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CICC June meeting. IUPUI team: Kelsey Forsythe Malika Mahoui Deepthi Jonnala Usha Cheemakurthi. Outline. Distributed Drug Discovery project Adopting Biofacets for Chemical Informatics Workflow automation. Adopting Biofacets for Chemical Informatics. What is Biofacets?

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cicc june meeting

CICC June meeting

IUPUI team:

Kelsey Forsythe

Malika Mahoui

Deepthi Jonnala

Usha Cheemakurthi

  • Distributed Drug Discovery project
  • Adopting Biofacets for Chemical Informatics
  • Workflow automation
adopting biofacets for chemical informatics
Adopting Biofacets for Chemical Informatics
  • What is Biofacets?
    • Faceted based integration system for biological databases
    • Features a meta-search engine that target variegated biological databases
    • Supported by a set of biological facets used to dynamically categorize query results facilitating results browsing and query refinement
adopting biofacets for chemical informatics1
Adopting Biofacets for Chemical Informatics
  • Biofacets variations
    • As a Web server integrating a diversified set of biological databases and a rich set of facets (
    • A framework to be used for generating custom versions; with user specific collection of scientific databases and facets
    • Chemical informatics version: currently being developed by Usha Cheemakurthi
workflow automation
Workflow automation
  • Problem statement:
    • Workflow environments such as Taverna are too complex for non-IT fluent chemists.
    • As a consequence, the efforts made for web services will be useful for a very limited audience.
    • Need to reach out normal chemists to help them leverage on the wealth of databases and analytical tools to advance their research.
workflow automation1
Workflow automation
  • Proposed solution:
    • Provide researchers with a high level query language (serialized through a GUI) that helps users formulate queries
    • Workflow automation will translate researcher query into executable workflow(s)
    • Provide users with different levels for workflow composition to account for different levels of user expertise
workflow automation3
Workflow automation
  • Example of existing solutions: SIBIOS project (
    • Workflow automation component under construction
    • Solution using enhanced graph planner algorithm to translate user query into a workflow
    • Current status: the user needs to specify:
      • the input and output of the workflow
      • Potential intermediate services and their ordering
workflow automation4
Workflow automation
  • Example:
    • User inputs Swissprot entry (input) and needs to find associated nucleic acid definitions and organism names (output)
    • He also wants to query PDB service before GenBank service.
workflow automation5
Workflow automation
  • Future work:
    • Allow users to enter semantic queries using biological/bioinformatics concepts.
    • Generate more than one workflow as a solution for user query