Data Formatting: Challenges and Potential Solutions
Transcript of Data Formatting: Challenges and Potential Solutions
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
© 2004 Pearson Education, Inc.
Central Nervous
System (CNS)
Injury is Complex!
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
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
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
-volume
-velocity
-variety
CNS Injury as a ‘big data’ problem?
Ferguson et al., Nat Neuro 2014; Huie et al., 2019, Curr Opin. Neurology
-volume
-velocity
-variety
Ferguson et al., Nat Neuro 2014; Huie et al., 2019, Curr Opin. Neurology
CNS Injury as a ‘big data’ problem?
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
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
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
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
Raw DataSources
MultispeciesData Repository
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
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
Private Public
Fouad et al., 2021 Journal of Neurotrauma
HTTP://ODC-SCI.ORG
Fouad et al., 2021 Journal of Neurotrauma
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
So you now have big data…THEN WHAT??
?? ?
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Abel Torres-Espin, PhDNow: Assistant Prof. UCSF
Jessica Nielson, PhDNow: Assistant Professor University of MinnesotaDept. Psychiatry and Institute of Health Informatics (IHI)
Long-tail data archive: Multicenter animal spinal cord
injury study (MASCIS) 1994-1996
Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
LocomotorRecovery
Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
LocomotorRecovery
Why are these groups different?
Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
Blood Pressure During Surgery
LocomotorRecovery
Why are these groups different?
Multicenter Animal SCI Study (MASCIS 1994-96)
Nielson et al., 2015Nature Communications
Blood Pressure During Surgery
Jessica Nielson, PhD
LocomotorRecovery
Carlos Almeida, MSCurrent PhD Student, University of Louisville
Example Reuse Case
Almeida et al., 2021. Neuroinformatics
Almeida et al., 2021. Neuroinformatics
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.
Lab
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
Questions?