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 Discussion of functionality testing of the UI v Updated repo list v Updated UI based on suggestions Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Updates- action items v User list Ron, Ian, Alison, Dawei v Prepare an template about the prototype release for the user list that NIH will send - Anu v Test out the new prototype UI functionality before the release; share link for the CDT Trello board Anu v Add the contact name of each repository to the repository spreadsheet CDT Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
4 Current Repository Targets Repositories in v0.2 in v0.5 Ingest Status Team Protein Data Bank (PDB) Yes Yes Completed CRBS Gene Expression Omnibus (GEO) Yes Yes Completed CRBS Gemma Yes Yes Completed CRBS ArrayExpress Yes Yes Completed CRBS LINCS Incomplete Yes Completed CRBS BioProject Yes Completed CRBS The Cardiovascular Research Grid (CVRG) Yes Completed CRBS ClinicalTrials.gov Yes Completed UTHealth Dryad Yes Completed UTHealth NeuroMorpho.org Yes Completed CRBS Dataverse Yes Completed DBMI ASCB Cell Image Library Indexing CRBS database of Genotypes and Phenotypes (dbgap) Incomplete Ongoing UTHealth Sequence Read Archive (SRA) Incomplete Ongoing UTHealth ICPSR Ongoing CRBS National Database for Autism Research (NDAR) Ongoing DBMI GeneNetwork To be started DBMI Eukaryotic Pathogen Database Resources (EuPathDB) To be started UTHealth MousePhenomeDatabase (MPD) To be started UTHealth Nuclear Receptor Signaling Atlas (NURSA) To be started CRBS Supported by the NIH grant 1U24 AI to the University of California, San Diego 4
5 Current Repository Targets Repositories in v0.2 in v0.5 Ingest Status Team Additional Repositories (from dknet/jeff) PeptideAtlas Yes Completed CRBS Clinical Trials Network NIDDK Central Repository OpenFMRI Physiobank ProteomeXchange YPED EU Clinicat Trials Register Supported by the NIH grant 1U24 AI to the University of California, San Diego 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: 13 finished 3 ongoing 4 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 Supported by the NIH grant 1U24 AI to the University of California, San Diego 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 Supported by the NIH grant 1U24 AI to the University of California, San Diego 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 Implemented 5.3 Share search results Implemented 5.4 User account Implemented 6 Searching/Ranking algorithms 6.1 Similar datasets Implemented 6.2 Data repositories search Implemented 6.3 Boolean/advanced search Implemented 6.4 Refine search results based on user s selection Not Started Supported by the NIH grant 1U24 AI to the University of California, San Diego 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 Implemented 8.2 Grants Implemented 9 Feedback 9.1 GitHub Implemented 9.2 Feedback form Implemented Supported by the NIH grant 1U24 AI to the University of California, San Diego 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 Supported by the NIH grant 1U24 AI to the University of California, San Diego 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
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
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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
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
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
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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
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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