Executive Committee Meeting

Transcription

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:

2 Agenda Overall Action Items BD2K and biocaddie All-Hands Meeting Supplement Projects Working Group/Core Development Team Actions/Discussions Upcoming Deliverables Pilot Project on Harvester Proposals Discussion Supported by the NIH grant 1U24 AI to the University of California, San Diego 2

3 Executive Committee Discussion Task Working Group Titles WG7: Machine Actionable Licenses > Accessibility Metadata for Datasets WG8: Ranking Algorithms > No change WG6: Criteria for Being Included in the DDI Leadership Suggest WG7 and WG8 members by adding names to invitee spreadsheet Google Drive > Working Groups LINCS/DCIC Face-to-Face Meeting Scheduled for September 23. Jeff and Ron will participate in person; remote participation is being discussed Who Executive Committee George? Executive Committee Tech Team Supported by the NIH grant 1U24 AI to the University of California, San Diego 3

4 Actions Items Task Year 1 Carryforward Funds Provide suggestions for invitees to the biocaddie All-Hands meeting and review invitation letters Google Drive > All-Hands Meeting 2015 Visit datamed.biocaddie.org and provide feedback via the prototype_issues repository in GitHub Contact user interview candidates for permission to release de-identified interview files Who Executive Committee Executive Committee All Anu Supported by the NIH grant 1U24 AI to the University of California, San Diego 4

5 biocaddie All-Hands Meeting Date: December 4, 2015 Location: Telemedicine Building Upper Auditorium, UCSD campus Workshop proposals: Journal publishers and DDI Identifiers and metadata information Minimal information and processes to allow indexing and sharing of digital objects FORCE11 supplement addresses this topic DDI beyond the prototype Engage users and stakeholders to explore how to scale the DDI prototype beyond biomedical data Draft agenda is in progress Supported by the NIH grant 1U24 AI to the University of California, San Diego 5

6 BD2K All-Hands Meeting Date: November 12-13, 2015 (NIH) Prototype Demo Status: Undecided, dependent on the prototype development within the next few weeks biocaddie Sessions Short plenary presentation of revised goals for biocaddie, in particular a metadata discussion Possible pilot projects and supplements introduction Estimate of biocaddie attendees Contact Cleo or Cassie if you are planning to attend Please respond by 09/17 Supported by the NIH grant 1U24 AI to the University of California, San Diego 6

7 Supplement Projects Supplement start date: September 1 Title Description PIs Count Everything: Integrating Clinical, Genomics, and mhealth APIs across the BD2K Program FORCE11 Omics Discovery Index Aim 1: Establish a covering set of interoperable APIs to answer simple quantitative questions integrating over clinical, omic, and mobile-sensor data; Aim 2: Create a software toolkit that implements APIs in one easily deployable package; Aim 3: Deploy the toolkit to create a network of data providers serving a common view of a large swath of biomedical data Aim 1: Support a pilot project with MGH to test data citation implementation; Aim 2: Launch and support a software citation group to define relevant principles and implementation Provide dataset discovery across heterogeneous, distributed group of omics data resources spanning 8 repositories in 2 continents and 6 organizations, includes both open and controlled access data resources. David Haussler, Isaac Kohane, Ida Sim Maryann Martone Peipei Ping, Eric Deutsch, Henning Hermjakob, Susanna Sansone Supported by the NIH grant 1U24 AI to the University of California, San Diego 7

8 WG2 Identifiers (Grethe) Task/Description/Topic 1 st Meeting: Presented initial draft for DDI prototype s handling of identifiers. Feedback: agreed with basic internal handling of identifiers Initial Meetings: Began discussion of identifier ecosystem via working group participants Review Meeting: Based on initial meetings and discussion, develop a list of specific deliverables for biocaddie WG2 to address 4 topics selected 1 discussed and closed Continue work on specific deliverables discussed as in scope during the review meeting. 3 topics remaining 2 discussed and closed Date 6/11 6/25 7/23 8/6 9/3 Continue work on final topic discussed as in scope 9/17 Initial draft of topic responses from working group 10/1 Supported by the NIH grant 1U24 AI to the University of California, San Diego 8

9 WG3 Metadata Specifications (Sansone) Task/Description/Topic Phase 1 = completed Metadata Specification v1, released: doi: zenodo Document describing the process, the material reviewed (Appendix I), the use cases used to identify an initial set of metadata elements (Appendix II); a JSON schemata and examples. Live Google document open for comments Files also shared with BD2K Metadata WG (with George and Mark s approval) Evaluation phase = started Model being implemented with Dev. Team. The WG3 members will be consulted only if needed, see below. Phase 2 = planned The results of the evaluation will inform this phase, where the metadata elements and the model may be revised, simplified and/or enriched, as needed. Date 7/14 ongoing TBD Supported by the NIH grant 1U24 AI to the University of California, San Diego 9

10 WG4 Use Cases and Testing Benchmarks (Xu) Progress Date WG4 membership First meeting: Discussed goals and deliverables; White paper, use cases document reviewed; Use cases and datasets to be prioritized for benchmark development Second meeting: Use cases document (from George) and competency questions (from WG3) discussed. Competency questions to be grouped into higher level clusters for use case prioritization. Completed 8/6 9/3 Third meeting scheduled 9/17 User needs interviews: Initial round of interviews finished Analysis completed Report 7/22 8/25 Supported by the NIH grant 1U24 AI to the University of California, San Diego 10

11 WG5 Dataset Citation Metrics (Grethe & Sansone) Progress Date 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 Developing initial working group document outlining information on current efforts highlighting what biocaddie could potentially adopt and implement. Completed 6/26 8/27 Supported by the NIH grant 1U24 AI to the University of California, San Diego 11

12 WG7 Accessibility Metadata for Datasets (Alter) Task/Description/Topic GOAL: The DDI should present users with information about licenses and terms of access for data. Access conditions should be described using a standard machine readable format and terminology. Many of the resources in the DDI will be accessed by automated processes. License information should be both human and machine readable. Date ACTIVITIES/RESPONSIBILITIES: Review existing models of data access conditions (e.g., RDA Practical Policies WG). Review mechanisms (e.g., Schema.org) for embedding license information with the data it covers. DELIVERABLES: Metadata model and controlled vocabularies for data access that can be incorporated in the DDI core metadata. Recommendations for implementing the machine readable portion of the license. Expect group activities to take 2-3 months. ACTION Discuss participation invitation list: biocaddie > Working Groups > WG7 > Invitation List (need experts on data use agreements for genomics data and clinical trials data) Begin meeting with group (expect 2-3 months of activities) 10/08 Supported by the NIH grant 1U24 AI to the University of California, San Diego 12

13 WG8 Ranking Algorithm (Xu) Task/Description/Topic Date 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. 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 Discuss participation invitation list: biocaddie > Working Groups > WG8 > Invitation List Supported by the NIH grant 1U24 AI to the University of California, San Diego 13

14 Core Dev. Team - Progress Task ElasticSearch Endpoint API Keys available for developers ElasticSearch EndPoint Documentation Deployed to GitHub wiki ElasticSearch Endpoint Enhancements Index ingestion transitioned to using API keys Configured NGINX to allow use of ES plugins Installed ES plugins - Data Ingestion Pipeline Cross data source transformations algorithms updated Determine best practices for versioning of index deployments Reconciliation of indices with WG3 metadata model Data Set Ingestion LINCS, GEO: re-indexing due to needed updates/fixes to cross source transformation algorithms dbgap, BioProject: next data sets in-line ICPSR: scheduled discussion with George s group. Already in contact regarding data access Due Operational Deployed Supported by the NIH grant 1U24 AI to the University of California, San Diego 14

15 Core Dev. Team - Progress Task Pilot project integration PP 1.1 Integration of specialized advanced search PP 2.1 Ranking function based on citation metrics PP 2.2 isee similarity metric in ElasticSearch, Search expansion, DELVE integration PP 3.2 Data Mention Pipeline for PDB UI Development Includes integration of PP 2.2 (DELVE part) as an exploratory search and visualization option. Preliminary UI ready for demo Improvements/additional functions based on feedback Ontology web services: Integration with search and indexing pipelines Due 9/30 Done Done Supported by the NIH grant 1U24 AI to the University of California, San Diego 15

16 Deliverables June-August Core Dev. Team Data identifier implementation - ON TARGET Index datasets using metadata standards, tested on 2-3 datasets from BD2K centers (per WG3) - ON TARGET Set up testing benchmarks ON TARGET Design a repository search function ON TARGET Working Groups (WG)/Pilot Projects (PP) WG4 - Use cases and testing benchmarks (Hua, Anu) ON TARGET WG5 Dataset Citation Metrics (Jeff, Susanna, Steph) ON TARGET Wrap-up of Pilot Projects (Cleo) COMPLETED RFA for Pilot on Harvester for DDI schema (metadata compliant sets) (per WG3) IN PROGRESS Supported by the NIH grant 1U24 AI to the University of California, San Diego 16

17 Deliverables September-November Core Dev. Team Implement a search function for 2-3 repositories (including recommendations from WG4, results from PP2.2) IN PROGRESS PP integration IN PROGRESS Working Groups (WG)/Pilot Projects (PP) WG6 Criteria for being included in the DDI (TBD) WG7 Accessibility Metadata for Datasets (George, Steph) ON TARGET WG8 Ranking Algorithm (Hua, Anu) ON TARGET Pilot on Harvester for DDI schema (metadata compliant sets) (PP4) DELAYED, START DATE: OCT. 1 Supported by the NIH grant 1U24 AI to the University of California, San Diego 17

18 Deliverables Supported by the NIH grant 1U24 AI to the University of California, San Diego 18

19 Deliverables Supported by the NIH grant 1U24 AI to the University of California, San Diego 19