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 –InfoChems SPRESI Web Service Provides access to the SPRESI molecule database Status: Perl scripts for accessing SPRESI Web Service To do: Developing a Web service wrapper to utilize InfoChems SPRESI Web Service

BCI Clustering URL Service Methods Service MethodDescription InputURLOutput makebitsURLGene rate Generate fingerprints from a SMILES structure SMIstringFingerprint and program output divkmURLGenerat e Cluster fingerprints with Divkmeans SCNstringDKM data and program output smile2dkmURLMakebits + divkmSMIstringAll SMI, DKM and std. outputs optclusURLGenera te Generate the best levels in a hierarchy SMIstring DKMstring Best data and program output rnnclusURLGenera te Extract individual cluster partitions SMIstring DKMstring New partition and std. output smile2ClusterPartiti onedURL Generate a new SMILES structure w/ extra col. SMIstringAll intermediate data and output

Workflow for smile2ClusterPartitionedURL

Workflow for Toxic Hazard in Verbose

Diagram of Workflow2 Input/Output Web Services Beanshell Scripting