Evidence map›Paper›PMID 35441678›Full record

ArticleBioinformatics (Oxford, England)2022

Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories.

Alexander M Waldrop, John B Cheadle, Kira Bradford, Alexander Preiss, Robert Chew, Jonathan R Holt, Yaphet Kebede, Nathan Braswell, Matt Watson, Virginia Hench and 9 more

Abstract 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. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Alexander M WaldropCenter for Genomics, Bioinformatics, and Translational Research, RTI International, Research Triangle Park, NC 27709-2194, USA.ORCID 0000-0002-4502-7894
John B CheadleResearch Computing Division, RTI International, Research Triangle Park, NC 27709-2194, USA.
Kira BradfordRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.
Alexander PreissCenter for Data Science, RTI International, Research Triangle Park, NC 27709-2194, USA.
Robert ChewCenter for Data Science, RTI International, Research Triangle Park, NC 27709-2194, USA.
Jonathan R HoltCenter for Data Science, RTI International, Research Triangle Park, NC 27709-2194, USA.
Yaphet KebedeRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.
Nathan BraswellResearch Computing Division, RTI International, Research Triangle Park, NC 27709-2194, USA.
Matt WatsonRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.
Virginia HenchCenter for Genomics, Bioinformatics, and Translational Research, RTI International, Research Triangle Park, NC 27709-2194, USA.
Andrew CrerarCenter for Genomics, Bioinformatics, and Translational Research, RTI International, Research Triangle Park, NC 27709-2194, USA.
Chris M BallResearch Computing Division, RTI International, Research Triangle Park, NC 27709-2194, USA.
Carl SchreepRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.
P J LinebaughRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.
Hannah HilesRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.
Rebecca BoylesResearch Computing Division, RTI International, Research Triangle Park, NC 27709-2194, USA.
Chris BizonRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.ORCID 0000-0002-9491-7674
Ashok KrishnamurthyRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.
Steve CoxRenaissance Computing Institute, University of Chapel Hill, North Carolina, Chapel Hill, NC 27599-7568, USA.

Funding

A Strategy for Heal Federated Data EcosystemOT2OD031940 · OD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Suparna Goswami · 2021 to 2026
$25.5M
The Integration of Trans-omics for Precision Medicine (TOPMED) and Other Heart, Lung, Blood and Sleep (HLBS) Data Sets with the Data CommonsOT3HL142479 · NHLBI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI KRISHNAMURTHY, ASHOK KUMAR · 2017 to 2020
$6.1M
Biomedical Data Translator Technical Feasibility Assessment and Architecture DesignOT3TR002020 · NCATS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI AHALT, STANLEY CARLTON, TROPSHA, ALEXANDER · 2016 to 2019
$3.1M
Helping to End Addiction Long-Term (HEAL) Office 1-OT2-OD031940-01National Center for Advancing Translational Sciences (NCATS) 1-OT3-TR002020-01National Heart, Lung, and Blood Institute (NHLBI) 1-OT3-HL142479-01NCATS NIH HHS OT3 TR002020NHLBI NIH HHS OT3 HL142479NIH HHS OT2 OD031940
6 · The paper itself

Abstract

motivationAs the number of public data resources continues to proliferate, identifying relevant datasets across heterogenous repositories is becoming critical to answering scientific questions. To help researchers navigate this data landscape, we developed Dug: a semantic search tool for biomedical datasets utilizing evidence-based relationships from curated knowledge graphs to find relevant datasets and explain why those results are returned.

resultsDeveloped through the National Heart, Lung and Blood Institute's (NHLBI) BioData Catalyst ecosystem, Dug has indexed more than 15 911 study variables from public datasets. On a manually curated search dataset, Dug's total recall (total relevant results/total results) of 0.79 outperformed default Elasticsearch's total recall of 0.76. When using synonyms or related concepts as search queries, Dug (0.36) far outperformed Elasticsearch (0.14) in terms of total recall with no significant loss in the precision of its top results. AVAILABILITY AND IMPLEMENTATION: Dug is freely available at https://github.com/helxplatform/dug. An example Dug deployment is also available for use at https://search.biodatacatalyst.renci.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Search EngineSemanticsAbstracting and IndexingEcosystem

Identifiers

PMID35441678
PMCPMC9991886

What Socratic holds

Textmetadata
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 Socratic graph.