Tutorial: Open Data. Open Source EHR Summit & Workshop October 17-18, 2012 National Harbor, MD

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1 Open Source EHR Summit & Workshop October 17-18, 2012 National Harbor, MD Tutorial: Open Data Fred Prior, Ph.D. Dir. Electronic Radiology Laboratory Dir. Center for High Performance Computing Co-Dir. Center for Biomedical Informatics Washington University School of Medicine

2 What is Open Data??? The Open Definition: A piece of data or content is open if anyone is free to use, reuse, and redistribute it subject only, at most, to the requirement to attribute and/or share-alike. - Open Data: Availability and Accessibility Reuse and Redistribution Universal Participation

3 Doesn t that describe much of the Internet? In a sense yes, BUT without caveat emptor Focus on Facts as distinct from: Rumors, opinions, distortions, misrepresentations Facts are: objective and verifiable observations or measurements Open Data in the context of Open Science

4 Open Science A somewhat nebulous concept in the scientific community which has been construed to mean... Using Open Source software in scientific research; Making data and tools available to the public to enhance basic science education; Freely sharing tools, data and results among scientists; Making scientific results available in Open Access journals; Finding innovative solutions to scientific problems via crowd sourcing. Using Open Source software to capture and manage Open Data to encourage and support research and education. Creating Research Communities around an Open Data resource.

5 Characteristics of Open Scientific Data Useful for scientific research and/or technology development/validation Properly Curated If the data is biomedical and relates to a human subject, curation must include de-identification Properly Licensed If the data relates to a human subject, did that subject give informed consent, were laws governing human subject research followed Available and Accessible

6 Fact Sheet: Big Data Across the Federal Government March 29, 2012 The Cancer Imaging Archive (TCIA) is an image data-sharing service that facilitates open science in the field of medical imaging. TCIA aims to improve the use of imaging in today's cancer research and practice by increasing the efficiency and reproducibility of imaging cancer detection and diagnosis, leveraging imaging to provide an objective assessment of therapeutic response, and ultimately enabling the development of imaging resources that will lead to improved clinical decision support. The NIH Human Connectome Project is an ambitious effort to map the neural pathways that underlie human brain function and to share data about the structural and functional connectivity of the human brain. The project will lead to major advances in our understanding of what makes us uniquely human and will set the stage for future studies of abnormal brain circuits in many neurological and psychiatric disorders.

7 TCIA encourages and supports cancer-related open science communities by hosting and managing the image archive, providing project wiki space, and is in the process of adding searchable clinical trial data repositories to facilitate collaborative research.

8 The Human Connectome Project in a Nutshell fmri, DTI, T1, T2 MEG Parcellation x x x

9 ConnectomeDB: the Open Data Repository for HCP Select cohort based on search criteria Dynamically compute average connectivity maps for that cohort (dense or parcellated connectome) Visualize and compare connectivity maps Marcus D, et al. (2011) Frontiers Neuroscience

10 Is the Data Scientifically Useful? An NCI committee selects data for inclusion in TCIA. NCI s goal in providing the TCIA service is to ensure that data included in this retrospective collection meets one or more of the following research objectives: Meeting the data sharing requirements set forth by an NCI grant or contract award Sharing data for analyzing imaging features to be used as biomarkers Sharing data for comparing image features to other data types such as genetics, pathology, or clinical information to create correlative signatures as biomarkers Sharing data for the creation of automated or semi-automated algorithms for detection of cancer Sharing data as a reference collection for testing and validating quantitative analysis techniques or algorithms in image processing Sharing data with unique characteristics for clinical training

11 Utility can be Measured Number of times the data is accessed Research communities that are actively supported Gigabytes 3,500 3,000 2,500 2,000 1,500 1, Downloads by Month Publication output peer reviewed publications (29) presentations (9) Doctoral/Master s Thesis (2) Educational Exhibits (4) Posters (21) Community TCGA Glioma Phenotype Group TCGA Breast Phenotype Group TCGA Renal Phenotype Group Quantitative Imaging Network National Lung Screening Trial Related Groups Collaborative Projects Active Researchers 11 >20 TCIA Collections Utilized TCGA-GBM, TCGA-LGG 4 >12 TCGA-BRCA 1 >13 TCGA-KIRC >16 >190 QIN Breast, QIN Phantom, QIN Lung, QIN Prostate 8 25 NLST

12 Curation Concept well understood in the art world Authenticity Provenance Is this the original A Sunday Afternoon on the Island of La Grande Jatte? Can I trace the chain of custody from the work s creation in the studio of Georges Seurat in 1886 to Now? Can I verify the work has not been modified? Is this a work of interest to the community so it warrants being included in our collection?

13 TCIA Curation Process A B C D E F G H A CTP pipeline de-identifies images in compliance with DICOM PS 3.15, Appendix E: and queues them for transmission to the intake server. The intake server accepts multiple concurrent submissions. These are curated (quality control review) before being moved to the public server and made open access. The TCIA wiki supports research groups by providing a platform to describe the scope and intent of collections and to provide metadata, including the posting of conference abstracts and publications. Privileged image consumers have been granted special permissions to query/download collection-specific limited-access images, while general consumers cannot. The public server hosts curated images available for download and the OS NBIA application for doing so. Downloads are noted in NBIA s MySQL database. The operations management Support Center s trouble-ticket system tracks image-consumers issues and resolutions. Consumers reach the support center via or telephone. Image consumers view and download images from TCIA and can save lists of images that may be shared with colleagues. TCIA supports searches by collection, anatomy, modality, scanner manufacturer, dates, and many modality-event specific criteria. A dashboard reporting system provides TCIA management with current and historical consumer counts, collection image counts, and image downloads. Clark, et al., SIIM 2012,

14 Curation in the Human Connectome Project (HCP) HCP is a prospective study so curation is built into the data accumulation and release process Acquisition protocols and experimental paradigms are published Provenance tracking is generated by processing pipeline software QC is performed at each stage of processing Provenance and QC data are part of each data release and on the HCP Wiki

15 Provenance Logs in HCP <?xml version="1.0" encoding="utf-8"?> <megconnectome xmlns:xsi=" xsi:nonamespaceschemalocation="megconnectome.xsd"> <version> <matlab> <Name>MATLAB</Name> <Version>8.0</Version> <Release>(R2012b)</Release> <Date>20-Jul-2012</Date> </matlab> <megconnectome> <Name>megconnectome</Name> <Version>0.3.x</Version> <Release>(HCP Phase2MEG)</Release> <Date>08-Aug-2013</Date> </megconnectome> <fieldtrip> <Name>FieldTrip</Name> <Version>r8422</Version> <Release>fieldtriptoolbox.org</Release> <Date>23-Aug-2013</Date> </fieldtrip> </version> <time>24-aug :50:22</time> <username>user</username> <hostname>node165</hostname> In megconnectome at 45 </matlabstack> <script> <filename>/home/user/matlab/megconnectome/pipeline_scripts/hcp_datache ck.m</filename> <md5sum>cc cbbcde6422d39e04bd306</md5sum> XML Schema for MEG Connectome MATLAB version information Compiled Pipeline version Function Library version Date-time and user who ran the pipeline Output log file with Checksum

16 Licensing Open Scientific Data Why is a license necessary? Databases and their content are covered by Copyright and other IP laws that vary from country to country Licensing makes your intent to share information legally clear The rights to a database and the data it contains may be different Creative Commons licensing for content Open Data Commons licensing for open databases PDDL license places the data(base) in the public domain ODdL license share-alike license for databases

17 Accessibility As the volume and of data in open repositories grows, it becomes increasingly difficult to make it easily accessible Query interfaces become complex and multifaceted Data volumes may make internet downloads impractical

18 Accessibility The Open Definition says that data should be freely accessible by anyone. Some times this isn t legally possible. When the data concerns human beings, laws governing Personally Identifiable Information (PII) or Protected Health Information (PHI) or other legal complications may require access be restricted to users who agree to comply with data use agreements. For example, the genome of a specific human being is the ultimate biometric signature. Repositories such as dbgap have both controlled and public components to their collections.

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20 Why Should Open Data Repositories be Created?

21 Why Should Open Scientific Data Repositories be Created? Scientific data is difficult and expensive to gather Data reuse and repurposing reduces costs Repeatable experiments Efforts are underway to reward publishing data Nature Publishing Group s Scientific Data initiative Web of Knowledge Data Citation Index

22 Conclusions Open Data: A piece of data or content is open if anyone is free to use, reuse, and redistribute it Open Scientific Data Supports new research through data reuse Reduces costs and preserves rare and difficult to acquire data Useful Open Scientific Data must be: Valuable Well Curated Properly Licensed Accessible to anyone subject to legal limitations