Core Technology Development Team Meeting
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1 Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: Access Code: For international call in numbers, please visit:
2 Agenda v Harvester PP presentation: Guoqian Jiang, Mayo Clinic College of Medicine : Feasibility Study of Indexing Clinical Research Data Using HL7 FHIR v Updates of last meeting action items v biocaddie All-Hands meeting v Discussion of index mappings and naming strategies v Brief updates from All Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Feasibility Study of Indexing Clinical Research Data Using HL7 FHIR biocaddie Pilot Project on Harvester Guoqian Jiang, MD, PhD Mayo Clinic College of Medicine biocaddie Core Development Team Meeting October 13, MFMER slide-1
4 Introduction biocaddie to promote data integration through the adoption of content standards and alignment to common data elements and high-level schema. A prototype of clinical research data discovery index (crddi) Standards-based representation Scalable Semantic Web technologies 2015 MFMER slide-2
5 Data Integration Challenges in Clinical and Translational Research Electronic Medical Records and Genomics (emerge) Network Genotype data The database of Genotypes and Phenotypes (dbgap) Phenotype data from EMR The Cancer Genome Atlas (TCGA) Pan-Cancer Project Genomic data generated on different platforms Clinical data vary widely by cancer type Ultimate comparability and consistency of heterogeneous data sources can be enhanced by data standards, manifest through standard formats and vocabularies MFMER slide-3
6 Meaningful Use A national strategy in the US A roadmap for the advancement of health information exchange Using certified EHR technology to improve quality, safety, efficiency and reduce health disparities 2015 MFMER slide-4
7 Vocabulary Standards in Meaningful Use MFMER slide-5
8 Data Model Standards Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems Standardization of DCM modeling Clinical Information Modeling Initiative (CIMI) HL7 Fast Healthcare Interoperability Resources (FHIR) 2015 MFMER slide-6
9 2015 MFMER slide-7
10 Clinical Information Modeling Initiative Goals Create a shared repository of detailed clinical information models Using an approved formalism Archetype Definition Language (ADL) Archetype Modeling Language (AML) Based on a common set of base data types With formal bindings of the models to standard coded terminologies Repository is open to everyone and models are licensed free for use at no cost Source from Dr. Stan Huff, CIMI 2015 MFMER slide-8
11 Source from Dr. Stan Huff, CIMI 2015 MFMER slide-9
12 Draft Standard for Trial Use (DSTU) 2 within HL7 Resources, Datatypes, Value Sets and REST API 2015 MFMER slide-10
13 FHIR Resources (~100 atomic structure) To provide a consistent, easy to implement, and rigorous mechanism for exchanging data between healthcare applications MFMER slide-11
14 FHIR Datatypes (Common structure for core meaning) 2015 MFMER slide-12
15 FHIR Value Sets 2015 MFMER slide-13
16 FHIR Profiles meta model used to describe resources 2015 MFMER slide-14
17 FHIR Interchangeable Formats Formats XML (released) JSON (released) RDF (under development) The goal Round-trippable, lossless translation between XML, JSON and RDF 2015 MFMER slide-15
18 Semantic Web Technologies The W3C standards Resource Description Framework (RDF) A model of directed, labeled graphs Using a set of triples (subject, predicate, object) - statements SPARQL A query language for RDF graphs Web Ontology Language (OWL) A standard ontology language used for ontology modeling Leveraging Description Logic for reasoning 2015 MFMER slide-16
19 Semantic Web Technologies RDFa (RDF in attributes) and JSON-LD (JavaScript Object Notation for Linked Data) Enables the embedding of machine-readable metadata in the web documents Adopted for use with schema.org (i.e., a shared vocabulary) by major search engines (e.g., Google) 2015 MFMER slide-17
20 Semantic Web Communities in Biomedical Domains W3C HCLS Semantic Web Health Care and Life Science Interest Group The mission is to develop, advocate for, and support the use of Semantic Web technologies across health care, life sciences, clinical research and translational medicine. HL7 ITS RDF Work Group RDF for Semantic Interoperability Use of RDF as a common semantic foundation for healthcare IT E.g., HL7 FHIR Ontology The Yosemite Project A roadmap for healthcare information interoperability A collaborative effort to achieve semantic interoperability of all structured healthcare information, using RDF as a universal information representation MFMER slide-18
21 Semantic Web Applications in Biomedical Domains National Center of Biomedical Ontologies (NCBO) NCI cabig project UK cancergrid project WHO ICD-11 Revision Bio2RDF Linked Open Data 2011 MFMER slide MFMER slide-19
22 MFMER slide MFMER slide-20
23 Related Projects cacde-qa: a quality assurance (QA) platform for cancer study common data elements (CDEs) (NCI U01, PI: Jiang) ISO/IEC metadata standard Leveraging Semantic Web technologies Main_Page PhEMA: a phenotype execution and modeling architecture (NIH R01, co-pi: Jiang) Developing a data element repository and its services to support phenotype authoring and execution applications. Loaded with data elements from HL7 FHIR MFMER slide-21
24 NIH Pilot Data Commons dbgap The database of Genotypes and Phenotypes (dbgap) was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. As of October 12, 2015, there are Variables, 3927 Analyses, 3576 Documents, and 3823 Datasets in 616 Studies TCGA The Cancer Genome Atlas As of October 8, 2015, there are cases with data (clinical and genomic data) in TCGA covering 34 cancer types. TCGA Data Dictionary aligned with NCI cadsr 2015 MFMER slide-22
25 Approach We will demonstrate the feasibility of indexing clinical research datasets through the transformation of corresponding data dictionaries into a common format using an indexing schema tailored from the HL7 FHIR MFMER slide-23
26 Specific Aim 1 Create methods for indexing phenotype variables in the clinical research datasets using HL7 FHIR 1) Examine an existing data element repository and its services for its suitability to HL7 FHIR 2) Create mappings between phenotype variables in clinical research datasets and standard data elements in HL7 FHIR 3) Building indexing services 2015 MFMER slide-24
27 MFMER slide-25
28 0_5_0/attribute/Patient.gender Indexing Services 2015 MFMER slide-26
29 Specific Aim 2 Create methods for exposing and validating embedded standard metadata for clinical research datasets. 1) Methods for embedding and exposing standard metadata using alternative formats 2) Methods for creating schema.org extension 3) Methods for validating embedded standard metadata 2015 MFMER slide-27
30 Data Dictionary in XML Data Dictionary in JSON Data Dictionary in JSON-LD 2015 MFMER slide-28
31 RDF/Turtle Embedding FHIR Elements 2015 MFMER slide-29
32 Timeline 2015 MFMER slide-30
33 Project Team biocaddie crddi Harold Solbrig, Mayo Clinic cacde-qa Harold Solbrig, Mayo Clinic Deepak Sharma, Mayo Clinic Eric Prod Hommeaux, MIT/W3C PhEMA Rick Kiefer, Mayo Clinic 2015 MFMER slide-31
34 Questions & Discussion 2015 MFMER slide-32
35 Updates Action Items v Visit datamed.biocaddie.org and provide feedback for the new version, v0.2 via the prototype_issues repository in GitHub v LINCS notes to be completed Jeff v Contact Anu if you plan on attending the CEDAR meeting during the biocaddie All- Hands v Send the biocaddie All-Hands Meeting agenda to Dawei or Ron once it is finalized - Anu Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
36 biocaddie AHM v Meeting with the CEDAR (Center for Expanded Data Annotation and Retrieval) group Tentative agenda v biocaddie presentation v Broad overview of bioacddie by Lucila v Technical requirements, approach, and current status of the biocaddie DDI prototype by CDT members v In a similar vein, we would be pleased to present similar detail about CEDAR. v CEDAR presentation v Broad overview of CEDAR by Mark v Technical requirements, approach, and current status of the CEDAR metadata creation interface by the technical team members v biocaddie metadata model, its scope, and ways to relate it to the CEDAR metadata model(s) Susanna and team with discussion v Future collaborations, opportunities, challenges, and preferences for interrelating these models and systems Supported by the NIH grant 1U24 AI to the University of California, San Diego 4
37 Index Mapping and Naming Strategies v DISCUSSION Supported by the NIH grant 1U24 AI to the University of California, San Diego 5
38 Ongoing work Task Status 1 Metadata Ingestion Import repositories PDB,GEO 2. LINCS 3. BioProject, ArrayExpress, GEMMA, dbgap 4. ICPSR Stable API details Ongoing Sample files 1.2 Metadata mapping Ongoing 1.3 Metadata management Ongoing 1.4 Indexing Ongoing 2 Terminology server 2.1 Develop terminology server 1) Imported terminologies (6) and validated them 2) Created UI-Browser for TS 3) Integration to Scigraph API 4) Create auto complete feature 09/01 10/09 Ongoing Ongoing 2.2 Integrate terminology server Ongoing Supported by the NIH grant 1U24 AI to the University of California, San Diego 6
39 Pilot project integration (Task 3) PP Presented to CDT / / / /01 As Integrated Specialized advanced search for GWAS datasets Ranking function based on citation metrics for GEO series data a) isee similarity metric in ElasticSearch b) DELVE implementation as exploratory search and visualization option. (i) for PDB (ii) for gene expression data Ranking function based on citation metrics (dataset mentions) for PDB data Completed On 09/22 Ongoing (10/20) 9/01 Ongoing (11/10) Ongoing (10/27) Supported by the NIH grant 1U24 AI to the University of California, San Diego 7
40 Ongoing work Task Status 4 Interface Design 4.1 Global statistics Implemented 4.2 Design interface Ongoing 4.3 Implement new design Ongoing 4.4 Breadcrumb for website navigation Not started 4.5 Display most Accessed Datasets Not Started 5 Personalized search 5.1 Search history Implemented 5.2 Save search results Not Started 5.3 Share search results Not Started 5.4 User account - - Discussion Not Started 6 Searching/Ranking algorithms 6.1 Similar datasets Implemented 6.2 Data repositories search Ongoing 6.3 Boolean/advanced search Not Started 6.4 Refine search results based on user s selection Not Started Supported by the NIH grant 1U24 AI to the University of California, San Diego 8
41 Ongoing work Task Status 7 Display of results 7.1 Sort datasets Ongoing 7.2 Browsing (grouping facets/metadata) Not started 7.3 Accessibility information Not started 8 Link to external resources 8.1 Pubmed Ongoing 8.2 Grants Not Started 9 Feedback 9.1 GitHub Implemented 9.2 Feedback form Not Started 10 Documentation 10.1 Source code Not Started 10.2 Tutorials Not Started 11 Usability studies 11.1 UI Analysis Completed 11.2 User studies Not Started 12 Data Duplication issue Supported by the NIH grant 1U24 AI to the University of California, San Diego 9
42 Other issues v Please deposit codes in GitHub. Please contact me at Anupama.E.Gururaj@uth.tmc.edu if you need access v Any other issues? v Thank You
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Executive Committee Meeting
Executive Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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Steering Committee Meeting
Steering Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Executive Committee Meeting
Executive Committee Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
Core Technology Development Team Meeting
Core Technology Development Team Meeting To hear the meeting, you must call in Toll-free phone number: 1-866-740-1260 Access Code: 2201876 For international call in numbers, please visit: https://www.readytalk.com/account-administration/international-numbers
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