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:
2 Agenda v Core Dev Updates v Discussion Points v Working Groups Updates v Upcoming Deliverables
3 DATS 2.1 Mapping Recently Completed UCSD - DBMI UTHealth UCSD CRBS LSDB, NDAR, HMP, American Gut Project (in EBI), IRD-JCVI, GeneNetwork Retina, EMDB, BMRB, TCGA, NBIA, Epigenomics, RGD, ClinVar, Vectorbase, IntAct (10) Currently Working On Nature Scientific SRA, Dryad, Clinical Trials, dbgap, Phenogen Informatics, Human Proteinpedia (6) YPED, Uniprot - Swisprot, CIL, NURSA, ICPSR, Neuromorpho, openfmri, NIDDK CR, Physiobank, CIA-Datacite, ICPSR, PeptideAtlas, CVRG, Gemma, GEO, ArrayExpress, CTN, LINCS,PDB, NeuroVault Results, NeuroVault Atlas, NeuroVault Collections, MPD, ProteomeXChange, NITRC, ASCB Cell Image Library (25) Uniprot Trembl, Mendeley Data (OAuth connection), IMEx (waiting for source data feed), bioproject, Datacite Biomedical Repositories (30 selected based on content) (33) Up Next Waiting for new assignment EuPathDB, Diabetic Retinopathy Clinical Research Network, Diabetes Research in Children Network, Candida Genome Database (4) EU Clinical Trials Network, OmicsDI, ImmPort (Contacted source for feed info), Cancer Nanotechnology Laboratory portal (Contacted source) (4) Waiting on repository response SimTK
4 DataMed Ingestion Recently Completed Currently Working On Up Next Waiting on repository response UCSD - DBMI UTHealth UCSD CRBS LSDB, GeneNetwork AmericanGut, (EBI), HMP, NDAR IRD (JCVI), NatureScienti fic Retina, EMDB, Epigenomics, ClinVar, BMRB, TCGA (4) NSRR, RGD, Vectorbase, IntAct (4) Phenogen Informatics, Human Proteinpedia, Diabetic Retinopathy Clinical Research Network, Diabetes Research in Children Network, Candida Genome Database (5) SimTK, EuPathDB YPED, Uniprot - Swisprot, CIL, NURSA, ICPSR, Neuromorpho, openfmri, NIDDK CR, Physiobank, CIA-Datacite, ICPSR, PeptideAtlas, CVRG, Gemma, GEO, ArrayExpress, CTN, LINCS,PDB, NeuroVault Results, NeuroVault Atlas, NeuroVault Collections, MPD, ProteomeXChange, NITRC, ASCB Cell Image Library (25) Uniprot Trembl, Mendeley Data (OAuth connection), IMEx (waiting for source data feed), bioproject, Datacite Biomedical Repositories (30 selected based on content) (33) EU Clinical Trials Network, OmicsDI, ImmPort (Contacted source for feed info), Cancer Nanotechnology Laboratory portal (Contacted source) (4)
5 Core Dev. Team - Progress Task Public ElasticSearch and Datamed Endpoint Public ElasticSearch EndPoint Documentation Development ElasticSearch Endpoints Data Ingestion Pipeline Deployment of pipeline to UT Health and DBMI Development of index enhancers: Primary publication epansion, Award/grant expansion Reconciliation of indices with WG3 metadata model v2 reviewing metadata model v2.1 implementation Metadata transformation scripts generation: CRBS, DBMI & UTHealth Wewow5lmqlGJKQc0/edit#gid=0 Data Set Ingestion Tracking metadata in context of recently released metadata standard update k8p1gycuula4lpdteeqmd0bgvrk/edit#gid=0 Develop curator guidelines ( CEDAR Interactions: Meet once a month during CDT meeting Testing biocaddie template (CEDAR tools) with synthetic data Status Implemented Operational Operational 5
6 Core Dev. Team - Progress Task Status UI Development Tutorials DataMed (v1.0) deployed Improvements/additional functions based on feedback (for v1.5): Improved response time, Sorting on publication date and authors, Visualization 06/30/201 6 Documentation : Source code, overviews of major modules, Help menu, Tutorials Ontology web services: 1) Integrate terminology server (Indexing) Usability & User testing: 1) Survey deployed for receiving feedback 2) Formative testing 3) Planning of Summative testing 4) User Persona and Workflow descriptions To be Supp orted by the NIH grant 1U24 AI to the Univ ersit y of Calif ornia, San Dieg o Generation of an Ontology for Data Type Pilot project integration: Integration plans for two being discussed & third to be scheduled LINCS Interactions: Supplement: Meet once a month during CDT meeting For visualization of DataMed search results started Initiated 6
7 DataMed Issues New Issues since 10/25/16 5 Total Issues 158 Number Open 58 Number Closed 100 Short Description of the latest issues 1.Title on datamed does not match the LINCS dataset landing pages : DataMed says Dataset 4 of 7 while LINCS says Dataset 4 of 15 2.GWAS Dataset Finder not finding an expected GWAS: Disease not found in GWAS finder 3.CYP12B1 suggestion: spelling corrected and suggested but no results exist 4.Github registering: registration seen as tedious biocaddie Data Types Ontology and markup multiple issues reported - #90, #123, #140, #143 expected resolution date: February, 2017
8 DataMed version 1.5 release vrelease before BD2K all hands meeting vtesting on November 17 th vrelease on November 22 nd vwhy should we release version 1.5? w We will have repositories that are mapped to DATS 2.1 (Previous 23 remapped) and new repositories w We have additional functions that are implemented vnew datasets and features we could have ready for version 1.5 w #1 Improved response time w #2 Sorting on publication date and authors w #3 Visualization w #4 Previous 23 repositories updated to DATS 2.1 w #5 New Data Repositories: 18 vdatamed v1.5 on Development server:
9 Other Discussion Items v biocaddie papers Susanna writing DATS paper and talking with NatGen to coordinate paper releases v Repository ranking updates v BD2K all hands w 1 demo (Hua), 5 posters (Jeff, Nansu, Ram (2x) and Harold), 2 presentations (Lucila, Susanna) v Presentation at Emory Feb 22 Lucila will go unless someone else wants to
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 (Xu/Johnson) Task/Description/Topic DATE 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- based on technical evaluation Users for the testing- User persona and workflow development by Jina Supported by the NIH grant 1U24 AI to the University of California, San Diego FIFTH MEETING: Summative testing Users for the testing- User persona and workflow development by Jina JULY 22 AUGUST 24 SEPTEMBER 7 OCTOBER 19 DECEMBER 14 11
12 WG11: Repository Contact Workflow Chair: George Alter v Repository Prioritization w Rubric for calculating priority scores proposed for EC review v Repository ingest workflow documentation w Tracking columns added to repository ingest spreadsheet w Team monitors selected to update spreadsheet 12
13 WG12: Standard Driven Curation Best Practices Chair: TBA v a. Goals: w Assist repositories in creating DATS metadata from the information that they hold and will make their data objects more easily discoverable in DataMED. w Draw lessons about data curation from experiences adding repositories to DataMED w Encourage best practices that make data FAIR v b. Activities/responsibilities: v v c. Deliverables: w A document that Provides use cases for describing data in DATS Offers lessons learned working with DATS Generalizes biocaddie experience in the context of FAIR principles and the longer term goal of semantic interoperability w Conference presentation at International Biocuration Conference, Palo Alto, March
14 Repository Prioritization Rubric Data Repository Ingest Prioritization Rubric The priority score is computed from the five criteria below using the formula: Priority Score = (3*Prominence + 2*Scope + Quality + Sustainability + Access) When ingest is complete Priority Score will be set to -1. Prominence Scope/Diversity Quality Sustainability Access 1.Repository does not prioritize biomedical research; No funding from NIH or other biomedical research sponsors 2.Funding from NIH or other biomedical research sponsors; repositories adopted by a research community as documented in downloads, citations, or other measures of impact 3.Repositories designated by NIH program officers 1.Data types already represented in DataMed; metadata harvested from other aggregator or other site; data not used in biomedical research 2.Repository expands coverage of data types underrepresented in DataMed 3.New data type not represented in DataMed 1.No data curation; no standard formats for data or metadata 2.No data curation; standard formats for data and metadata 3.Data curated by repository; standard formats for data and metadata 1.Less than 2 years in operation; funding from a single source with a time limit 2.More than two years in operation; funding dependent on grants 3.More than five years in operation; diversified funding sources or long-term institutional commitment 1.Data are available; metadata is not available online 2.Data are available with access controls; metadata is available online in a format appropriate for DataMed ingest 3.Data are available without access controls; metadata is available online in a format appropriate for DataMed ingest
15 WG13: EVALUATION OF HARVESTING AND NLP PILOT PROJECTS Chair: Hua Xu Organizing committee members Hua Xu Trevor Cohen Kirk Roberts Dina Demner-Fushman Bill Hersh CALL FOR PARTICIPATION SENT/REGISTRATION OPENED SEPTEMBER 9 DATASET AND SAMPLE QUERIES RELEASED SEPTEMBER 16 TOTAL NUMBER OF REGISTRATIONS: 25 OCTOBER 10 Submission route: Via biocaddie website: Challenge evaluation: by organizing committee- Draft criteria : Top n results to be evaluated with m% of remaining results (upto top 100) where n & m will be decided based on number of submissions and time available Participants: will submit results and a draft paper describing the methods used by the team with detailed descriptions of each run Supported by the NIH grant 1U24 AI to the University of California, San Diego Subcontract award committee: organizing committee + biocaddie EC members + NIH officers: Criteria : 1) Ranking in the challenge 2) Methodology used TEST QUERIES RELEASE NOVEMBER 14 SYSTEM OUTPUT DUE NOVEMBER 28 DATE 15
16 Timeline Evaluation score released December, 15, 2016 Registration SAC meeting to determine awardees September 9, 2016 Test queries released January 10, 2016 Subcontracts setup Subcontract ends November 14, 2016 Mid-February, 2017 End of May, 2017 SEPTEMBER OCTOBER NOVEMBER DECEMBER JANUARY FEBRUARY MARCH APRIL MAY September 16, 2016 Datasets and sample queries released November 28, 2016 System submission January 13, 2017 Decision sent to participants Subcontract period December, 19, 2016 Top 10 systems sent to Subcontract Award Committee (SAC)
17 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
18 Deliverables Time Deliverables Core team WG/PP Y3 Q1 Sept 2016 to Nov Pilot Project evaluation - Evaluation by users - Demonstration of prototype in professional meetings - Standard- driven curation best practices (WG12) - Pilot/Challenge on innovative methods of metadata generation and capture (PP 6) Y3 - Q2 Dec 2016 to Feb PP tool integration - Prototype v.2 - Evaluation of harvesting and NLP PPs (WG13) 18
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
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
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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
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
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Steering Committee Meeting
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Core Technology Development Team Meeting
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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
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
Steering Committee Meeting
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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
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
Steering Committee Meeting
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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
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
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Core Technology Development Team Meeting
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