ArticlebioRxiv : the preprint server for biology2026
The Common Fund Data Ecosystem (CFDE).
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92 authors.
Julie A JurgensPrograms in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0003-4822-9384
Andreas BueckleDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.ORCID 0000-0002-8977-498X
Jeet VoraDepartment of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA.
Mano R MauryaDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Taha Mohseni AhooyiDepartment of Biomedical and Health Informatics (DBHi), the Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Erika ZhengDepartment of Physiology, UCLA School of Medicine, Los Angeles, CA, USA; Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA, USA.
Benjamin StearDepartment of Biomedical and Health Informatics (DBHi), the Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Ding WangDepartment of Physiology, UCLA School of Medicine, Los Angeles, CA, USA; Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA, USA.
Caitlin ReeDepartment of Physiology, UCLA School of Medicine, Los Angeles, CA, USA; Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA, USA.
Srinivasan RamachandranDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Anton NekrutenkoHuck Institutes for Life Sciences, Penn State University, University Park, PA, USA.
MacKenzie BrandesPrograms in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Swathi ThakerSystems Pharmacology AI Research Center, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA.
Daniel H KatzDivision of Computational Medicine, Stanford University, Stanford, CA, USA; Division of Cardiovascular Medicine, Stanford University, CA, USA.
Monica C Munoz-TorresDepartment of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, CO, USA.
Ido DiamantDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Hye-Jung E ChunDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
J Alan SimmonsDepartment of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Sarah K TasianDepartment of Pediatrics and Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.ORCID 0000-0003-1327-1662
Sherry L JenkinsDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
John Erol EvangelistaDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Hardik DodiaDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Surya SahaVelsera, Charlestown, MA, USA.
Martin A LindquistDepartment of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
Vennela GajjalaTexas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA.
Christopher NemarichCenter for Data-Driven Discovery in Biomedicine (D3B), the Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Jimmy ZhenDepartment of Medicine, Stanford University, Stanford, CA, USA.
Karen E RossDepartment of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA.
Anna I ByrdDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Alex ShilinPrograms in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Vincent T MetzgerDepartment of Internal Medicine, University of New Mexico, Albuquerque, NM, USA.
Cristian G BologaDepartment of Internal Medicine, University of New Mexico, Albuquerque, NM, USA.
Sumana SrinivasanDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Dongkeun JangPrograms in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Praveen KumarDepartment of Internal Medicine, University of New Mexico, Albuquerque, NM, USA.
Lily D TaubDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Mia P LevantoDepartment of Medicine, Stanford University, Stanford, CA, USA.
Varduhi PetrosyanDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Manju AnandakrishnanCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
Mariia KimDepartment of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA.
Daniel J B ClarkeDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Adriana IvichDepartment of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, CO, USA.
Daniel J CrichtonJet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
Shava SmallenSan Diego Supercomputing Center, The University of California San Diego, La Jolla, CA, USA.
Dominic BordelonPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA.
Chuming ChenCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
Andrew J SchroederDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Ashish MahabalCalifornia Institute of Technology, Pasadena, CA, USA.
Ivan Cao-BergPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA.
Sean KimDepartment of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA.
Daniall MasoodDepartment of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA.
Keyang YuDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Kyle J GaultonDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
David Jimenez-MoralesDepartment of Medicine, Stanford University, Stanford, CA, USA.
John Michael RinconDepartment of Physiology, UCLA School of Medicine, Los Angeles, CA, USA; Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA, USA.
Brendan J HonickPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA.
Wei WangDepartment of Physiology, UCLA School of Medicine, Los Angeles, CA, USA; Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA, USA.
Cathy H WuCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
Aleksandar MilosavljevicDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Philip D BloodPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA.
Jyl BolineInformed Minds Inc., Walnut Creek, CA, USA.
Tudor I OpreaDepartment of Internal Medicine, University of New Mexico, Albuquerque, NM, USA.ORCID 0000-0002-6195-6976
Christophe G LambertDepartment of Internal Medicine, University of New Mexico, Albuquerque, NM, USA.ORCID 0000-0003-1994-2893
Bernard de BonoIndiana University School of Medicine, Indianapolis, IN, USA; Auckland Bioengineering Institute, Auckland, NZ.
Peter J ParkDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID 0000-0001-9378-960X
Jonathan C SilversteinDepartment of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Jason FlannickPrograms in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Jeremy J YangDepartment of Internal Medicine, University of New Mexico, Albuquerque, NM, USA.
Jeffrey S GretheDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Shankar SubramaniamDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Michael TiemeyerComplex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
Timothy ClarkDepartment of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA.
Matthew T WheelerDepartment of Medicine, Stanford University, Stanford, CA, USA.
Ari KahnTexas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA.
Jennifer BurnetteOak Ridge Associated Universities (ORAU) Government Services, ORAU, Oak Ridge, TN, USA.
Rene RanzingerComplex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
Michael C SchatzDepartments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
LaFrancis GibsonOak Ridge Associated Universities (ORAU) Government Services, ORAU, Oak Ridge, TN, USA.
Noël P BurttPrograms in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
James P CarsonTexas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA.
Jake Y ChenSystems Pharmacology AI Research Center, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA.ORCID 0000-0001-8829-7504
Peipei PingDepartment of Biomedical Informatics, College of Medicine at Phoenix, University of Arizona, Phoenix, AZ, USA.
Sean DavisDepartment of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, CO, USA.
Deanne M TaylorDepartment of Biomedical and Health Informatics (DBHi), the Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Katy BörnerDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
Allissa DillmanBioData Sage, LLC, Bethesda, MD, USA.
Kelli BurseyOak Ridge Associated Universities (ORAU) Government Services, ORAU, Oak Ridge, TN, USA.
Avi Ma'ayanDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
CFDE Consortium
Raja MazumderDepartment of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA.
Matthew E RothDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Casey S GreeneDepartment of Biomedical Informatics, University of Colorado Anschutz School of Medicine, Aurora, CO, USA.ORCID 0000-0001-8713-9213
Funding
UniProt - Text Mining and Large Language models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's DiseaseU24HG007822 · NHGRI · GEORGETOWN UNIVERSITY · PI Alex Bateman, Alan James Bridge · 2018 to 2026
$53.0MKOMP2-Phase3 Production and Phenotyping by the DTCC Consortium TCP Transfer to UC DavisUM1OD023221 · OD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI KC KENT LLOYD · 2016 to 2026
$45.7MBridge2AI:Salutogenesis Data Generation ProjectOT2OD032644 · OD · WASHINGTON UNIVERSITY · PI BAXTER, SALLY LIU, CHUTE, CHRISTOPHER G · 2022 to 2025
$32.7MHigh-throughput targeted mutagenesis of mouse stem cell linesU01HG004080 · NHGRI · CHILDREN'S HOSPITAL & RES CTR AT OAKLAND · PI DE JONG, PIETER J. · 2006 to 2010
$28.1M Bridge2AI: Patient-Focused Collaborative Hospital Repository Uniting Standards (CHoRUS) for Equitable AIOT2OD032701 · OD · MASSACHUSETTS GENERAL HOSPITAL · PI BIHORAC, AZRA, CLERMONT, GILLES · 2022 to 2025
$24.6MSenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1MBridge2AI: Cell Maps for AI (CM4AI) Data Generation ProjectOT2OD032742 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jean-Christophe Bélisle-Pipon, TIMOTHY W CLARK · 2022 to 2026
$21.5MConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI HIMMELFARB, JONATHAN, IYENGAR, SRINIVAS RAVI V · 2017 to 2021
$21.0MFlexible 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
$20.4MBridge2AI: Voice as a Biomarker of Health - Building an ethically sourced, bioaccoustic database to understand disease like never beforeOT2OD032720 · OD · UNIVERSITY OF SOUTH FLORIDA · PI BENSOUSSAN, YAEL EMILIE, BÉLISLE-PIPON, JEAN-CHRISTOPHE · 2022 to 2025
$18.0MKOMP Phase II Mouse PhenotypingU54HG006364 · NHGRI · UNIVERSITY OF CALIFORNIA AT DAVIS · PI LLOYD, KC KENT · 2011 to 2015
$16.3MDissemination and Coordinating Center for the SCGE ConsortiumU24HG010423 · NHGRI · MEDICAL COLLEGE OF WISCONSIN · PI DWINELL, MELINDA R · 2019 to 2023
$15.0MNCI NIH HHS R01 CA293587NCI NIH HHS U01 CA232486NCI NIH HHS U01 CA243072NCI NIH HHS U24 CA268108NCRR NIH HHS U42 RR024244NHGRI NIH HHS U01 HG004080NHGRI NIH HHS U24 HG006620NHGRI NIH HHS U24 HG007822NHGRI NIH HHS U24 HG010423NHGRI NIH HHS U54 HG006364NHGRI NIH HHS U54 HG012510NHGRI NIH HHS U54 HG012513NHGRI NIH HHS U54 HG012517NHLBI NIH HHS K23 HL164980NHLBI NIH HHS U24 HL168712NIA NIH HHS U54 AG076043NIDA NIH HHS U54 DA036134NIDA NIH HHS U54 DA049098NIDA NIH HHS U54 DA049110NIDA NIH HHS U54 DA049113NIDA NIH HHS U54 DA049115NIDA NIH HHS U54 DA049116NIDA NIH HHS UM1 DA058230NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U24 DK141185NIDDK NIH HHS U2C DK114886NIDDK NIH HHS U2C DK119886NIGMS NIH HHS R24 GM146616NIGMS NIH HHS R35 GM141873NIH HHS OT2 OD026671NIH HHS OT2 OD026675NIH HHS OT2 OD030160NIH HHS OT2 OD030161NIH HHS OT2 OD030162NIH HHS OT2 OD030541NIH HHS OT2 OD030544NIH HHS OT2 OD030545NIH HHS OT2 OD030546NIH HHS OT2 OD030547NIH HHS OT2 OD032092NIH HHS OT2 OD032119NIH HHS OT2 OD032619NIH HHS OT2 OD032644NIH HHS OT2 OD032701NIH HHS OT2 OD032720NIH HHS OT2 OD032742NIH HHS OT2 OD033756NIH HHS OT2 OD033759NIH HHS OT2 OD036435NIH HHS OT2 OD036440NIH HHS OT2 OD037922NIH HHS OT2 OD037936NIH HHS R03 OD030600NIH HHS R03 OD039970NIH HHS U24 OD026629NIH HHS U24 OD036598NIH HHS U24 OD038421NIH HHS U24 OD038422NIH HHS U24 OD038423NIH HHS U24 OD038424NIH HHS U24 OD038425NIH HHS U54 OD036472NIH HHS UM1 OD023221NINDS NIH HHS U24 NS112873NINDS NIH HHS UM1 NS112874NINDS NIH HHS UM1 NS118922
Abstract
The NIH Common Fund Data Ecosystem (CFDE) integrates data resources from 18 NIH Common Fund programs for discovery and integrative analysis. These programs generate valuable but heterogeneous datasets that can be difficult to discover, access, and reuse. CFDE aims to provide a collaborative, community-built infrastructure that links and enriches Common Fund programs. We describe the evolution, structure, and core technologies of CFDE, including practical approaches that support submission, integration, visualization, and public release of multimodal data. Training programs and workforce initiatives lower barriers to adoption. CFDE has devised solutions to critical issues facing cross-program initiatives, including data scale and heterogeneity, dataset integration, and long-term sustainability. We demonstrate the utility of linking Common Fund resources through integrative tools and cross-dataset queries to yield insights that would otherwise be infeasible. Collectively, CFDE shows that a standards-driven, federated approach enhances and unifies cross-disciplinary resources, fostering collaboration and data-driven discovery.
Indexed as
analysis workflowbiomedical data integrationCFDEcloud computingcollaborative sciencedata visualizationdiscoveryinteroperabilitymetadata harmonizationsustainability
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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 Socratic graph.