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 regarding action items DataMed logo Updated repo list Discussion of functionality testing of the UI Feedback on DataMed Metadata issues 2
3 Updates- action items Finalized User list List from Ron, Ian, Alison, Dawei + biocaddie EC recommendations (all WG and PP members) Prepare an template about the prototype release for the user list that NIH will send Test out the new prototype UI functionality Include a link to a feedback form/survey in the prototype release 3
4 DataMed Logo 4
5 DataMed Logo
6 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 Nuclear Receptor Signaling Atlas (NURSA) Yes Completed CRBS MousePhenomeDatabase (MPD) Yes Completed UTHealth 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 6
7 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 Yes Completed CRBS NIDDK Central Repository Yes Completed CRBS OpenFMRI Yes Completed CRBS Physiobank Yes Completed CRBS ProteomeXchange Yes Completed CRBS YPED Yes Completed CRBS Cancer Imaging Archive Yes Completed CRBS EU Clinicat Trials Register 7
8 Feedback on DataMed The search results page is too cluttered (see attachment for proposed rearrangement of the results page) The search results are too slow The numbers for the various categories increase in a random inconsistent way Users always expect logo to be clickable. It's currently not. I would link the image to the homepage and remove the "Home" nav button. Not a fan of the banner text. TeXt seems to LooK like this Too MUch Banner text will look clearer if it's actually text instead of an image. Feedback is too prominent. It's on the nav and if people want to leave feedback, they'll find where to leave it. A lot of white space at the top right. Either combine the top white banner with the nav or put something there. Not really necessary to expand and contract the menus on the side of search results. That dropdown that opens when you start searching is a little confusing and a bit annoying. Let the user filter results once the search is complete. Filters shouldn't show if there are 0 results for them. Is the "unspecific" filter necessary? 8
9 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 9
10 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 10
11 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 11
12 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 12
13 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
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
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
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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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
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
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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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