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 DataMed UI Evaluation Inclusion of more repositories into DataMed : plan and course of action DataMed v1.5 release before BD2K AHM Metadata problems Data Type Ontology Updates from all team members Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Updates- action items Generate a HELP and FAQ page please start adding material here ASAP Robust server to host biocaddie to be set up ongoing work by Jeff and Claudiu Feedback on video Pilot Project Integration LinkOut Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
4 Inclusion of more repositories into DataMed : plan and course of action DK3ParoPWewow5lmqlGJKQc0/edit#gid=0 0BsVdI_tddAXZrXS5eQc8K8/edit#gid= 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 AI to the University of California, San Diego 4
5 DataMed release DataMed v1.5 release before BD2K AHM: Increased number of repositories mapped to DATS 2.1 : target ~ 40 repos mapped to DATS 2.1, 43 repos currently and more being added Additional functions sorting Visualization user activity tracking NLP at backend UI functionality needs testing before release November 21 st Release on November 23 rd Supported by the NIH grant 1U24 AI to the University of California, San Diego 5
6 Metadata problems 1. The field name of metadata should be consistent. landingpage, landpage taxonomicinformation,taxonomicinformation,taxonomyinformation,ta xonomicinformation cellline,cellline primarypublication,publication,primary Publications,PrimaryPublication,activity, Activityaccess, Access datastandard,datastandard biologicalentity,biologicalentity MolecularEntity,molecularEntity study, Study datasetdistributions,datasetdistribution,datasetdistribution Supported by the NIH grant 1U24 AI to the University of California, San Diego 6
7 Metadata problems The field of publication should be consistent. pmid: and Some of the accessurl in datasetdistrubtions is not working. NeuroMorpho.Org MPD CTN GEO Some error:yped, title field is the same as ID field Supported by the NIH grant 1U24 AI to the University of California, San Diego 7
8 Data Type Ontology Need to understand how datamed search engine currently works and indexes values found under 'data type'. Is there any documentation about any specific processing of this attributes and the entities cast so far under that category? Supported by the NIH grant 1U24 AI to the University of California, San Diego 8
9 Data Type Ontology Also, can we start documenting all the search 'pain point' associated with this attribute? i. "searching on 'gene expression' fails to return datasets whose topic is 'transcription profiling'?" ii. "i can not filter out 'gene expression' datasets which have been generated using DNA microarrays, I am only interested in RNA-Seq"? Supported by the NIH grant 1U24 AI to the University of California, San Diego 9
10 Github Issues Total Issues 168 Number Open 62 Number Closed 106 Supported by the NIH grant 1U24 AI to the University of California, San Diego 10
11 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, 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 11
12 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 12
13 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 Generation of benchmark for the dataset Completed 14 Relationship Network Graph 15 Collaborative research support Supported by the NIH grant 1U24 AI to the University of California, San Diego 13
14 Other issues Please deposit codes in GitHub. Please contact me at if you need access hp 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
Minutes. Date: Location: UCSD BRF2 5A03. Attendees Present
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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
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
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
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
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 isit: 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
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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