Cicc june meeting
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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

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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 automation2

Example of existing solutions: Biomediator project (

Workflow automation

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

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