Building CICC Web services

Jungkee (Jake) Kim

Community Grids Laboratory

3/22/2006 CICC Project Meeting

CICC Web Services

• BCI Clustering– Provides Bernard Chemical Information (BCI) clustering

packages– Status: Done for a solid prototype

• Local Service for WWMM of Peter M-R’s group– Status: Done for InChiGoogle, InChIServer, OBServer, and

CMLRSSServer

• Other Planed Web Services– ToxTree

• Estimates toxic hazard by applying a decision tree approach• Status: Java application available, includes Java command line

– Open Source Chemistry Analysis Routines (OSCAR)• Status: Limited accessibility (Not for Unix), No new version yet

3/22/2006 CICC Project Meeting

Flow Chart of SMILES to Cluster Partitioned of BCI Web Service

SMILEString

Makebits

Dictionary(Default)

Fingerprint(*.scn)

DivKmeansCluster

Hierarchy(*.dkm)

Optclus RNNclusOne

ColumnProcess

MergeProcess

ExtractedCluster

Hierarchy(*.clu)

NewSMILEString

GeneratingFingerprints

ClusteringFingerprints

Generatingthe best levels

SMILES to DKM

Extracting individualcluster partitions

best

level

BCI Clustering Service Methods

Service Method Description Input Output

makebitsGenerate Generate fingerprints from a SMILES structure

SMIstring Fingerprint string

divkmGenerate Cluster fingerprints with Divkmeans

SCNstring Clustered Hierarchy

smile2dkm Makebits + divkm SMIstring Clustered Hierarchy

optclusGenerate Generate the best levels in a hierarchy

DKMstring Best partition cluster level

rnnclusGenerate Extract individual cluster partitions

DKMstring Indiv. cluster partitions

smile2ClusterPartitioned

Generate a new SMILES structure w/ extra col.

SMIstring New SMILES structure

Workflow for smile2ClusterPartitioned

Result of the workflow

Local Web Service Methods for WWMM of PMR’s Group

Services Descriptions Input Output

InChIGoogle Search an InChI structure through Google

inchiBasic

type

Search result in HTML format

InChIServer Generate InChI version

format

An InChI structure

OBServer Transform a chemical format to another using Open Babel

format

inputData

outputData

options

Converted chemical structure string

CMLRSSServer

Generate CMLRSS feed from CML data

mol, title description link, source

Converted CMLRSS feed of CML data

SMILE to InChiGoogle Search

3/22/2006 CICC Project Meeting

Search ResultGoogle Search Results:The estimated total number of results returned for the query: 12The query string that generated this result: 1/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12) ====Result elements (8) =====The size in kilobytes of the cached version: 38kURL: http://nmrshiftdb.pharmazie.uni-marburg.de/portal/pane0/Results?nmrshiftdbaction=showDetailsFromHome&molNumber=20038075

The size in kilobytes of the cached version: URL: http://pubchem.ncbi.nlm.nih.gov/help.html

The size in kilobytes of the cached version: URL: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2244

……

toxTree

3/22/2006 CICC Project Meeting

Discussion

• We are considering some revisions for the services to use URL’s as input/output of services instead of sending/receiving the actual content.

• But there will be some privacy/security issues that may need be discussed. This would also simplify splitting BCI services across multiple machines.

3/22/2006 CICC Project Meeting

Web Sites for CICC Web Services

• Web Services Infrastructurehttp://www.chembiogrid.org/wiki/index.php/Web_Service_Infrastructure

• CICC Web Service Usagehttp://www.chembiogrid.org/wiki/index.php/CICC_Web_Service_Usage

• Workflowshttp://www.chembiogrid.org/wiki/index.php/Workflows

• List of the Local Web Serviceshttp://gf1.ucs.indiana.edu:7880/axis/servlet/AxisServlet