ArticleeLife2020
Wikidata as a knowledge graph for the life sciences.
Abstract read
In one paragraph
Article in eLife, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
0numbers the graph read from it
0cells of the map it votes in
48citing papers in PubMed
–field-weighted citation impact
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.
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.
Who cites it
48 citing papers in PubMed.
- pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources.Bioinformatics (Oxford, England) · 2026Article
- Protein Design Enters the Artificial Intelligence Era: Foundations, Tools, and Emerging Paradigms.Computational and structural biotechnology journal · 2026Review
- Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0.Briefings in bioinformatics · 2025Article
- Wikidata for botanists: benefits of collaborating and sharing Linked Open Data.Annals of botany · 2025Article
- Automated descriptive cell type naming in flow and mass cytometry with CytoPheno.Scientific reports · 2025Article
- Quantifying the impact of biobanks and cohort studies.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Overview and Prospects of DNA Sequence Visualization.International journal of molecular sciences · 2025Review
- Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions.Frontiers in immunology · 2025Review
- A framework for integrating biomedical knowledge in Wikidata with open biological and biomedical ontologies and MeSH keywords.Heliyon · 2024Article
- An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing.PLoS computational biology · 2024Article
- Integrating knowledge graphs into machine learning models for survival prediction and biomarker discovery in patients with non-small-cell lung cancer.Journal of translational medicine · 2024Article
- Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing.Scientific data · 2024Article
- The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources.Scientific data · 2024Article
- A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery.ACS central science · 2024Article
- The SIB Swiss Institute of Bioinformatics Semantic Web of data.Nucleic acids research · 2024Article
- Article
- Current and future directions in network biology.Bioinformatics advances · 2024Article
- BioBLP: a modular framework for learning on multimodal biomedical knowledge graphs.Journal of biomedical semantics · 2023Article
- Ten quick tips for editing Wikidata.PLoS computational biology · 2023Article
- Capturing Semantic Relationships in Electronic Health Records Using Knowledge Graphs: An Implementation Using MIMIC III Dataset and GraphDB.Healthcare (Basel, Switzerland) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
30 authors.
Andra Waagmeester *Micelio, Antwerpen, Belgium.ORCID 0000-0001-9773-4008
Gregory Stupp *Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0002-0644-7212
Sebastian Burgstaller-MuehlbacherCenter for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.ORCID 0000-0003-4640-3510
Benjamin M GoodDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0002-7334-7852
Malachi GriffithMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States.ORCID 0000-0002-6388-446X
Obi L GriffithMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, United States.ORCID 0000-0002-0843-4271
Kristina HanspersInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States.ORCID 0000-0001-5410-599X
Henning HermjakobEuropean Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.ORCID 0000-0001-8479-0262
Toby S HudsonSchool of Chemistry, The University of Sydney, Sydney, Australia.ORCID 0000-0002-3348-3622
Kevin HybiskeDivision of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, United States.ORCID 0000-0002-2967-3079
Sarah M KeatingEuropean Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.ORCID 0000-0002-3356-3542
Magnus ManskeWellcome Trust Sanger Institute, Cambridge, United Kingdom.ORCID 0000-0001-5916-0947
Michael MayersDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0002-7792-0150
Daniel MietchenSchool of Data Science, University of Virginia, Charlottesville, United States.ORCID 0000-0001-9488-1870
Elvira MitrakaUniversity of Maryland School of Medicine, Baltimore, United States.ORCID 0000-0003-0719-3485
Alexander R PicoInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States.ORCID 0000-0001-5706-2163
Timothy PutmanDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0002-4291-0737
Anders RiuttaInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States.ORCID 0000-0002-4693-0591
Nuria Queralt-RosinachDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0003-0169-8159
Lynn M SchrimlUniversity of Maryland School of Medicine, Baltimore, United States.ORCID 0000-0001-8910-9851
Thomas ShafeeDepartment of Animal Plant and Soil Sciences, La Trobe University, Melbourne, Australia.ORCID 0000-0002-2298-7593
Denise SlenterDepartment of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.ORCID 0000-0001-8449-1318
Ralf StephanRetired researcher, Berlin, Germany.ORCID 0000-0002-4650-631X
Katherine ThorntonYale University Library, Yale University, New Haven, United States.ORCID 0000-0002-4499-0451
Ginger TsuengDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0001-9536-9115
Roger TuDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0002-7899-1604
Sabah Ul-HasanDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0001-6334-452X
Egon WillighagenDepartment of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.ORCID 0000-0001-7542-0286
Chunlei WuDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0002-2629-6124
Andrew I SuDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.ORCID 0000-0002-9859-4104
Funding
Scripps Translational Science InstituteUL1TR002550 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI TOPOL, ERIC JEFFREY · 2018 to 2022
$28.9MTR&D 3 - Network Guided Machine LearningP41GM103504 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2012 to 2024
$17.3MReactome - CoreU41HG003751 · NHGRI · ONTARIO INSTITUTE FOR CANCER RESEARCH · PI STEIN, LINCOLN D. · 2012 to 2021
$14.5MTRAININGU54GM114833 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LINDSEY, MERRY L., PING, PEIPEI · 2014 to 2017
$13.8MFunctional genomics for ChlamydiaR01AI126785 · NIAID · UNIVERSITY OF WASHINGTON · PI HEFTY, P SCOTT, HYBISKE, KEVIN · 2016 to 2025
$7.1MThe Gene Wiki: Community intelligence applied to gene annotationR01GM089820 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI SU, ANDREW I · 2010 to 2021
$5.2MReactome: An Open Knowledgebase of Human PathwaysP41HG003751 · NHGRI · ONTARIO INSTITUTE FOR CANCER RESEARCH · PI STEIN, LINCOLN D. · 2007 to 2011
$4.5MStandardized and Genome-Wide Clinical Interpretation of Complex Genotypes for Cancer Precision MedicineU24CA237719 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, OBI L. · 2019 to 2023
$3.8MWikiPathways Project: At the Intersection of Big Data and Researcher KnowledgeR01GM100039 · NIGMS · J. DAVID GLADSTONE INSTITUTES · PI PICO, ALEXANDER R · 2012 to 2020
$3.4MDEVELOPMENT OF INFORMATICS RESOURCES FOR INTERPRETATION OF CLINICALLY ACTIONABLE VARIANTS IN CANCERU01CA209936 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, OBI L. · 2016 to 2018
$1.0MIntegrated Analysis & Interpretation of Whole Genome Exome & Transcriptome SequenR00HG007940 · NHGRI · WASHINGTON UNIVERSITY · PI GRIFFITH, MALACHI · 2017 to 2019
$724kNCATS NIH HHS UL1 TR002550NCI NIH HHS U01 CA209936NCI NIH HHS U24 CA237719NHGRI NIH HHS P41 HG003751NHGRI NIH HHS R00 HG007940NHGRI NIH HHS U41 HG003751NIAID NIH HHS R01 AI126785NIGMS NIH HHS P41 GM103504NIGMS NIH HHS R01 GM089820NIGMS NIH HHS R01 GM100039NIGMS NIH HHS U54 GM114833
Abstract
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.
Indexed as
Biological Science DisciplinesComputational BiologyDatabases, FactualGenomicsProteomicsHumansPattern Recognition, Automatedcomputational biologydata miningdrug repurposingknowledge graphsnonescience forumsystems biologywikidata
Identifiers
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.