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Towards Biomedical Research as a Digital Enterprise
 

Towards Biomedical Research as a Digital Enterprise

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Presented at the American College of Medical Informatics (ACMI) Winter Symposium in Phoenix, Arizona, February 14, 2014

Presented at the American College of Medical Informatics (ACMI) Winter Symposium in Phoenix, Arizona, February 14, 2014

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    Towards Biomedical Research as a Digital Enterprise Towards Biomedical Research as a Digital Enterprise Presentation Transcript

    • Towards Biomedical Research as a Digital Enterprise Philip E. Bourne University of California San Diego pbourne@ucsd.edu 2/14/14 2014 ACMI Winter Symposium 1
    • My Background/Bias • Limited Biomedical Informatics Experience – IAIMS, Pharmacy Informatics • RCSB PDB/IEDB Database Developer – Views on community, quality, sustainability … • PLOS Journal Co-founder – Open Science Advocate • Associate Vice Chancellor for Innovation – Business models, interaction with the private sector, sustainability • Professor – Mentoring, reward system, value (or not) of research 2/14/14 2014 ACMI Winter Symposium 2
    • Why Am I Here? • In two weeks I will take on the NIH role of Associate Director for Data Science (ADDS):     NIH Data Science Point Person Reports to NIH Director Lead the BD2K initiative Trans-NIH responsibilities for data  Eric Green, Acting [Modified slide from Eric Green] 2/14/14 2014 ACMI Winter Symposium 3
    • Disclaimer • These comments are currently being made as an employee of the University of California system and reflect my own opinions. 2/14/14 2014 ACMI Winter Symposium 4
    • I want to engage with this community to: • • • • Understand the most pressing problems Begin a dialog Inform you of what I am currently thinking Inform you of NIH initiatives that are underway or planned • Have you change my thinking appropriately 2/14/14 2014 ACMI Winter Symposium 5
    • The NIH Process Thus Far An external advisory group provided a valuable blueprint for what should be done acd.od.nih.gov/diwg.htm 2/14/14 2014 ACMI Winter Symposium 6
    • Blueprint Recommendations • Promote central and federated catalogs – Establish minimal metadata framework – Tools to facilitate data sharing – Elaborate on existing data sharing policies • Support methods and applications – Fund all phases of software development – Leverage lessons from National Centers • Training – More funding – Enhance review of training apps – Quantitative component to all awards • On campus IT strategic plan – Catalog of existing tools – Informatics laboratory – Ditto big data • Sustainable funding commitment 2/14/14 2014 ACMI Winter Symposium acd.od.nih.gov/diwg.htm 7
    • Special Considerations for Phenotypic Data Relevant to ACMI • Definition: From cellular to human; sensitive or non-sensitive • Need: – Provide transparency regarding current policies – Develop a common language for appropriate data access – Establish the appropriate forum to establish policies 2/14/14 2014 ACMI Winter Symposium 8
    • Some of the Phenotypic Data Issues • Data Governance – Needs a balance of technology and policy solutions • Data Sharing – Query with or without data release • Data Characterization – Local vs standard nomenclature and associated mapping Aligns well with: Hripcsak et al. J. Am. Med. Inform. Assoc. 2014 21:204-211 2/14/14 2014 ACMI Winter Symposium 9
    • Let Me Outline Then in General Terms Where I See My Effort Being Spent Going Forward http://pebourne.wordpress.com/2013/12/ 2/14/14 2014 ACMI Winter Symposium 10
    • ADDS Initial Thrusts • • • • • • • • How data are currently being used Lightweight metadata standards Data & software registries Expanded policies on data sharing, open source software Training programs & reward systems Institutional incentives Private sector incentives Data centers serving community needs 2/14/14 2014 ACMI Winter Symposium 11
    • ADDS Initial Thrusts • • • • • • • • How data are currently being used Lightweight metadata standards Data & software registries Expanded policies on data sharing, open source software Training programs & reward systems Institutional incentives Private sector incentives Data centers serving community needs 2/14/14 2014 ACMI Winter Symposium 12
    • We Need to Start By Asking How Are We Using the Data Now! Only Then Can We Make Rational Decisions About Data – Large or Small 2/14/14 2014 ACMI Winter Symposium 13
    • How Data Are Used Structure Summary page activity for H1N1 Influenza related structures Jan. 2008 Jul. 2008 * http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm Jan. 2009 Jul. 2009 Jan. 2010 Jul. 2010 3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir 1RUZ: 1918 H1 Hemagglutinin 2/14/14 14 2014 ACMI Winter Symposium [Andreas Prlic]
    • We Need to Learn from Industries Whose Livelihood Addresses the Question of Use 2/14/14 2014 ACMI Winter Symposium 15
    • ADDS Initial Thrusts – More Detail • Now: – – – – – Data centers (under review) Data science training grants (call out) Pilot data catalog consortium (call out) Genomic Data Sharing Policy (being finalized) Piloting “NIH-drive” • What Is Planned: – Extended public-private programs specifically for data science activities – Interagency activities – International exchange programs – Cold Spring Harbor-like training facilities – by-coastal? – Programs for better data descriptions – Reward institutions/communities – Policies to get clinical trial data into the public domain 2/14/14 2014 ACMI Winter Symposium 16
    • ADDS Initial Thrusts – More Detail • Now: – – – – – Data centers (under review) Data science training grants (call out) Pilot data catalog consortium (call out) Genomic Data Sharing Policy (being finalized) Piloting “NIH-drive” • What Is Planned: – Extended public-private programs specifically for data science activities – Interagency activities – International exchange programs – Cold Spring Harbor-like training facilities – by-coastal? – Programs for better data descriptions – Reward institutions/communities – Policies to get clinical trial data into the public domain 2/14/14 2014 ACMI Winter Symposium 17
    • Pilot NIH-Drive • Investigator A from the NCI makes frequent reference to the over expression of genes x and y. • Investigator B from the NHLBI makes frequent reference to the under expression of genes x and y • Automatic notification of a potential common interest before publication or database deposition 2/14/14 2014 ACMI Winter Symposium 18
    • Let Me Bring Us Back to a More Far Reaching View Embodied in the Title of This Talk: Towards Biomedical Research as a Digital Enterprise 2/14/14 2014 ACMI Winter Symposium 19
    • First Consider What We Do (or Wish We Could Do) Every Day: We take actions on digital data increasingly across boundaries 2/14/14 2014 ACMI Winter Symposium 20
    • Actions on Biomedical Data Implies: • • • • • • • • • Insuring data quality and hence trust Making data sustainable Making data open and accessible Making data findable Providing suitable metadata and annotation Making data queryable Making data analyzable Presenting data as to maximize its value Rewarding good data practices 2/14/14 2014 ACMI Winter Symposium 21
    • Actions on Biomedical Data Implies: • • • • • • • • • Insuring data quality and hence trust Making data sustainable Making data open and accessible Making data findable Providing suitable metadata and annotation Making data queryable Making data analyzable Presenting data as to maximize its value Rewarding good data practices 2/14/14 2014 ACMI Winter Symposium 22
    • Boundaries on Biomedical Data Implies: • Working across biological scales • Working across biomedical disciplines • Working across basic and clinical research and practice • Working across institutional boundaries • Working across public and private sectors • Working across national and international borders • Working across funding agencies 2/14/14 2014 ACMI Winter Symposium 23
    • Boundaries on Biomedical Data Implies: • Working across biological scales • Working across biomedical disciplines • Working across basic and clinical research and practice • Working across institutional boundaries • Working across public and private sectors • Working across national and international borders • Working across funding agencies 2/14/14 2014 ACMI Winter Symposium 24
    • These Issues Have Been Around Almost As Long As Biomedical informatics The Good News is That “Big Data” Has Bought More Attention to the Problem 2/14/14 2014 ACMI Winter Symposium 25
    • What Are Big Data? • Large datasets from high throughput experiments • Large numbers of small datasets • Data which are “ill-formed” • The why (causality) is replaced by the what • A signal that a fundamental change is taking place – a tipping point? 2/14/14 2014 ACMI Winter Symposium 26
    • That Change is Embodied in The Digital Enterprise • Consists of digital assets • E.g. datasets, papers, software, lab notes • Each asset is uniquely identified and has provenance, including access control • E.g. publishing simply involves changing the access control • Digital assets are interoperable across the enterprise 2/14/14 2014 ACMI Winter Symposium 27
    • The Enterprise Is Almost Anything.. Your Lab, your Institution, the NIH…. 2/14/14 2014 ACMI Winter Symposium 28
    • Consider an Academic Institution As A Digital Enterprise • Jane scores extremely well in parts of her graduate on-line neurology class. Neurology professors, whose research profiles are on-line and well described, are automatically notified of Jane’s potential based on a computer analysis of her scores against the background interests of the neuroscience professors. Consequently, professor Smith interviews Jane and offers her a research rotation. During the rotation she enters details of her experiments related to understanding a widespread neurodegenerative disease in an on-line laboratory notebook kept in a shared on-line research space – an institutional resource where stakeholders provide metadata, including access rights and provenance beyond that available in a commercial offering. According to Jane’s preferences, the underlying computer system may automatically bring to Jane’s attention Jack, a graduate student in the chemistry department whose notebook reveals he is working on using bacteria for purposes of toxic waste cleanup. Why the connection? They reference the same gene a number of times in their notes, which is of interest to two very different disciplines – neurology and environmental sciences. In the analog academic health center they would never have discovered each other, but thanks to the Digital Enterprise, pooled knowledge can lead to a distinct advantage. The collaboration results in the discovery of a homologous human gene product as a putative target in treating the neurodegenerative disorder. A new chemical entity is developed and patented. Accordingly, by automatically matching details of the innovation with biotech companies worldwide that might have potential interest, a licensee is found. The licensee hires Jack to continue working on the project. Jane joins Joe’s laboratory, and he hires another student using the revenue from the license. The research continues and leads to a federal grant award. The students are employed, further research is supported and in time societal benefit arises from the technology. From What Big Data Means to Me JAMIA 2014 21:194 2/14/14 2014 ACMI Winter Symposium 29
    • The NIH is Starting to Think About the Digital Enterprise, Witness… bd2k.nih.gov 2/14/14 2014 ACMI Winter Symposium 30
    • What Will Define the NIH Digital Enterprise? • • • • • • • • • NCBI/NLM Trans-NIH collaboration – a culture change Long-term NIH strategic planning The BD2K Initiative A “hub” of data science activities International cooperation Interagency cooperation Data sharing policies External forces…. 2/14/14 2014 ACMI Winter Symposium 31
    • External Forces: Science Will Continue to Become More Open • The public (and hence the politicians demand it) • Its the right thing to do • Its part of the modern psyche • The scholarly enterprise is broken and more stakeholders are acknowledging it 2/14/14 2014 ACMI Winter Symposium 32
    • Result: Discovery is Too Slow [Josh Sommer] 2/14/14 http://sagecongress.org/Presentations/Sommer.pdf 2014 ACMI Winter Symposium 33
    • Result: Discovery is Too Slow [Josh Sommer] 2/14/14 http://sagecongress.org/Presentations/Sommer.pdf 2014 ACMI Winter Symposium 34
    • Personal Evidence for a Broken System • I have a paper with 16,000 citations that no one has ever read • I have papers in PLOS ONE that have more citations than ones in PNAS • I have data sets I am proud of but no place to put them • I “cant” reproduce work from my own lab…. 2/14/14 2014 ACMI Winter Symposium 35
    • Personal Evidence for a Broken System • I cant immediately reproduce the research in my own laboratory: • It took an estimated 280 hours for an average user to approximately reproduce the paper • Workflows are maturing and becoming helpful • Data and software versions and accessibility prevent exact reproducibility Daniel Garijo et al. 2013 Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome PLOS ONE 8(11) e80278 . 2/14/14 2014 ACMI Winter Symposium 36
    • Politicians Demand It: G8 open data charter http://opensource.com/government/13/7/open-data-charter-g8 2/14/14 2014 ACMI Winter Symposium 37
    • External Forces: The Deinstitutionalization of Science Daniel Hulshizer/Associated Press 2/14/14 2014 ACMI Winter Symposium 38
    • External Forces: The Deinstitutionalization of Science Daniel Hulshizer/Associated Press 2/14/14 2014 ACMI Winter Symposium 39
    • An Example of That External Force: The Story of Meredith http://fora.tv/2012/04/20/Congress_Unplugged_Phil_Bourne 2/14/14 2014 ACMI Winter Symposium 40
    • External Forces: The Deinstitutionalization of Science Daniel Hulshizer/Associated Press 2/14/14 2014 ACMI Winter Symposium 41
    • External Forces: The Deinstitutionalization of Science Daniel Hulshizer/Associated Press 2/14/14 2014 ACMI Winter Symposium 42
    • There Still Needs to be a Reward System The Wikipedia Experiment – Topic Pages  Identify areas of Wikipedia that relate to the journal that are missing of stubs  Develop a Wikipedia page in the sandbox  Have a Topic Page Editor Review the page  Publish the copy of record with associated rewards  Release the living version into Wikipedia 2/14/14 2014 ACMI Winter Symposium 43
    • One Possible End Product of Open Science 0. Full text of PLoS papers stored in a database 4. The composite view has links to pertinent blocks of literature text and back to the PDB 4. 1. 1. A link brings up figures from the paper 2. 2/14/14 3. A composite view of journal and database content results 3. 2. Clicking the paper figure retrieves data from the PDB which is analyzed 1. User clicks on thumbnail 2. Metadata and a webservices call provide a renderable image that can be annotated 3. Selecting a features provides a database/literature mashup 4. That leads to new papers PLoS Comp. Biol. 2005 1(3) e34 44
    • If This Vision of a Digital Enterprise Comes to Pass Based Upon: • • • • More open science Deinstitutionalization New modes of scholarly communication Changing rewards for scholarship What Will Biomedical Research Look Like? 2/14/14 2014 ACMI Winter Symposium 45
    • The Research Life Cycle will Persist IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION 2/14/14 2014 ACMI Winter Symposium 46
    • Tools and Resources Will Continue To Be Developed Authoring Tools Lab Notebooks Data Capture Analysis Tools Software Scholarly Communication Visualization IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION
    • Those Elements of the Research Life Cycle will Become More Interconnected Authoring Around a Common Framework Tools Lab Notebooks Data Capture Software Analysis Tools Scholarly Communication Visualization IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION
    • New/Extended Support Structures Will Emerge Authoring Tools Data Capture Lab Notebooks Analysis Tools Scholarly Communication Software Visualization IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION Commercial & Public Tools DisciplineBased Metadata Standards Community Portals Git-like Resources By Discipline Data Journals New Reward Systems Training Institutional Repositories 2/14/14 2014 ACMI Winter Symposium Commercial Repositories 49
    • Change in the Way we Support the Research Lifecycle Authoring Tools Data Capture Lab Notebooks Software Analysis Tools Scholarly Communication Visualization IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION Commercial & Public Tools DisciplineBased Metadata Standards Community Portals Git-like Resources By Discipline Data Journals New Reward Systems Training Institutional Repositories 2/14/14 2014 ACMI Winter Symposium Commercial Repositories 50
    • Conclusion: Biomedical Research Will Increasingly Become a Digital Enterprise in the Way I Have Described Agree/Disagree? If Agree Where Should Resources be Put? If Disagree What is Your Vision? 2/14/14 2014 ACMI Winter Symposium 51
    • Provocative Questions Perhaps? • Do BMI’s see openness in the same way as computational biologists; if not why not? • Is there indeed perturbation in what it means to be a research scholar and if so is that disruption as prevalent in clinical research as basic research? • What would you do in my shoes? 2/14/14 2014 ACMI Winter Symposium 52