Evidence map›Paper›PMID 40832351›Full record

ArticlebioRxiv : the preprint server for biology2025

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data.

Taha Mohseni Ahooyi, Benjamin Stear, J Alan Simmons, Vincent T Metzger, Praveen Kumar, John Erol Evangelista, Daniel J B Clarke, Zhuorui Xie, Heesu Kim, Sherry L Jenkins and 34 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

44 authors.

Taha Mohseni AhooyiDepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia PA USA.
Benjamin StearDepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia PA USA.
J Alan SimmonsDepartment of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh PA USA.
Vincent T MetzgerDepartment of Internal Medicine, Division of Translational Informatics, University of New Mexico Health Sciences Center, University of New Mexico NM USA.
Praveen KumarDepartment of Internal Medicine, Division of Translational Informatics, University of New Mexico Health Sciences Center, University of New Mexico NM USA.
John Erol EvangelistaDepartment of Pharmacological Sciences; Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York NY USA.
Daniel J B ClarkeDepartment of Pharmacological Sciences; Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York NY USA.
Zhuorui XieDepartment of Pharmacological Sciences; Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York NY USA.
Heesu KimDepartment of Pharmacological Sciences; Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York NY USA.
Sherry L JenkinsDepartment of Pharmacological Sciences; Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York NY USA.
Mano R MauryaDepartment of Bioengineering, University of California San Diego, San Diego CA USA.
Srinivasan RamachandranDepartment of Bioengineering, University of California San Diego, San Diego CA USA.
Eoin FahyDepartment of Bioengineering, University of California San Diego, San Diego CA USA.
Thomas H GillespieDepartment of Neuroscience, School of Medicine, University of California San Diego, San Diego CA USA.
Fahim T ImamDepartment of Neuroscience, School of Medicine, University of California San Diego, San Diego CA USA.
Natallia KokashInstitute of Informatics, University of Amsterdam, the Netherlands.
Matthew E RothDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston TX USA.
Robert FullemDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston TX USA.
Dubravka JevticPersida Bio, Brooklyn NY USA.
Aleks MihajlovicPersida Bio, Brooklyn NY USA.
Michael TiemeyerComplex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
Clara BakkerDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Andrew J SchroederDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Julia MarkowskiDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Jared NedzelBroad Institute of MIT and Harvard, Cambridge MA USA.
Dave D HillDepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia PA USA.
James TerryDepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia PA USA.
Christopher NemarichCenter for Data Driven Discovery, The Children's Hospital of Philadelphia, Philadelphia PA USA.
Jyl BolineInformed Minds Inc. Walnut Creek, CA USA.
Peter J ParkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID 0000-0001-9378-960X
Kristin G ArdlieBroad Institute of MIT and Harvard, Cambridge MA USA.
Jeet VoraDepartment of Biochemistry and Molecular Medicine, George Washington University, Washington DC USA.
Raja MazumderDepartment of Biochemistry and Molecular Medicine, George Washington University, Washington DC USA.
Rene RanzingerComplex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
Bernard de BonoAuckland Bioengineering Institute, University of Auckland, Auckland NZ.
Shankar SubramaniamDepartment of Bioengineering, University of California San Diego, San Diego CA USA.
Jeffrey S GretheDepartment of Neuroscience, School of Medicine, University of California San Diego, San Diego CA USA.
Jeremy J YangDepartment of Internal Medicine, Division of Translational Informatics, University of New Mexico Health Sciences Center, University of New Mexico NM USA.
Christophe G LambertDepartment of Internal Medicine, Division of Translational Informatics, University of New Mexico Health Sciences Center, University of New Mexico NM USA.
Adam ResnickCenter for Data Driven Discovery, The Children's Hospital of Philadelphia, Philadelphia PA USA.
Aleks MilosavljevicDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston TX USA.
Avi Ma'ayanDepartment of Pharmacological Sciences; Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York NY USA.
Jonathan C SilversteinDepartment of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh PA USA.
Deanne M TaylorDepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia PA USA.ORCID 0000-0002-3302-4610

Funding

4D Nucleome Network Data Coordination and Integration CenterU01CA200059 · NCI · HARVARD MEDICAL SCHOOL · PI PARK, PETER J · 2015 to 2024
$24.4M
SenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1M
U2C Kids First Admin Supplement - data transferU2CHL138346 · NHLBI · CHILDREN'S HOSP OF PHILADELPHIA · PI RESNICK, ADAM CAIN · 2017 to 2022
$21.5M
Flexible Hybrid Cloud Infrastructure for Seamless Integration and Use of Human Biomolecular Data and Reference Maps [1 of 5]OT2OD033759 · OD · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D., SILVERSTEIN, JONATHAN C. · 2022 to 2025
$20.4M
National Metabolomics Data Repository - nextgen Metabolomics WorkbenchU2CDK119886 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2018 to 2021
$12.7M
Kids First Data Resource Center (KFDRC): Harnessing Data-Driven Opportunities in the Present on behalf of the Future of Common Fund Data Ecosystem (CFDE)OT2OD030162 · OD · CHILDREN'S HOSP OF PHILADELPHIA · PI DIGIOVANNA, JACK, HEATH, ALLISON · 2020 to 2025
$10.7M
K-CORE: Curation and Knowledge Management for SPARCOT2OD030541 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DE BONO, BERNARD, MARTONE, MARYANN E · 2020 to 2024
$10.3M
Functional Genomic Dissection of Alzheimer's Disease in Humans and Drosophila ModelsU01AG072439 · NIA · BAYLOR COLLEGE OF MEDICINE · PI BELLEN, HUGO J, BOTAS, JUAN · 2021 to 2025
$8.4M
The CFDE WorkbenchOT2OD036435 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI, SUBRAMANIAM, SHANKAR · 2023 to 2025
$7.2M
GlyGen growth and evolution into a central resource for glycans and glycoconjugatesR24GM146616 · NIGMS · UNIVERSITY OF GEORGIA · PI Raja Mazumder, Rene Ranzinger · 2022 to 2026
$5.5M
Proteogenomic translator for cancer biomarker discovery towards precision medicineU24CA271114 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Avi Ma'ayan, Pei Wang · 2022 to 2026
$5.0M
Scientific Outreach ComponentU54DA049098 · NIDA · BAYLOR COLLEGE OF MEDICINE · PI MILOSAVLJEVIC, ALEKSANDAR · 2019 to 2022
$5.0M
NCI NIH HHS U01 CA200059NCI NIH HHS U24 CA264250NCI NIH HHS U24 CA268108NCI NIH HHS U24 CA271114NHLBI NIH HHS U2C HL138346NIA NIH HHS U01 AG072439NIDA NIH HHS U54 DA049098NIDDK NIH HHS U24 DK141185NIDDK NIH HHS U2C DK119886NIGMS NIH HHS R24 GM146616NIH HHS OT2 OD030160NIH HHS OT2 OD030162NIH HHS OT2 OD030541NIH HHS OT2 OD030544NIH HHS OT2 OD030545NIH HHS OT2 OD030546NIH HHS OT2 OD030547NIH HHS OT2 OD032092NIH HHS OT2 OD032619NIH HHS OT2 OD033759NIH HHS OT2 OD036435NIH HHS R03 OD030600NIH HHS U24 OD038422NIH HHS U24 OD038423
6 · The paper itself

Abstract

The Data Distillery Knowledge Graph (DDKG) is a framework for semantic integration and querying of biomedical data across domains. Built for the NIH Common Fund Data Ecosystem, it supports translational research by linking clinical and experimental datasets in a unified graph model. Clinical standards such as ICD-10, SNOMED, and DrugBank are integrated through UMLS, while genomics and basic science data are structured using ontologies and standards such as HPO, GENCODE, Ensembl, STRING, and ClinVar. The DDKG uses a property graph architecture based on the UBKG infrastructure and supports ontology-based ingestion, identifier normalization, and graph-native querying. The system is modular and can be extended with new datasets or schema modules. We demonstrate its utility for informatics queries across eight use cases, including regulatory variant analysis, tissue-specific expression, biomarker discovery, and cross-species variant prioritization. The DDKG is accessible via a public interface, a programmatic API, and downloadable builds for local use.

Identifiers

PMID40832351
PMCPMC12363844

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

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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.