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 Updates on action items Presentation outline of CDT at AHM Mapping to DATS 2.0/transformation script Dataset in GEO Login (sharing) with CEDAR Inclusion of more repositories into DataMed Updates from all team members Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Updates- action items Other repositories should be sent to UTHealth team for integration Jeff to be mapped to DATS 2.0 Video Jeff Record the timestamps for queries and results retrieved to determine the response time completed on Dev server, checking DataMed server Linkout discussion get someone from NCBI involved here Login (sharing) with CEDAR Ruiling Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
4 Core Dev. Team Presentation for the biocaddie AHM Presentation Introduction to DataMed: 1) Overall architecture 2) Demonstration of DataMed Prototype 3) PP integration 4) Feedback mechanism Ingestion & Indexing pipeline: 1) Ingestion pipeline 2) Indexing pipeline User Interface: 1) Technical details 2) Features in v1.0 System Evaluation: 1) Evaluation Plan 2) Benchmark Dataset Supported by the NIH grant 1U24 AI to the University of California, San Diego Usability & User testing: 1) Phase I survey 2) Phase II completed results + plans for next one 3) Phase III Plan outline 2016 biocaddie DataSet Retrieval Challenge: 1) CFP 2) Queries/Benchmark Datasets from WG3, WG4 & CDT Person Hua Jeff Hua Trevor Todd Hua 4
5 Mapping to DATS 2.0/ transformation script Based on call and discussion with Alejandra on 08/25, changes were incorporated master/transformations/pdb.trs Supported by the NIH grant 1U24 AI to the University of California, San Diego 5
6 Datasets in GEO In the latest version of GEO, there are only 3,848 datasets. But in the previous version, there were 105,035 datasets. w Dataset Browser - there are now 4,348 datasets (increase since last time we crawled it) Supported by the NIH grant 1U24 AI to the University of California, San Diego 6
7 Datasets in GEO This is related to the GitHub issue 84. Using HIV as a search term, there are only 121 hits from GEO in DataMed, while there are 7610 hits from the NCBI GEO site. Should we be indexing at the dataset level itself or at the sample level (DataSet -> Series -> Sample & Platforms)? Dataset definition by biocaddie important issue to be addressed ASAP? Supported by the NIH grant 1U24 AI to the University of California, San Diego 7
8 Log in to datamed using CEDAR account Install Keycloak OAuth 2.0 package for PHP Add a button to allow users to log in using CEDAR account Install authentication server Create a new realm for DataMed website Provide the information below Validate login information using the authentication server 8
9 Inclusion of more repositories into DataMed 1CT9ozn0_91W8Ul8nYHzDK3ParoPWewow5lm qlgjkqc0/edit#gid=0 1RYNe5WNIsAb7eW4JSHX5cDarSodkkERZOOR g9s6_q9a/edit#gid= JHfPyxziUMqGbOmW5hCWOQia6sCpjFsHIAn CFFmZytI/edit#gid= Supported by the NIH grant 1U24 AI to the University of California, San Diego 9
10 Github Issues Total Issues 142 Number Open 65 Number Closed 77 Associated with v1.0 Usability Issues Associated with v0.5 Number of Bugs Number of Enhancements Number of QuesJons Number Open 10 Number Closed 1 Number Open 27 Number Closed 4 Number Open 38 Number Closed 48 Number Open 7 Number Closed 10 Number Open 25 Number Closed 22 Number Open 9 Number Closed 9 Supported by the NIH grant 1U24 AI to the University of California, San Diego 10
11 Ongoing work Task Status 1 Metadata Ingestion 1.1 Import repositories expansion Ongoing 1.2 Data repository suggestion form at DataMed George/ Xiaoling / Sanda Ongoing 1.3 Metadata mapping review/ reconciliation between curators Ongoing 1.4 Metadata management Ongoing 1.5 Indexing Ongoing NLP-based indexing : Gene/protein, Disease, Drug/chemical, 1.6 Implemented at backend Biological process, Organism, Format, Access, Cell types 1.7 Bulk download of indices Not Started 2 Terminology server 2.3 Integrate terminology server (Indexing) Ongoing 4 Interface Design 4.2 Design interface usability issues Ongoing 4.5 Display most Accessed Datasets Not Started Supported by the NIH grant 1U24 AI to the University of California, San Diego 11
12 Ongoing work Task Status 5 Personalized search 5.1 Improve the tracking system Ongoing 6 Searching/Ranking algorithms 6.1 Similar datasets to be expanded Ongoing 7 Display of results 7.1 Sort datasets author, published date, repository, title Ongoing 7.2 What fields should be displayed? Ongoing 7.3 Additional filters: File type Data Restrictions (data use agreement, restricted, unrestricted) Data Level (participant/aggregate) Population (mouse, human, etc) Not started 8 Link to external resources Pubmed: click through to pubmed records of citing publications: copy citation to clipboard 2. Scholix Framework for Linking Data and Literature 3. Linkout Not Started Supported by the NIH grant 1U24 AI to the University of California, San Diego 12
13 Ongoing work Task Status 10 Documentation 10.1 Source code Ongoing 10.2 Tutorials Not Started 10.3 Help menu Not Started 10.4 Video Ongoing 11 Usability studies 11.2 User studies Ongoing Data Duplication issue: Create a plan for how to best display/represent the duplicate in the metadata records and set up a meeting to discuss the workflow for displaying the duplicates in the metadata records Jeff/Anu 12 Additional field in index 13 Generation of benchmark for the dataset 13.4 Execute designed queries and annotate results Ongoing 14 Relationship Network Graph 15 Collaborative research support Supported by the NIH grant 1U24 AI to the University of California, San Diego 13
14 Other issues Please deposit codes in GitHub. Please contact me at if you need access Any other issues? 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
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
Minutes. Date: Location: UCSD BRF2 5A03. Attendees Present
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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
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
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
Metadata Ingestion and Processinng
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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
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
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
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
Agenda. Clarification of issues Quarter definition Steering and Executive Committee composition Dissemination and community outreach activities
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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 isit: 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
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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