Chris Orton Data Project Manager Swansea University. Webinar- 30 th January am (GMT)

Transcription

1 Chris Orton Data Project Manager Swansea University Webinar- 30 th January am (GMT)

2 Identify Access Analyse Data Portal homepage

3 Four levels of metadata Cohort snapshot and details (website, contacts) Cohort study overview (themes, data collection overview) Data dictionaries and variable profiles Interactive tooling for variable discovery according to participant counts and values (query level discovery, MMSE score, age, sex etc).

4 Cohort Matrix

5 Cohort Directory

6 Tony Brookes University of Leicester Tooling background and development potential

7 In order to FREE (SHARE) THE DATA people must first FIND THE DATA PRECISELY [ie AT THE RECORD AND REGULATORY LEVEL] so beyond metadata catalogues and central databases, there is a need for STANDARDS-BASED, INTER-OPERABLE DISCOVERY SOFTWARE, WRAPPED AROUND LINKED/LINKABLE DATASETS (OR SHOP WINDOWS VERSIONS OF DATASETS) WITHIN A HUMAN+MACHINE READABLE DISCOVERY LATTICE.

8 Target Listings & Catalogs Record-Level Discovery Sharing & Analysis Resources Subjects & Samples Datasets Data Context Data Latest Real Data Versioned Real Data Graphical Data Enhanced Data Query Limited, Canned Flexible Unlimited Response Yes/No, Counts, etc Contacts, Links, etc Graphical Displays Interpretive Results

9 Universal EAV+ model, split by sources : true or obfuscated data, summary data, omics data, [chemical structures] Multi-component data items Federated, dynamic lists and values Query API Search Discover Basic, advanced & canned queries Field subsets Record subsets Userspecified Time relationships Yes/No, counts Key features, Thresholds User-specified Networks, subnetworks, overlapping networks Data use conditions (IRDiRC & GA4GH) IDs, field subsets, record subsets Sharing requests User-specified Summarise Share All aspects locally controlled Inbuilt CMS & messaging Rich admin interface Premade summaries Runtime summaries Graphical summaries User-specified Activity logs

10 Mature modular platform Query Builder CafeVariome Federated Access Control User, group and record access control management Output

11 Primary data EAV Format Harmonised/Enhanced data GA4GH Standard? Query Builder Process numbers & text in db API JSON doc omics info in files ES Syntax DIVA translator Indexed data Process ES Output DIVA Output Process DISPLAY

12 Centralised or networked, in (m)any combinations External searches Internal searches Head node Searches are performed through one nominated head node. Searches can be performed from any paired node, or registered online person, that is so approved.

13 Privacy control One-way encryption of local IDs done by DerIDIOM tool In firewalled Parent Cohort systems, subjects are identified by their Local ID Ex: In EPAD network, subjects are identified by their DerIDs Ex: 7cc567261ed386335ecbb7e2 3d0d1dde X

14 Phenotype Semantics Allow the phenotypic consequences of genetic entities to be described using public ontologies. Many terms from many ontologies can be associated with one entity. Allow the phenotypic consequences of genetic entities to be described using a local vocabulary or list. Enable hierarchical viewing and querying of the phenotype ontology data.

15 Federated queries > Basic QB - unlimited AND query items (queries logged) > Advanced QB - unlimited AND + OR query items (queries logged) - save queries for re-use (queries saved) > Canned QB - rerun saved queries (queries and results logged) User-specific query permissions

16 User-specific responses

17 Consent and data use conditions

18 ADA-M Profile Creation Tool...auto-validation

19 List of Café Variome adopters Café EDS EDS Mendelian mutations private network PREPAD population & dementia cohorts private network Café REQUITE Radiotherapy toxicity data [public] Café Cardiokit CVD mutation frequencies public BRC Network Cohort, Biobank & Omics data private network Café etox Drug company toxicity data [public] HDR-Midlands Healthcare & biobank data [private network] Solve-RD EU RD data (inc. matchmaking) [mixed network] Beacon Option for all installations public

20 Application Form Application form

21 Analysis Environment Analysis Environment Page

22 USE YOUR OWN DATA PRE-LOADED SOFTWARE SECURE ENVIRONMENT Analysis Environment

23 Portal Launch Research Platform

24 VM Real Windows look

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