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 Engaging Users All stakeholders, testing Discrete implementation of DataMed Visualization module demonstration Data Type Ontology Inclusion of more repositories into DataMed : plan and course of action Updates from all team members Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Updates- action items 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 Ian Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
4 Usability Analysis 1. To collect feedback from users that use the DDI interface in the project. We will interact with this group remotely and use the information collected to inform the functionality, usability and design of the user interface : 2. Gather information from beta (test) users about researchers dataset seeking needs, strategies, and challenges. We will use this data also to refine the design of the BioCADDIE DDI user interface and its functions : Round One completed Round Two being planned 3. Determine whether integrating several data sources in one place would improve discoverability of biomedical data by comparing biocaddie to researchers standard approach to finding data : being discussed in WG9 Supported by the NIH grant 1U24 AI to the University of California, San Diego 4
5 Discrete implementation of DataMed The biocaddie path forward with DataMed needs to be considered in terms of recommendations and observations made at the AHM with discrete implementation as (e.g.) v1.1, v1.2, etc leading up to the all-important v2.0. By doing so we show the community that their concerns are being addressed in a timely fashion, as development moves along toward the larger impact v2.0. Continued development of DataMed should proceed and we should have some defined deliverables expressed through milestones with timelines. Supported by the NIH grant 1U24 AI to the University of California, San Diego 5
6 Visualization module demo Supported by the NIH grant 1U24 AI to the University of California, San Diego 6
7 Timeline Chart Date Fields Repository datereleased datecreated pdb_ dataset.datereleased dataset.datecreated gemma_ datasetdistribution.daterel eased cvrg_ datasetdistribution.daterel eased nursadatasets_ dataset.datereleased neuromorpho_ dataset.datereleased peptideatlas_ dataset.datereleased cia_ dataset.datereleased dataset.datecreated yped_ dataset.datereleased *These repositories have been mapped to DATS 2.1
8 Generate Data for Word Cloud Search hemangioma Returns 29 search results NLP web service Returns NLP concepts Cavernous Tufted Benign Tumor Kasabach Cavernous Cavern Tufted ous Hemangioendotheliomas Tufted involution phace merritt NLP Concepts Frequency Cavernous 20 Tufted 15 Kasabach 1
9 Data type Ontology bxzomm6tqbn6geyl51yfzcvmaaqm/edit#gid= Needs work!!! Supported by the NIH grant 1U24 AI to the University of California, San Diego 9
10 Inclusion of more repositories into DataMed : plan and course of action DK3ParoPWewow5lmqlGJKQc0/edit#gid=0 0BsVdI_tddAXZrXS5eQc8K8/edit#gid= Supported by the NIH grant 1U24 AI to the University of California, San Diego 10
11 Github Issues Total Issues 148 Number Open 49 Number Closed 99 Associated with v1.0 Usability Issues Associated with v0.5 Number of Bugs Number of Enhancements Number of Questions Number of Help Wanted Number Open 11 Number Closed 7 Number Open 23 Number Closed 10 Number Open 38 Number Closed 46 Number Open 5 Number Closed 12 Number Open 20 Number Closed 28 Number Open 8 Number Closed 11 Number Open 2 Number Closed 0 Supported by the NIH grant 1U24 AI to the University of California, San Diego 11
12 Ongoing work Task Supported by the NIH grant 1U24 AI 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, Access, Cell types Implemente d at backend 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 12
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 Scholix Framework for Linking Data and Literature 3. Linkout Not started Not Started Supported by the NIH grant 1U24 AI to the University of California, San Diego 13
14 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 Additional field in index 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 14
15 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
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
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
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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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 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
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
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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