SDM center Supporting Heterogeneous Data Access in Genomics Terence Critchlow Ling Liu, Calton Pu GT Reagan Moore, Bertam Ludaescher, SDSC Amarnath Gupta.

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Presentation transcript:

SDM center Supporting Heterogeneous Data Access in Genomics Terence Critchlow Ling Liu, Calton Pu GT Reagan Moore, Bertam Ludaescher, SDSC Amarnath Gupta Mladen Vouk NCSU Tom Potok ORNL Matt Coleman LLNL September 2002 UCRL-PRES-???????

SDM center Outline l Motivation l System architecture l Status

SDM center Different users end up doing the same thing. Motivated by current state of the art in genomics data access. Source Specific Schema The user is required to perform all data management tasks. dbEST SCoP SWISS-PROT User applications Transform Map data format similar concepts ParseAccess input/the data output PDB

SDM center What is a realistic environment? A single location that provides effective access to of data and tools from many sources through an intuitive and useful interface. Transform Map data format similar concepts Parse Access input/ the data output : User applications

SDM center Motivating use case: Identifying model sequences Matt MILLAFSSGRRLDFVHRSGVF FFQTLLWILCATVCGTEQYFN Hundreds of sequences Clusfavor Gene name / accession # Genbank Sequence Blast against HTGS Model builder Homologs Filter Subseq to 2000bp Accession # Transfac Sequence Model sequence

SDM center SDM Center Data Integration Infrastructure Program Data Source DB Interface User (Matt) Data Sources

SDM center SDM Center Data Integration Infrastructure Data Source User (Matt) Workflow Agent Service registry and brokering Data Integration Agent(s) Communication Protocol Gateway Program DB Interface Data Sources

SDM center SDM Center Data Integration Infrastructure Data Source User (Matt) Workflow Agent Service registry and brokering Data Integration Agent(s) Other Agents (e.g., VIPAR) Database Access Communication Protocol Gateway Program Interfacing Other I/O Agents Program DB Interface Data Sources

SDM center SDM Center Data Integration Infrastructure XML Wrapper Data Source User (Matt) Workflow Agent Service registry and brokering Data Integration Agent(s) Wrapper based Agent Other Agents (e.g., VIPAR) Database Access Communication Protocol Gateway Program Interfacing Other I/O Agents Program DB Interface Data Sources Extraction Rules Human Knowledge GUI Code Generator

SDM center SDM Center Data Integration Infrastructure XML Wrapper Data Source User (Matt) Workflow Agent Service registry and brokering Data Integration Agent(s) Data Mediation Wrapper based Agent Other Agents (e.g., VIPAR) Database Access Communication Protocol Gateway Program Interfacing Other I/O Agents Extraction Rules Human Knowledge GUI Code Generator Program DB Interface Data Sources Executable Workflow Plan: “Matt’s WF”

SDM center SDM Center Data Integration Infrastructure User (Matt) Workflow Agent Service registry and brokering Data Integration Agent(s) Data Mediation Wrapper based Agent Other Agents (e.g., VIPAR) Database Access Communication Protocol Gateway XML Wrapper Data Source Executable Workflow Plan: “Matt’s WF” Program Interfacing Other I/O Agents Parameterized Workflow Specification (PWS) Source Capabilities (SC) Binding Patterns User Agent User constraints & parameters Workflow Resolution Service (WRS) Domain Map/Ontology Workflow Instantiation Service (WIS) WF feasible WF infeasible: report reason Data RegistrationServices Registration DB Program DB Interface Data Sources Extraction Rules Human Knowledge GUI Code Generator

SDM center Status l Focus has been on developing a prototype of Matt’s workflow  Demonstrate basic infrastructure functionality  Provide a useful tool for Matt to use in his research efforts l Flushed out the details of architecture  Interconnections between components better defined l We have a prototype of that system in place  Wrappers generated from XWrap by GT  Combined into coherent workflow by SDSC  Workflow based interface completed by NCSU l The following presentations will go into more details about what has been accomplished and what our current tasks are

SDM center Questions?

SDM center People LLNL l Terence Critchlow (lead) Georgia Tech l Calton Pu l Ling Liu l David Buttler l Dan Rocco l Henrique Paques l Wei Han Target Users l Matt Coleman (LLNL)  Allen Christian (LLNL)  Phil Bourne (PDB) SDSC l Bertram Ludaescher l Amarnath Gupta l Ilkay Altintas Agent Technology l Tom Potok (ORNL) l Joel Reid (ORNL) l Mladen Vouk (NCSU) l Munindar Singh (NCSU) l Sandeep Chandra (NCSU) l Zhengang Cheng (NCSU) l Sangeeta Bhagwanani (NCSU)

SDM center This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W ENG-48.