Steering Committee Meeting

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1 Steering Committee 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 v v v v v Brief review development roadmap Deliverables Overview Discussion Items Working Groups Updates biocaddie Challenge Core Dev Team Updates

3 Development Roadmap Personalized search Share/save search results User account Link dataset to external resources PubMed Grants Search algorithm Boolean/advanced search Data repository search function Core Development Roadmap Usability study User study Track user s action Ranking algorithm Refine search results based on user s selection Report from WG 8 on Ranking Data duplication problem Metadata management February 2016 Version 0.5 June 2016 Version 1.0 We are here

4 Upcoming WG12 Standards- Driven Curation Best Practices DataMed Prototype February 2017 Version 2.0 Integration of all pilot projects Dataset Retrieval Challenge WG13 Evaluation of Pilot Projects and NLP Published report and recommendations

5 Deliverables Overview What s on track? What s Delayed? Coming up next DATS 2.1 released Sept 10 Supplement Projects (CountEverything, Force 11 and Omics DI) are finishing up New BD2K Supplements (FAIR and LINCS-bioCADDIE) underway Pilot projects 4.3 will not finish until end of October Dataset ingestion slowed due to needing to remap the metadata of the first repositories to DATS 2.0 Working Group 12 will begin shortly Point paper is complete and under review Nature Genetics Presentations/demos/ posters at AMIA 2016 and BD2K All Hands meeting

6 Discussion Items v Assessing how DataMed is used need to develop a plan of how practicing scientists are using it v Executive Committee versus Steering Committee meetings how can we make them more useful? v Bring Your Repository hackathon - could we have it just after the BD2K all hands meeting in Bethesda?

7 BD2K All Hands Nov v Need to discuss what we will present during All-Hands v Posters v Presentation v Demo?

8 Updates v California BD2K Sept 30-Oct 1: Elizabeth, Jeff and Lucila attended v NHGRI workshop: Lucila and Heidi attended

9 Completed Working Groups Completed! Working Group 2 - Identifiers Working Group 4 Use Cases and Testing Benchmarks Working Group 5 Dataset Citation Metrics Working Group 6/10 Criteria for Inclusion in the DDI (CRISIS) Working Group 7 Accessibility Metadata for Datasets Working Group 8 Ranking Search Results Chair Jeff Grethe Chair Hua Xu Chairs Jeff Grethe and Susanna Sansone Chairs Lucila Ohno-Machado, Ian Fore, George Alter Chair George Alter Chairs - Hua Xu, Trevor Cohen

10 WG3 Metadata Phase 2 Chair: Susanna Sansone Main community phases completed; work carry out internally, interacting with selected external groups as needed Task/Description/Topic Model and its serializations DATS V1 (Aug 2015) and v1.1 release (May 2016) DATS v2 release (June 2016) DATS v2.1 release (Sept 2016) DATS v2.2 release Date completed completed completed DATS and related communities Mapping DATS with metadata for repository landing pages (DCIP admin supplement) Mapping DATS with omicdi model Communication with schema.org to ensure (additional) DATS elements are enclosed Work with DataCite (Martin Fenner) to export in DATS format completed completed Work with core dev team Create list/taxonomy of data type terms: need to classify datasets in DataMed DATS paper outlining the community work; Scientific Data possible target journal To be started To be started

11 WG9: End User Evaluation Criteria Chairs: Hua Xu and Todd Johnson Task/Description/Topic DATE GOAL Engage with various stakeholders (End Users) to enumerate primary characteristics that need to be used to evaluate DataMed. The primary end-users as defined by the biocaddie White Paper are the users looking for the datasets (biomedical researchers, clinicians, funders, data scientist, external search engines, and general public) and the data producers (Individual researchers, data repositories, centers producing large amounts of data, publishers, health care providers and curators) ACTIVITIES/RESPONSIBILITIES The working group will review common evaluation criteria for a DDI with specific relevance to the biomedical domain and the current usability testing plans by DataMed development team to determine appropriate evaluation metrics for DataMed. DELIVERABLES Report defining the user-centric criteria for evaluation of DataMed that will be used to evaluate the prototype and refine the usability testing plans for DataMed. FIRST MEETING: Introduction to the WG Discussion of the CDT user testing plans SECOND MEETING: Survey: Summative testing draft outline : Goal: Compare Usability of biocaddie to a standard control Proposed control: Hyperlinks of all repositories indexed by biocaddie (being discussed) Tasks: 4 tasks from benchmarking effort (being discussed) THIRD MEETING: Survey finalized Summative testing draft outline discussion FOURTH MEETING: Summative testing draft outline discussion Users for the testing Supported by the NIH grant 1U24 AI to the University of California, San Diego JULY 22 AUGUST 24 SEPTEMBER 7 OCTOBER 5 11

12 WG11: Repository Contact Workflow Chair: George Alter v Workflow process status w 10 repositories being tracked in Github w Repository Submission form automatically generates a Github issue w All repositories have been assigned to an ingest team w Evaluation forms under review for 2 repositories not on the CDT Repository list 12

13 Chair: Hua Xu WG13: Evaluation of NLP pilots 13

14 Challenge 2016 biocaddie DataSet Retrieval Challenge Timeline Registration: begins September 9, 2016 DataSets and Sample Queries Release: September 16, 2016 Test Queries Release: November 14, 2016 System Outputs Due: November 28, 2016 Relevance Judgements and Evaluation Scores Released: December 15, 2016 Workshop: TBD Might have some complications subcontracting to international attendees we are working out whether we

15 Challenge Registrants Douglas Teodoro Ram Gouripeddi Guoqian Jiang MayoNLPTeam Guido Zuccon Kyle Copas Sofiane Lagraa Craig Willis Johannes Starlinger Alexander Garcia Jiangshigen Yue Wang Wei Wei SIB Swiss Institut of Bioinformatics University of Utah Mayo Clinic Mayo Clinic Queensland University of Technology (QUT) GBIF Secretariat Inria University of Illinois Humboldt-Universität zu Berlin Universidad Politecnica de Madrid Shanghai Lilian Information Technology Corporation LTD University of Michigan UCSD Zengjian Liu Eugene Agichtein Venkat Srinivasan Natasha Noy Bevan Koopman Caty Chung Marek Grabowski William Hersh Martin Krallinger Antony Scerri Chunlei Wu Czeslaw Jedrzejek Harbin Institute of Technology Shenzhen, China Emory University Independent Scientist Google Research CSIRO UM University of Virginia Oregon Health & Science University Spanish National Cancer Research Centre (CNIIO) Elsevier The Scripps Research Institute Poznan University of Technology

16 Core Dev. Team - Progress Task Public ElasticSearch and Datamed Endpoint Public ElasticSearch EndPoint Documentation Development ElasticSearch Endpoints Data Ingestion Pipeline Deployment of index enhancers: NLP Entity Recognition, metadata summarizer, Citation count New enhancers to be added: Primary publication, Award/grant expansion Reconciliation of indices with WG3 metadata model v2 Continuing to work with Oxford group in reviewing metadata model v2.1 implementation Metadata transformation scripts generation: CRBS, DBMI & UTHealth lgjkqc0/edit#gid=0 Data Set Ingestion Supporte Curators using GitHub for sharing transformation d by files the Web service has been deployed for checking transformations NIH grant Review current data sources 1U24 Tracking metadata in context of recently released AI metadata standard update -01 to the k8p1gycuula4lpdteeqmd0bgvrk/edit#gid=0 Universit Develop curator guidelines ( y of Remapping of previously ingested and new repositories Californi to DATS 2.1: meeting to discuss model implementation between the three groups a, San Diego CEDAR Interactions: Finalizing biocaddie template using CEDAR tools Due Implemented Operational Operational 16

17 Core Dev. Team - Progress Task UI Development Preliminary UI (v0.1) demo UI (v0.2) deployed (new design) DataMed (v0.5) deployed Tutorials DataMed (v1.0) deployed Improvements/additional functions based on feedback (for v1.5 or 2.0): 1. NLP-based term identification and indexing 2. Improved response time 3. Bulk download of indices 4. Most accessed datasets 5. User activity tracking system 6. Sorting on publication date and authors 7. Visualization 8. Primary repository vs aggregators 9. Linkout 10.Duplicate dataset display 11.More as we get more feedback. Supported by the NIH grant 1U24 AI to the University of California, San Diego Documentation : Source code, overviews of major modules, Help menu, Tutorials Google Analytics for datamed.orghttps://analytics.google.com/analytics/web/#home/a w p / 2016 biocaddie DataSet Retrieval Challenge CFP : sent Dataset & Sample queries released Registrations: 21+ registrants so far Due 09/01 10/09 03/13 06/30/

18 Core Dev. Team - Progress Task Ontology web services: 1) Integrate terminology server (UI) 2) Integrate terminology server (Indexing) Benchmark dataset generation/system Evaluation: 23 repositories frozen for use 1) Four search engines: INDRI, Terrier, Lucene, Semantic Vectors 2) Specific queries from competency questions 3) Execute queries 4) Generate list of returned datasets 5) Annotate results: queries for training annotators, Supported annotation by guideline development, IAA agreement the NIH grant 6) Used for biocaddie Dataset Retrieval Challenge1U24 Usability & User testing: AI to the 1) First set of 5 interviews completed (for Phase II), Data Analysis University of 2) Recruitment of users for 5 additional interviews (for Phase II): 3 interviews completed, California, data analysis completed: San Diego 3) User recruitment/feedback for Phase I: 4) Planning of next Phase II/Phase III Pilot project integration: 1) Guoqian Jiang : Feasibility Study of Indexing Clinical Research Data Using HL7 FHIR 2) Ram Gouripeddi: Metadata Discovery and Integration to Support Repurposing of Heterogeneous Data using the OpenFurther Platform Due 1/19 Completed 02/22, 03/22 5/02 08/09 10/11 18

19 Issues Total Issues 148 Number Open 49 Number Closed 99 Associated with v1.0 Usability Issues Associated with v0.5 Number of Bugs Number of Enhancements Number of Questions Number of Help Wanted Number Open 11 Number Closed 7 Number Open 23 Number Closed 10 Number Open 38 Number Closed 46 Number Open 5 Number Closed 12 Number Open 20 Number Closed 28 Number Open 8 Number Closed 11 Number Open 2 Number Closed 0 19

20 Pilot Project Updates v v v Feasibility study of Indexing Clinical Research Data Using HL7 FHIR (Dr. Guoqian, Mayo Clinic) w Completed Metadata Discovery and Integration to Support Hetergeneous Data using the OpenFurther Platform (Drs. Gouripeddi & Facelli, U of UT) w Completed except for write-ups Distributed data Discovery using GYM: Github, YAML, and Markdown (Dr. Mungall, Lawrence Berkeley National Laboratory) w Expected completion: October 2016

21 Other Discussions Comments/Questions Next Steering Committee Meeting: October 6, 2016

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