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 v Updates regarding action items v Demo of updated UI v0.5 v Discussion of functionality testing of the UI v Updated repo list v Metadata discussion (time permitting) 2
3 Updates- action items v Prepare an template about the prototype release for the user list that NIH will send - Anu v Schedule a meeting with George to go over a potential script for the tutorial video after EC meeting per George v User list Ron, Ian, Alison, Dawei v Add the contact name of each repository to the repository spreadsheet CDT v Test out the new prototype UI functionality before the release 3
4 Demo of UI v datamed.biocaddie.org v Username biocaddie v Password biocaddie 4
5 Functional testing of UI v FdkGD2cM/biocaddie-testplan 5
6 Current Repository Targets Repository Protein Data Bank (PDB) database of Genotypes and Phenotypes (dbgap) Gene Expression Omnibus (GEO) Gemma ArrayExpress BioProject Sequence Read Archive (SRA) LINCS ICPSR 20 Total: 7 finished 7 ongoing 6 to be started Repository 1ZIPnkkPpbF3PHkF5- yq9f29cquvvz6z9otkaewrexli/edit#gid=0 The Cardiovascular Research Grid (CVRG) - CRBS GeneNetwork - DBMI EukaryoMc Pathogen Database Resources (EuPathDB) - UTHealth Mouse Phenome Database (MPD) - UTHealth Nuclear Receptor Signaling Atlas (NURSA) - CRBS NaMonal Database for AuMsm Research (NDAR) - DBMI ClinicalTrials.gov - UTHealth NeuroMorpho.org - CRBS ASCB Cell Image Library - CRBS Dryad - UTHealth Dataverse - DBMI 6
7 Ongoing work Task Status 1 Metadata Ingestion 1.1 Import repositories please see previous 1.2 Metadata mapping Ongoing 1.3 Metadata management Ongoing 1.4 Indexing Ongoing 1.5 NLP-based indexing : Gene/protein, Disease, Drug/chemical, Biological process, Organism, Format, Access, Cell types Ongoing 2 Terminology server Develop terminology server 1) Imported terminologies (6) and validated them 2) Created UI-Browser for TS 3) Integration to Scigraph API 4) Create auto complete feature /01 10/09 11/20 10/ Integrate terminology server (UI) 01/ Integrate terminology server (Indexing) Ongoing 7
8 Ongoing work Task Status 4 Interface Design 4.1 Global statistics Implemented 4.2 Design interface Ongoing 4.3 Implement new design Ongoing 4.4 Breadcrumb for website navigation Ongoing 4.5 Display most Accessed Datasets Not Started 5 Personalized search 5.1 Search history Implemented 5.2 Save search results Ongoing 5.3 Share search results Ongoing 5.4 User account Ongoing 6 Searching/Ranking algorithms 6.1 Similar datasets Implemented 6.2 Data repositories search Ongoing 6.3 Boolean/advanced search Ongoing 6.4 Refine search results based on user s selection Not Started 8
9 Ongoing work Task Status 7 Display of results 7.1 Sort datasets Implemented 7.2 What fields should be displayed? Ongoing 7.3 Browsing (grouping facets/metadata) Implemented 7.4 Accessibility information Ongoing 7.5 Allow users to select multiple repositories Implemented 7.6 Improve faceted browsing Ongoing Use a common way throughout records to access the Implemented 7.7 data from the record 8 Link to external resources 8.1 Pubmed Ongoing 8.2 Grants Ongoing 9 Feedback 9.1 GitHub Implemented 9.2 Feedback form Implemented 9
10 Ongoing work Task Status 10 Documentation 10.1 Source code Not Started 10.2 Tutorials Not Started 11 Usability studies 11.1 UI Analysis Completed 11.2 User studies Ongoing 12 Data Duplication issue 13 Generation of benchmark for the dataset 13.1 Select search engine: Lucene, Terrier, Indri Completed 13.2 Dump elasticsearch data into JSON file and convert JSON file to XML format Completed 13.3 Install Indri, Lucene, Terrier, Semantic Vectors Completed 13.4 Execute designed queries To be started 10
11 Other issues v Please deposit codes in GitHub. Please contact me at Anupama.E.Gururaj@uth.tmc.edu if you need access v Any other issues? v 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
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
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
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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
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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
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
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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
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