The BioDA Project

1
Data Integration in Bioinformatics Using OGSA-DAI

• The BioDA Project
• Shirley Crompton, Brian Matthews (CCLRC)
• Alex Gray, Andrew Jones,
• Richard White (Cardiff University)

2
Overview

• Bioinformatics Data Access and Integration
  Requirements
• Generic
• BioDA Workshop and Questionnaire
• BDWorld-specific
• OGSA-DAI exemplar

3
The BioDA Project

• Independent Evaluation of OGSA-DAI
• the suitability of that software in its present
  form
• how to leverage OGSA-DAI in bioinformatics GRID
• OGSA-DAI Product Improvement
• Feedbacks to the DAIT Team
• Knowledge Dissemination
• Evaluation Report
• Publications/Presentations
• Workshop on OGSA-DAI for the bioinformatics
  eResearch community

4
Bioinformatics

• The Application and development of computing of
  mathematics to the management, analysis an
  understanding of data to solve biological
  question.
• Attwood, TK and Parry-Smith, DJ 1999

Data Management
Data Analysis
5
Grid Computing

• ... flexible, secure, coordinated resource
  sharing among dynamic collections of individuals,
  institutions and resources
• Foster, Kesselman and Tuecke, 2001

6
1st BioDA Workshop(NeSC, 8 Dec 2004)

• Workshop Objectives
• examine bioinformatics communitys needs for data
  access and integration (DAI) on the grid, and
• to explore the application of OGSA-DAI, a
  middleware developed expressly to address DAI
  requirements of eScience projects

7
The BioDA Survey
8
The Results

• 17 key requirements, top of the list include
• schema integration
• schema mapping
• mixed language query
• complex join across databases
• provenance data
• flexible resource discovery
• RDF database access

9
The BioDA Exemplar

• The BioDiversity World
• To create a GRID-based problem solving
  environment. 
• Enable collaborative exploration and analysis of
  global biodiversity patterns using workflow and
  rich data sources from around the world
• Example applications would be modeling species
  distributions against climate change,
  conservation prioritization and linking
  evolutionary changes to past climates. 

10
BDWorld(Source BDWolrd)
11
BDWorld Data Resources Key Issues

• geographically distributed and autonomous
• heterogeneous in structure and data standards
• mainly read via HTTP/XML protocols using custom
  wrappers
• SQL queries are limited to the EBI EMBL store and
  BDWorld cache databases
• potentially resource-intensive to harvest
• a single taxa name may resolve into a large
  number of accepted taxon names
• same query repeated on different data collections

12
Resource Wrapping(SourceBDWorld)
User
Remote Resource
Workflow enactment engine
Wrapper
The GRID
13
Implications for BioDA

• abstraction layer (BGI) ? Proprietary invocation
  mechanism
• InvokeOperation
• (ResourceHandler, Operation, XmlDataCollection)
• prepared search statements defined in individual
  data resource wrapper
• BGI protocols ? BDW communication objects.
  Search parameters and results passed as
  XmlDataCollecton

14
BioDA Exemplar

• Two main possibilities within BDW
• Augment BGI to support inclusion of queries in
  workflows and to be sent directly to OGSA-DAI
  enabled databases.
• Define precise search parameters, exclude
  ineligible data early on
• Potential application of OGSA-DQP
• Very major revision to BDW protocols also,
• many resources of interest are simply not exposed
  as databases.
• Provide facilities within individual wrappers
  that benefit from OGSA-DAI.

15
OGSA-DAI Prototype(What wed have liked)
OGSA-DAI R5 GDS
3. Invoke wrapper
Wrapper Module
BDWQueryActivity
2. Create GDS and query
6. Download url
7. url
deliverFromURL(url)
5. Download URL
OGSA-DAI Client
deliverFromURL(xsl)
8. XSL transform to BDW format
XSLTransform
9. To WF unit
deliverToURL/GFTP
16
Key Issues encountered

• Complex client-side coding to orchestrate the
  application flow
• require several GDS perform requests
• Difficult to synchronise
• Remote web databases have different response time
  (or not response at all!)
• Different data transformation series applicable
  to different data resources
• BDW Protocols specify data returned as a BDW
  XmlDataCollection object

17
OGSA-DAI Prototype(What we ended up doing)
OGSA-DAI R5 GDS
BDWQueryActivity
6. return XmlRemoteData
3. Invoke wrapper/s
4. Query, transform
OGSA-DAI Client
18
Conclusion

• Highlighted key bioinformatics eScience project
  requirements for OGSA-DAI
• support for a metadata-driven two-step access to
  data and data integration
• Reviewed BDWorld DAI requirements
• uniform access to disparate, heterogeneous data
  resources
• including anonymous access to web information
  system
• Reviewed the BDWorld OGSA-DAI exemplar and
  issues encountered