CICC Web services and Issues

Jungkee (Jake) Kim

Community Grids Laboratory

CICC Web Services I• BCI Clustering

– Provides Bernard Chemical Information (BCI) clustering packages– A module of the workflow for HTS data organization and flagging– Status:

• Added URL output support to the previous solid prototype (Multi-user durable)

• Taverna Beanshell Scripting for data format adjusting (e.g. Filtering out the head part listing column names)

– To do: Evaluating the URI(URL) based workflow design• ToxTree

– Estimates toxic hazard by applying a decision tree approach– A module of the workflow for HTS data organization and flagging– Status: A test prototype producing the level of toxicity in a brief or

verbose explanation against a SMILE structure– To do:

• Refining the Web service for cluster input and external property support• The Taverna Beanshell scripting for data merging not used in some modules

CICC Web Services II• Workflow for HTS data organization and flagging

– Demonstrates how screening data can be flagged and organized for human analysis

– Status: Individual modules except the visualization are in prototype– To do:

• Defining at least XML schema or DTD for the workflow data (at most the Ontology)

• Redefining current workflow model to reflect the new feature of Taverna 1.4 supporting complex data structures and the provenance plugin

• Other Planed Web Services– Open Source Chemistry Analysis Routines (OSCAR)

• Extracts chemical information from text and produces an XML instance highlighting the chemical information

• A module of the PMR workflow• Status: OSCAR3 is available and works fine as a Java application• To do: Studying XML instances for extracting chemical names

BCI Clustering URL Service Methods

Service Method Description Input URLOutput

makebitsURLGenerate

Generate fingerprints from a SMILES structure

SMIstring Fingerprint and program output

divkmURLGenerate

Cluster fingerprints with Divkmeans

SCNstring DKM data and program output

smile2dkmURL Makebits + divkm SMIstring All SMI, DKM and std. outputs

optclusURLGenerate

Generate the best levels in a hierarchy

SMIstring

DKMstring

Best data and program output

rnnclusURLGenerate

Extract individual cluster partitions

SMIstring

DKMstring

New partition and std. output

smile2ClusterPartitionedURL

Generate a new SMILES structure w/ extra col.

SMIstring All intermediate data and output

Workflow for smile2ClusterPartitionedURL

Workflow for Toxic Hazard in Verbose

Diagram of Workflow2Input/Output

Web Services

Beanshell Scripting