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
Agenda Updates on action items Discussion with CEDAR folks: Ø Ø Ø AMIA presentation Keycloak integration Synthetic dataset for CEDAR biocaddie interaction Video demonstration Inclusion of more repositories into DataMed : plan and course of action DataMed v1.5(?) release before AMIA Reminders Updates from all team members Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 2
Updates- action items Video demonstration - Jeff Generate a HELP and FAQ page Robust server to host biocaddie to be set up Synthetic dataset for use Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 3
HELP & FAQ page In the biocaddie CDT folder: w https://docs.google.com/document/d/1sbgr4arxoh7ki88lwoy PuFb6cxwRuteqwbONB3LbwYc/edit Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 4
Discussion with CEDAR biocaddie AMIA presentation: 45 minute presentation on Nov. 15 (Tuesday) from 11.15am-12pm in Salon A3 (Lobby Level 1) Current plan is: w w Lucila introduce biocaddie Hua will present DataMed and do the demo w Presentations will be similar to that from biocaddie-ahm : https://biocaddie.org/biocaddie-all-hands-meeting-1 Poster session for the ingestion pipeline poster is from on Nov. 14 (Monday) from 5pm-6.30pm in the Stevens Salon D (Lobby Level 1) Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 5
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
Discussion with CEDAR Synthetic Dataset: w w w Benerator, http://databene.org/databene-benerator.html IBM Quest Synthetic Data Generator, https://sourceforge.net/projects/ibmquestdatagen/ https://www.mockaroo.com/ Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 7
Video demonstration https://youtu.be/s4yhpy-jedo - Jeff Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 8
Inclusion of more repositories into DataMed : plan and course of action https://docs.google.com/spreadsheets/d/1ct9ozn0_91w8ul8nyhz DK3ParoPWewow5lmqlGJKQc0/edit#gid=0 https://docs.google.com/spreadsheets/d/19uxgo9tya6ahtua3zs_r 0BsVdI_tddAXZrXS5eQc8K8/edit#gid=193660278 Each site should get at least 2 repos mapped/team per week Progress to be reported every CDT meeting with plans for next set of repos for mapping Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 9
DataMed release DataMed v1.5 (?) release before AMIA: w Increased number of repositories mapped to DATS 2.1 : 10 completed, how many more? w Additional functions sorting Visualization user activity tracking NLP at backend Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 10
Reminders Next CDT meeting PP presentation by Ramkiran Gouripeddi : Metadata Discovery and Integration to Support Repurposing of Heterogeneous Data using the OpenFurther Platform BD2K AHM demo set up BD2K AHM Abstract submission deadline is October 27 Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 11
Github Issues Total Issues 150 Number Open 50 Number Closed 100 Associated with v1.0 Number Open 12 Number Closed 8 Usability Issues Number Open 23 Number Closed 10 Associated with v0.5 Number Open 23 Number Closed 63 Number of Bugs Number Open 5 Number Closed 12 Number of Enhancements Number Open 21 Number Closed 28 Number of Questions Number Open 9 Number Closed 11 Number of Help Wanted Number Open 3 Number Closed 0 Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 12
Ongoing work Task Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 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 1.6 NLP-based indexing : Gene/protein, Disease, Drug/chemical, Biological process, Organism, Format, Implemented at backend 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 13
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 Additional filters: File type Data Restrictions (data use agreement, restricted, unrestricted) Data Level (participant/aggregate) 7.3 Population (mouse, human, etc) 8 Link to external resources 1. Pubmed: click through to pubmed records of citing publications: copy citation to clipboard 8.1 2. Scholix Framework for Linking Data and Literature 3. Linkout Not started Not Started Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 14
Ongoing work Task Status 10 Documentation 10.1 Source code Ongoing 10.2 Tutorials Not Started 10.3 Help menu Ongoing 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 Additional field in index 12 13 Generation of benchmark for the dataset Completed 14 Relationship Network Graph 15 Collaborative research support Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego 15
Other issues Please deposit codes in GitHub. Please contact me at Anupama.E.Gururaj@uth.tmc.edu if you need access Any other issues? Thank You