Executive Committee Meeting
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1 Executive Committee Meeting To hear the meeting, you must call in Toll-free phone number: Access Code: For international call in numbers, please visit: Supported by the NIH grant 1U24 AI to the University of California, San Diego
2 Agenda v Discussion Points v Core Dev Updates v Working Groups Updates v Upcoming Deliverables Supported by the NIH grant 1U24 AI to the University of California, San Diego
3 Discussion Items v Metadata for accessibility questions - Anu v New pilot RFA for NLP Anu and Hua drafting v June 23 workshop who will lead technical session - Jeff? v Special invitees for workshop? Only have 12 workshop representatives attending so far v Lucila to recap meeting she attended May 13 th Supported by the NIH grant 1U24 AI to the University of California, San Diego
4 NIH progress report v Starting progress report now v All documents for pilots, supplements, subcontract awards, NIH biosketches, etc to Elizabeth and Hyeon-eui by June 20 v If you have presented biocaddie anywhere, please send information about it. Supported by the NIH grant 1U24 AI to the University of California, San Diego
5 Pilot Project Updates v v v Feasibility study of Indexing Clinical Research Data Using HL7FHIR - Dr. Guoqian Mayo w Expected completion: Completed! Metadata Discovery and Integration to Support Hetergeneous Data using the OpenFurther Platform Drs. Gouripeddi & Facelli Utah w Expected completion: July 2016 Distributed data discovery using GYM: GitHub, YAML and Markdown Dr. Mungall LBNL w Expected completion: October 2016 Supported by the NIH grant 1U24 AI to the University of California, San Diego
6 Core Dev. Team - Progress Task Public ElasticSearch Endpoint - Increasing VM size and update to latest ES version Public ElasticSearch EndPoint Documentation Development ElasticSearch Endpoints Due Upgrade Operational Operational Data Ingestion Pipeline Development of index enhancers: synonyms & semantic relationships, metadata summarizer, Citation count External (web) services for remote pipeline control Reconciliation of indices with WG3 metadata model Providing feedback for updated metadata model Data Set Ingestion Dataset ingestion process tested at three sites: UT-Health; UCSD-DBMI; and UCSD-CRBS Curators using GitHub for sharing transformation files Web service has been deployed for checking transformations Review current data sources O8kjEikFpewpn9GWQ6K_4erJ9Bz8w/edit#gid= Continue working on data sources; Reconcile curator differences Develop curator guidelines ( Meeting with CEDAR: Access to generate biocaddie Supported template by the NIH grant 1U24 AI to the University of California, San Diego 6
7 Core Dev. Team - Progress Task UI Development Preliminary UI (v0.1) demo UI (v0.2) deployed (new design) DataMed (v0.5) deployed NLP-based term identification and indexing Tutorials Improvements/additional functions based on feedback (for v1.0): 1. Spelling correction 2. Breadcrumb for website navigation - completed 3. Visualization 4. Export to citation managers; copy citation to clipboard 5. Search/sort on any column by clicking on column header 6. Display all records from one repository - completed 7. Select number of results per page Documentation : Source code, Help menu, Tutorials Data Duplication issue: 1. Strategies at the backend: additional field in index or separate table for multiple relations? 2. Strategies for display in UI: Display duplicates together and Supported by the NIH grant 1U24 AI to the University of remove repeating instances California, San Diego Due 09/01 10/09 03/13 Evaluation Discussed in Meeting 7
8 Issues Aggregated in GitHub from those reported via GitHub, Contact Us form and Questionnaire We have started pushing issues generated via the Contact Us form into GitHub using the GitHub API Total Issues 105 Number Open 51 Number Closed 54 Associated with v0.5 Number of Bugs Number of Enhancements Number of Questions Number Open 41 Number Closed 38 Number Open 3 Number Closed 6 Number Open 23 Number Closed 16 Number Open 7 Number Closed 7 Supported by the NIH grant 1U24 AI to the University of California, San Diego 8
9 Core Dev. Team - Progress Task Ontology web services: 1) Imported terminologies (6) and validate them 2) Created UI-Browser for TS 3) Created auto complete feature 4) Integration to Scigraph API 5) Integrate terminology server (UI) 6) 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, annotation guideline development, IAA agreement Due 08/31 09/30 10/20 11/20 1/19 Annotation Usability & User testing: 1) First set of 5 interviews completed (for Phase II), Data Analysis 2) Recruitment of users for 5 additional Supported interviews by the (for NIH grant Phase 1U24 II): 3 AI interviews completed, to the University data analysis of completed: California, San Diego a) We received very few negative comments, most were positive. 65 positive, 58 challenge, 5 negative b) We categorized the problem and challenge areas - most were in the search results page and had to do with display of data. c) Metadata issues overall there were not any major issues with metadata. 3) User recruitment/feedback for Phase I 02/22, 03/22 5/02 9
10 Working Groups Updates v Working Group 2 Jeff v Working Group 3 Susanna v Working Group 4 Hua v Working Group 5 - Jeff v Working Group 6+10 Lucila/Ian/George v Working Group 7 George v Working Group 8 Hua v Working Group 9 Hua Supported by the NIH grant 1U24 AI to the University of California, San Diego
11 WG2 Identifiers (Grethe) Completed Task/Description/Topic Identifiers Working Group 2 completed its activities. Follow-on discussions occurring via a number of separate groups Date Feb 2016 Data Citation Implementation Pilot (DCIP) Provide basic coordination between publishers, repositories and identifier / metadata services for early adopters of data citation according to the JDDCP Identifiers Expert Group of technical experts on web-resolvble biomedical data identification which is supporting harmonization of identifier resolution services (e.g. CDL N2T, identifiers.org) biocaddie Supplement Minid: A BD2K Minimal Identifier Pilot Minimal Viable Identifier (minid) infrastructure for uniquely and unambiguously identifying research data products throughout their life from data generation -> data release. BD2K Collaboration Identifier implementation within the biocaddie prototype Initial discussions with Dataverse on how to better represent primary repository biocaddie 11
12 Supported by the NIH grant 1U24 AI to the University of California, San Diego WG3 Metadata Phase 2 (Sansone)
13 WG4 Use Cases and Testing Benchmarks (Xu) - Details 13 members Completed Functioned from August December 2015 Deliverables: v User needs analysis report v Usability tests v Benchmarking dataset collection v Testing queries Report: Final auwapavw/edit Supported by the NIH grant 1U24 AI to the University of California, San Diego 13
14 WG5 Dataset Citation Metrics (Grethe & Sansone) Progress Identifying groups outside of biocaddie working on Citation Metrics (CASRAI/RDA, PLOS/CDL/DataOne, ) Initial conference call held with CASRAI/RDA group and PLOS/CDL/NISO group Action Items: Additional participants identified (THOR) Conference call to review PLOS/CDL/DataONE, NISO and THOR groups Agenda: Get lesson learned and/or recommendation they can share; also get DDI qualitative and quantitative metrics in their use cases On hold until external projects progress: Date Completed Completed Completed Setup doodle poll for next meeting Supported by the NIH grant 1U24 AI to the University of California, San Diego 14
15 WG6 Criteria for being included in the DDI (Ohno-Machado & Fore) Completed Last meeting occurred 5/06/16 Report being formulated by group members on Google Drive Repository Workshop 6/23/16 Executive Summary: Repositories considered for inclusion in the BioCADDIE Prototype (DataMed) will be evaluated on five dimensions. Key aspects of those dimensions are: Prominence: Priority should be given to types of data that testers of the prototype will expect to find. Less prominent repositories should be considered if they introduce diversity. Sustainability: Repositories should actively maintain their holdings and have sustainable funding. Scope: Additional repository included in biocaddie should introduce diversity and new data. Quality: Data sets should be accompanied by sufficient metadata to make them findable, usable, and interoperable. Data formats should follow community standards Access: Data should be accessible to the scientific community. Metadata must be in a format usable by the biocaddie team for ingest to the DataMed index. Objects must be uniquely identified and web-resolvable by persistent identifiers. Supported by the NIH grant 1U24 AI to the University of California, San Diego 15
16 WG7: Accessibility Metadata for Datasets (Alter) Deliverables v Metadata model and controlled vocabularies for data access that can be incorporated in the DDI core metadata. v Recommendations for implementing the machine readable portion of the license Status v Final draft agreed December 2015 v Recommended items will be added to the biocaddie metadata schema by WG3 Completed
17 WG8 Ranking Search Results (Xu/Cohen) Task/Description/Topic GOAL Bring together information retrieval experts and biomedical domain experts with expertise in searching and using large datasets to identify priorities for the system users to facilitate aggregation and sorting of the results. Date ACTIVITIES/RESPONSIBILITIES Define the characteristics of a set of ranking metrics for relevance. Examples might include number of citations to the dataset and/or initial publication or a PageRank-like metric, number of downloads (if available), completeness of metadata, and an estimate of the relative importance of indexed metadata fields to users. DELIVERABLES Report that identifies the categories that are useful features (based on user needs) for ranking of search results for implementation in the prototype. ACTION 15 members in the WG First meeting: Discussed goals and deliverables; Current ranking algorithm reviewed briefly 01/14 Second meeting: earlier WG outputs discussed (WG4), relevance ranking algorithms discussed (language models etc), review families of ranking algorithms for next meeting 02/11 Third meeting: Various default ES plugin ranking algorithms discussed, others to be reviewed for discussion in next meeting Fourth meeting: ES plugin as well as state of the art ranking algorithms were reviewed. First draft report of the WG is ready. Fifth meeting: To collect feedback on draft report. Attending members needed another week s time 05/19 03/10 04/07 17
18 WG9 End User Evaluation Criteria (Xu/Johnson) Task/Description/Topic 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. MEMBERS Being recruited ( s sent to potential members) Require recommendation of potential members from the following communities: Biomedical researchers Clinicians Funders Data scientist General public Data Repositories Centers Publishers Curators Supported by the NIH grant 1U24 AI to the University of 6 MEMBERS AGREED TO PARTICIPATE, 2 DECLINED, WAITING California, ON San RESPONSE Diego FROM 3 MORE INVITEES SCHEDULING OF FIRST MEETING IS ONGOING 18
19 WG11- OUTREACH MEETING: REPOSITORY OPERATORS v Will begin after Repository Workshop in June Supported by the NIH grant 1U24 AI to the University of California, San Diego
20 Deliverables Time Deliverables Core team WG/PP Y2 Q3 Mar 2016 to May Development of search algorithms/interfaces leveraging repositories (informed by WG10) - - Database of literature-dataset links - Pilot on machine actionable licenses (per WG7) Y2-Q4 June 2016 to August Data indexing tools for individual researchers to submit data to repositories - - User experience evaluation - - Prototype v RFA for Pilot on NLP capture of metadata without standards - Outreach meeting: Repository operators (WG11) Supported by the NIH grant 1U24 AI to the University of California, San Diego 20
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
Steering Committee Meeting
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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
Steering Committee Meeting
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Core Technology Development Team Meeting
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Steering Committee Meeting
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Core Technology Development Team Meeting
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Minutes. Date: Location: UCSD BRF2 5A03. Attendees Present
Executive Committee Meeting Location: UCSD BRF2 5A03 Date: 8-16-16 Start time: 10:00 am PDT End time: 11:30 am PDT Meeting Objective Attendees Present Minute Taker Executive Committee Meeting UCSD: Lucila
Agenda. Clarification of issues Quarter definition Steering and Executive Committee composition Dissemination and community outreach activities
Agenda Clarification of issues Quarter definition Steering and Executive Committee composition Dissemination and community outreach activities Progress and updates Y1Q3 and plans for Y1Q4 Plan for the
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
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
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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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
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