSITY OF WASHINGTON · PI GLAZIER, JAMES ALEXANDER, SAURO, HERBERT M. · 2019 to 2023
$1.5M
EPA RD840027NCI NIH HHS U01 CA200059NIBIB NIH HHS U24 EB028887NIGMS NIH HHS R01 GM122424NIH HHS OT2 OD026671Wellcome Trust
6 · The paper itself

Abstract

Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by the quality of the samples, the experimental methods, and the data analysis. Therefore, a comprehensive and precise documentation of the pre-analytical conditions, the analytical procedures, and the data processing are essential to be able to assess the validity of the research results. With the increasing importance of the exchange, reuse, and sharing of data and samples, procedures are required that enable cross-organizational documentation, traceability, and non-repudiation. At present, this information on the provenance of samples and data is mostly either sparse, incomplete, or incoherent. Since there is no uniform framework, this information is usually only provided within the organization and not interoperably. At the same time, the collection and sharing of biological and environmental specimens increasingly require definition and documentation of benefit sharing and compliance to regulatory requirements rather than consideration of pure scientific needs. In this publication, we present an ongoing standardization effort to provide trustworthy machine-actionable documentation of the data lineage and specimens. We would like to invite experts from the biotechnology and biomedical fields to further contribute to the standard.

Indexed as

biotechnologyInternational Organization for Standardizationprovenance informationstandardization

Identifiers

PMID38249839
PMCPMC10797572

What OpenQuestion holds

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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.