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CICC June meeting

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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  1. CICC June meeting IUPUI team: Kelsey Forsythe Malika Mahoui Deepthi Jonnala Usha Cheemakurthi

  2. Outline • Distributed Drug Discovery project • Adopting Biofacets for Chemical Informatics • Workflow automation

  3. 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

  4. Adopting Biofacets for Chemical Informatics • Biofacets variations • As a Web server integrating a diversified set of biological databases and a rich set of facets (http://biofacets.informatics.iupui.edu:8080/biofacets/) • 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

  5. 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.

  6. 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

  7. Example of existing solutions: Biomediator project (http://www.biomediator.org/publications/) Workflow automation

  8. Workflow automation • Example of existing solutions: SIBIOS project (http://sibios.engr.iupui.edu/) • 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

  9. 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.

  10. 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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