Data Formatting: Challenges and Potential Solutions
Transcript of Data Formatting: Challenges and Potential Solutions
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Adam R. Ferguson, Ph.D.Director of Data Science Brain and Spinal Injury Center (BASIC)
Associate Professor, Department of Neurological Surgery Weill Institute for Neurosciences, UCSF
Principal Investigator, SFVAHCS
Data Formatting: Challenges and Potential Solutions
Central Nervous System Injury as a Use Case
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© 2004 Pearson Education, Inc.
Central Nervous
System (CNS)
Injury is Complex!
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Gazillions of tiny measures of biofunction
Figure Sources: Rosenzweig et al., 2010; 2019 Nat Neurosci; Ferguson et al., 2013 PloS One; Nielson et al., 2014, J Neurotrauma; Nielson et al., 2015, Brain Res.; Friedli et al., 2015 Science TM; Rosenzweig et al., 2019 Nat Medicine
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Figure Sources: Rosenzweig et al., 2010; 2019 Nat Neurosci; Ferguson et al., 2013 PloS One; Nielson et al., 2014, J Neurotrauma; Nielson et al., 2015, Brain Res.; Friedli et al., 2015 Science TM; Rosenzweig et al., 2019 Nat Medicine
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Figure Sources: Rosenzweig et al., 2010; 2019 Nat Neurosci; Ferguson et al., 2013 PloS One; Nielson et al., 2014, J Neurotrauma; Nielson et al., 2015, Brain Res.; Friedli et al., 2015 Science TM; Rosenzweig et al., 2019 Nat Medicine
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-volume
-velocity
-variety
CNS Injury as a ‘big data’ problem?
Ferguson et al., Nat Neuro 2014; Huie et al., 2019, Curr Opin. Neurology
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-volume
-velocity
-variety
Ferguson et al., Nat Neuro 2014; Huie et al., 2019, Curr Opin. Neurology
CNS Injury as a ‘big data’ problem?
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Ferguson et al., 2014, Nature Neuroscience Huie et al., 2019, Current Opinion in NeurologyHawkins et al., 2019, Journal of Neurotrauma
TOWARD ‘DATAFICATION’ OF BIOMEDICAL RESEARCH
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Ferguson et al., 2014, Nature Neuroscience Huie et al., 2019, Current Opinion in NeurologyHawkins et al., 2019, Journal of Neurotrauma
TOWARD ‘DATAFICATION’ OF BIOMEDICAL RESEARCH
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Ferguson et al., 2014, Nature Neuroscience Huie et al., 2019, Current Opinion in NeurologyHawkins et al., 2019, Journal of Neurotrauma
TOWARD ‘DATAFICATION’ OF BIOMEDICAL RESEARCH
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Ferguson et al., 2014, Nature Neuroscience Huie et al., 2019, Current Opinion in NeurologyHawkins et al., 2019, Journal of Neurotrauma
TOWARD ‘DATAFICATION’ OF BIOMEDICAL RESEARCH
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Raw DataSources
MultispeciesData Repository
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Open Data
Commons for
SCI
https://odc-sci.org
Open Data
Commons for
TBI
https://odc-tbi.org
VA Gordon Mansfield SCI Consortium
Raw DataSources
MultispeciesData Repository
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FAIR-SCI Ahead
SCI Preclinical Community Readiness and Next Steps
Washington DC,
November 10, 2017
SCI Preclinical Community
Readiness and Next Steps
November 4, 2018
San Diego, CA
STREET-FAIRSCI Team Research, Enabling Expansion
and Translation of FAIR data sharing
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Private Public
Fouad et al., 2021 Journal of Neurotrauma
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HTTP://ODC-SCI.ORG
Fouad et al., 2021 Journal of Neurotrauma
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HTTP://ODC-TBI.ORG
Chou et al., submitted. Preprint: https://doi.org/10.1101/2021.03.15.435178
Open Data Commons for Traumatic Brain Injury Currently has 17 labs and 40 datasets. JOIN NOW
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So you now have big data…THEN WHAT??
?? ?
??
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Abel Torres-Espin, PhDNow: Assistant Prof. UCSF
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Jessica Nielson, PhDNow: Assistant Professor University of MinnesotaDept. Psychiatry and Institute of Health Informatics (IHI)
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Long-tail data archive: Multicenter animal spinal cord
injury study (MASCIS) 1994-1996
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Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
LocomotorRecovery
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Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
LocomotorRecovery
Why are these groups different?
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Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
Blood Pressure During Surgery
LocomotorRecovery
Why are these groups different?
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Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
Blood Pressure During Surgery
Jessica Nielson, PhD
LocomotorRecovery
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Carlos Almeida, MSCurrent PhD Student, University of Louisville
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Example Reuse Case
Almeida et al., 2021. Neuroinformatics
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Almeida et al., 2021. Neuroinformatics
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Takeaway Messages:
1) Long-tail and Dark data comprise majority of biomedical research data.
2) User-facing (community) repositories provide a way to make these data FAIR, open and reusable by both human and machine intelligence tools.
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Lab
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FERGUSON LAB:Carlos Almeida, BS, MA (cand.) Carla Arellano, DPTAustin Chou, PhDDaniel Fong, DPT Jenny Haefeli, PhDJ Russell Huie, PhDAnastasia V Keller, PhDSheena McCormack, DPT Kazuhito Morioka, MD, PhDJonathan Namnath, BSDave Namnath, BSJessica L Nielson, PhDCleopa Omondi, BS, MSEllen Stuck, DPT studentDolores Torres, BS, MS2Christina Tsutsumi, DPT studentJennifer Truong, DPT studentLauren VanCitters, DPTNadine Joseph, BS (cand.)
CollaboratorsUCSF Beattie/Bresnahan Lab:Michael S. Beattie, PhDJacqueline C. Bresnahan, PhDTomoo Inoue, MD,PhDAmity Lin, BSSang Mi Lee, PhDJeffery Sacramento, B.A.Ernesto Salegio, PhD
UCSF Manley Lab:Tomoo Inoue, MD,PhDGeoffery T Manley MD, PhDMary Vassar, RN, MSJohn Yue, BA, MS2
UCSF/PT Rehab:Susanna Rosi, PhD
UCSF Biostatistics:Mark R Segal, PhD
UCSF Neurology/SFVA:Ray Swanson, MDSteve Massa, MD/PhDRaquel Gardner, MD
UCSF/Anesth & Periop Care:Jonathan Pan, MD/PhDMervyn Maze, MDHua Su, MD
UCSF/Radiology:Esther Yuh, MD/PhDPratik Mukherjee, MD/PhDJason Talbott, MD/PhDSharmila Majumdar, PhD
UCSF Orthopedics:Jeff Lotz, PhDChelsey Bahney, PhDRalph Marcucio, PhD
UCSF Psychiatry:Bruno Biagianti, MDAoife O’donovan, PhDRachel Loewy, PhD
UCSD:Mark H. Tuszynski, MD, PhDEphron Rosenzweig, PhDJohn Brock, PhD
UCSD/NIF:Maryann Martone, PhDJeff Grethe, PhD
UCLA:Reggie Edgerton, PhDSharon ZdunowskiLeif Havton, MD,PhD
UC Davis:Rod MoseankoStephanie Hawbecker
Swiss Federal Institute of Technology:Gregoire Courtine, PhD
UC IrvineOs Steward, PhD
University of KentuckyJohn C. Gensel, PhD Sasha Rabchevsky, PhD
U Miami /Miami Project Vance Lemmon, PhDJohn Bixby, PhD
University of AlbertaKarim Fouad, PhD
Stanford:Karen-Amanda Irvine, PhDAlison Callahan, PhDSteve McKenna, MDGraham Creasey, MD
Funding US National Institutes of Health: R01NS088475,
R01CA213441, R01AG056770, R01MH116156,
U01NS086090, P30AR066262, UG3NS106899,
U19AR076737
US Veterans Affairs: 1I01RX002245, I01RX002787
US Department of Defense: SC150198, SC150177
US Department of Energy
Craig H. Neilsen Foundation
Wings for Life FoundationTexas A&M UniversityJim W. Grau, PhDMichelle A. Hook, PhD
University of ZurichArmin Curt, MD
University of MinnesotaJessica Nielson, PhDSophia Vinogradov, MD
Ohio State University:Phillip G. Popovich, PhDDana M. McTigue, PhDJan Schwab, MD,PhDMichele Basso, EdD
University of Louisville:David Magnuson, PhDDarlene Burke, MSScott Whittemore, PhD
NINDS TOP-NT
NIH/NINDS Patrick Bellgowan, PhD
University of FloridaKevin Wang, PhD
Johns Hopkins UniversityJinyuan Zhou, PhD
Georgetown UniversityMark Burns, PhD
UCLANeil Harris, PhDIna Wanner, PhD
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Questions?