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 Harvester PP presentation: Ramkiran Gouripeddi, Biomedical Informatics Research, University of Utah: Metadata Discovery and Integration to Support Repurposing of Heterogeneous Data using the OpenFurther Platform v Updates of last meeting action items v Discussion about BD2K AHM demo, meeting with LINCS v Features/timeline discussion v Brief updates from All Supported by the NIH grant 1U24 AI to the University of California, San Diego 2
3 Metadata Discovery and Integra2on to Support Repurposing of Heterogeneous Data using the OpenFurther Pla>orm Mee#ng with biocaddie Core Technology Development Team October 27 th, 2015
4 Peter Bernie Ram Team Ryan Phillip Naresh Randy Julio 2
5 Overview Proposal Presenta2on Background OpenFurther Goals Metadata Aim 1 Metadata Repository Aim 2 Evalua#on Future Steps 3
6 Biomedical Research Clinical trials Observa#onal Environmental (exposome) data Electronic health record (phenotypes) Genomic Annota#ons (genotypes) Compara#ve Effec#veness Health Services Data Popula#on Health Socio- economic Proteomics Environmental Genomic Biospecimen Metabolomics 4
7 Embedded Syntac2cs & Seman2cs Diagnosis? ICD9? Primary or Secondary Diagnosis? = 5
8 Current State of Art Relies on human manual cura#on Non- scalable Limits realiza#on of full poten#al of using big data technologies in biomedical science. Final number of metadata (fields/columns) and terminology manual mappings stored in OpenFurther for ini#al onboarding of laboratory, microbiology and radiology results for 6 hospitals in the PHIS+ network. (Numbers do not include ar#facts that were considered as poten#al matches in the preceding discovery phase.) 6
9 OpenFurther 7
10 Goals Prototype a computa#onal infrastructure that supports discovery and mapping of metadata ar#facts and terminologies to overcome current limita#ons. Automated/semi- automated depending on confidence threshold chosen at specific implementa#ons. Agnos#c to specific algorithms or tools as many of these are domain- specific and dependent on data. Choose best available solu#on(s) based on performance, and for specific metadata ar#facts. Leverage exis#ng components of OpenFurther framework to manage, integrate and share metadata in structured non- proprietary formats. 8
11 Aim 1 Catalogue, benchmark and evaluate exis#ng metadata discovery and mapping methods and tools that are applicable to clinical (PHIS+), environmental (Environmental Protec#on Agency s Air Quality) and genomic (ClinVar) data. 9
12 Metadata Data about data including all physical data contained in soeware and other media, business and technical processes related to the data, and rules, constraints, structures and provenance of data. Types of metadata Descrip#ve: describes content including seman#cs for purposes such as discovery and iden#fica#on Structural: describes rela#onships between compound objects Administra#ve: includes the crea#on, file type, and access 10
13 Common Metadata Embedded Sources Databases: Rela#onal, NoSQL and EAV In en##es, aiributes, inter- rela#ons, data types, constraints, ddl, data dic#onaries and sample data Spreadsheets XML messages: stored as schemas, aiributes and markups Web services Soeware source code used to generate, process or store data En#ty rela#onship specifica#ons Data descrip#on language (DDL) defining data structures & database schemas Unstructured documents: PDFs, word, text documents. 11
14 Metadata Discovery and Mapping Metadata Discovery & Mapping Service Human Expert: Understands metadata ar#facts and finds poten#al matches Automated Approach: Discovers metadata and generates poten#al match(es) 12
15 Metadata Discovery and Harves2ng Methods Classifica#on: Primarily focusing on discovery and extrac#on of metadata Those that combine discovery with mapping Majority Some metadata discovery methods (literature) Mercury Grid based metadata services Library cataloguing Soeware architectures 13
16 Metadata Mapping/Matching Next step in characterizing source s data: harmonize and map source s metadata with central metadata stores. Metadata matching requires considering descrip#ve ar#facts (data types, rules, constraints and possible values) Lexical (exact, synonym, paierns) Seman#c matching of metadata ar#facts (e.g. date of birth vs. birth date) Sta#s#cal matching Classifica#on Granularity Elements vs. structure Schema, instance, element, structure, language or constraints. Schema matching vs. ontology alignment Kinds of inputs they use. Well- known mappers use a hybrid approach by relying on both descrip#ve and structural metadata. 14
17 Some Metadata Mapping/Matching Methods Similarity Flooding Uses similarity propaga#on Artemis (Analysis of Requirements: Tool Environment for Mul#ple Informa#on) Affinity- based analysis and hierarchical clustering of source schema elements Cupid Computes similarity coefficients with of a domain specific dic#onary COMA (COmbina#on of MAtching algorithms) Mul#ple matching algorithms that can evaluated against one another Protoplasm Industrial strength matcher S- Match Compares structures (e.g., XML schemas or ontologies) and returns seman#c rela#ons) Seman#c matching methods and tools for analysis: Metamap MTERMS ctakes LOINC mappers Machine learning approaches Combing indirect matches and direct matches Mul#faceted approaches Distributed seman#cs and seman#c indexing approaches 15
18 Metadata Repository 16
19 Aim 2 Incorporate into OpenFurther a state of art prototype to integrate these metadata discovery and mapping tools that support expert review and provide measurements to inform on the uncertainty factor for the mappings. 17
20 Metadata Discovery and Mapping Service (MDMS) Framework to programma#cally characterize metadata of a source. Will consist of an extensible library of metadata discovery and mapping methods and tools. Service oriented architecture. MDMS will accelerate mul#ple data services. 18
21 Architectural Overview of MDMS 19
22 Evalua2on Expert curated metadata Clinical (PHIS+) Environmental (EPA s Air Quality) Genomic (ClinVar) 20
23 Expect Results and Future Steps Selec#on a suitable discovery and mapping methodology and providing the results for storage in the MDR and TS. Automated mapping for less tolerant applica#ons, with the op#on of domain expert review of single or ranked matches. Future work Biomedical metadata discovery and mapping plaqorm that accelerated availability of data for repurposing. Adding addi#onal discovery and mapping methods. Authors can submit their methods for evalua#on and use. Learning from previous mappings stored in MDR and TS along with similarity measures using machine learning. 21
24 Timeline 22
25 Ques2ons 23
26 Thank You 24
27 Updates Action Items v Visit datamed.biocaddie.org and provide feedback for the new version, v0.2 via the prototype_issues repository in GitHub v Follow up with Chris Mungall to add him to the biocaddie GitHub organization Anu v Create a diagram showing biocaddie with Aztec and other repositories and share with the group Jeff/ Ian v Send a draft of the Core Dev. Team poster abstract to the group for review - Anu v Share the list of planned prototype feature implementations with the biocaddie team - CDT Supported by the NIH grant 1U24 AI to the University of California, San Diego 3
28 BD2K AHM Demo v Things to be accomplished before the demo: ü Updated indices (following WG3 specifications) for following repositories: u PDB,GEO,LINCS, BioProject, ArrayExpress, GEMMA, dbgap ü ü Integrated PPs implemented on the datamed server Implement new design completely, group metadata/facets for each dataset Supported by the NIH grant 1U24 AI to the University of California, San Diego 4
29 BD2K AHM Demo v Usability feedback to be collected ü ü survey? Recruit interested users for formal user testing (both in person and remote) v Details for the demo: ü ü Demo in the lobby? Demo in a separate room: Ø Ø For how many people? How many computers to be setup? Supported by the NIH grant 1U24 AI to the University of California, San Diego 5
30 BD2K AHM v LINCS face-to-face meeting: ü ü ü ü ü Contact with LINCS program manager (Ron) When do we meet? Do we need a room? Who will participate all biocaddie members or just CDT? Agenda follow up meeting to the earlier one Supported by the NIH grant 1U24 AI to the University of California, San Diego 6
31 Timeline Y2 Q1 Sep. Nov., 2015 Y2 Q2 Dec Feb., 2016 Sep., 2015 Oct., 2015 Nov., 2015 Dec., 2015 Jan., 2016 Feb., 2016 Interface design Global sta)s)cs New interface for prototype v0.2 Improving interface based on feedback Searching algorithms Finder similar datasets Add Boolean search Add advanced search Add data repositories search Ranking algorithms Refine search results based on user's selec)on Report from WG 8 Dataset result display Sort datasets Group metadata Accessibility of dataset Summarize all returned results (isee- DELVE) Allow users to select mul)ple repositories Improve faceted browsering Personalized search Search history Share search results User account Save search results Link dataset to external resources PubMed Grants (via PubMed?) 7
32 Timeline Y2 Q1 Sep. Nov., 2015 Y2 Q2 Dec Feb., 2016 Sep., 2015 Oct., 2015 Nov., 2015 Dec., 2015 Jan., 2016 Feb., 2016 Data inges=on Data inges)on and indexing Metadata mapping Terminology server Import ontology Create UI broswer Integrate to Scigraph API Integrate autocomplete feature to core UI Integra=on of pilot projects Integrate PP 1.1 GWAS Finder Integrate PP 2.2 isee- DELVE for pdb Integrate PP 2.1 DataRank for GEO Explore gene expression data using PP 2.2 Integrate PP 3.2 for PDB Integrate PP 2.1 for other dataset Feedback collec=on Github Feedback form Documenta=on Source codes on github Tutorials Usability Study UI Analysis User Study Track user's ac)ons Data duplica=on problem Metadata management Architecture/Scalability Code refactoring Back up 8
33 Ongoing work Task Status 1 Metadata Ingestion Import repositories PDB,GEO 2. LINCS 3. BioProject, ArrayExpress, GEMMA, dbgap 4. ICPSR Stable API details Ongoing Sample files 1.2 Metadata mapping Ongoing 1.3 Metadata management Ongoing 1.4 Indexing Ongoing 2 Terminology server 2.1 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 09/01 10/09 Ongoing 10/ Integrate terminology server Ongoing Supported by the NIH grant 1U24 AI to the University of California, San Diego 9
34 Pilot project integration (Task 3) PP Presented to CDT / / / /01 As Integrated Specialized advanced search for GWAS datasets Ranking function based on citation metrics for GEO series data a) isee similarity metric in ElasticSearch b) DELVE implementation as exploratory search and visualization option. (i) for PDB (ii) for gene expression data Ranking function based on citation metrics (dataset mentions) for PDB data Completed On 09/22 10/21 9/01 Ongoing (12/31) Ongoing (11/30) Supported by the NIH grant 1U24 AI to the University of California, San Diego 10
35 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 Not started 4.5 Display most Accessed Datasets Not Started 5 Personalized search 5.1 Search history Implemented 5.2 Save search results Not Started 5.3 Share search results Not Started 5.4 User account - - Discussion Not Started 6 Searching/Ranking algorithms 6.1 Similar datasets Implemented 6.2 Data repositories search Ongoing 6.3 Boolean/advanced search Not Started 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 11
36 Ongoing work Task Status 7 Display of results 7.1 Sort datasets Ongoing 7.2 What fields should be displayed? - Discussion 7.3 Browsing (grouping facets/metadata) Not started 7.4 Accessibility information Not started 8 Link to external resources 8.1 Pubmed Ongoing 8.2 Grants Ongoing 9 Feedback 9.1 GitHub Implemented 9.2 Feedback form Not Started 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 Not Started 12 Data Duplication issue Supported by the NIH grant 1U24 AI to the University of California, San Diego 1
37 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
Metadata Discovery and Integration to Support Repurposing of Heterogeneous Data using the OpenFurther Platform
Metadata Discovery and Integration to Support Repurposing of Heterogeneous Data using the OpenFurther Platform biocaddie All Hands Meeting September 11 th, 2016 Ram Gouripeddi & Julio Facelli Department
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
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Executive Committee Meeting
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Core Technology Development Team Meeting
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Core Technology Development Team Meeting
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Core Technology Development Team Meeting
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Core Technology Development Team Meeting
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Executive Committee Meeting
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Core Technology Development Team Meeting
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Steering Committee Meeting
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