Web Service Infrastructure

From Chemical Informatics and Cyberinfrastructure Collaboratory

Completed services link to the WSDL

Contents 1 Indiana CICC hosted web services 1.1 Varuna Services 1.2 Database Services (see also Databases Projects) 1.3 Commercial Application Services 1.4 Cheminformatics Services 1.5 Statistics/Math Web Services 2 External chem/bio informatics web services 3 Potential Services 4 External general web services

Indiana CICC hosted web services

These are all under development. For example clients to these services, see Web Portal Development.

Varuna Services

• The file operation utilities help to convert file formats frequently used for Quantum mechanics and Molecular mechanics computation. These web services accept the input files and return the converted result in a string array. Some services need the support of the Openbabel. http://129.79.139.29/FileOper/FileOperation.asmx

• The result analysis utilities accept the computed result from Jaguar and ADF package and return the frequency and geometry optimization information. http://129.79.139.29/Utilites/Service.asmx

• The database query service helps the user to locate the project information in the Varuna database. This service also include executing command on the Avidd. http://129.79.139.29/RemoteOper/RemoteCmd.asmx

• The upload web service help user to interact with the Avidd, Varuna and local PC through SFTP or SCP protocol by using the open source SharpSSH library. These web services accept the input files, submit files to the Avidd and store the information into Varuna. http://129.79.139.29/RemoteOper/Service.asmx

Database Services (see also Databases Projects)

• • Local NIH Database
  • Local PubChem Database Rajarshi Guha. These services are essentially wrapped queries. Naturally there may be queries that you'd like to see but are not present. If so let me know.
    • PubChem Structure (Usage) Provides methods to get Pubchem Compound information
    • PubChem Synonyms (Usage) Provides methods to get synonyms given a compound or substance ID. SMILES support coming
    • PubChem Derived properties (Usage) Get calculated properties (SLogP and SMRef) given a compound ID. Can also search via exact values and ranges (but this is very slow at the moment).
    • PuBChem Docking results (Usage) Provides methods to get the docked structures (for a given target) for PubChem compounds based on CID, sorted score values or by SMARTS patterns. Ligands are returned in SDF format. Currently only the ligand structures are accessible and the actual score values are coming soon.
    • PubChem 3D structures (Usage) This service provides access to MMFF94 optimized 3D structures for PubChem compounds. Structures are returned in SD format and can be accessed by CID or by SMARTS patterns
  • Distributed Drug Discovery Database

Commercial Application Services

• OpenEye: These URLs are private and are available on request.
  • FRED Docking
  • FILTER Property Calculation and Filtering
  • OMEGA 2D-3D Conversion
• BCI: these services are private and available on request. Huapeng Yuan
  • Various BCI Clustering services (Usage)

Cheminformatics Services

• VOTables Sima Patel
  • Convert tab file to VoTables
  • Convert Votable to tab file
  • Convert Votable to Spreadsheet
  • Convert Spreadsheet to VoTable
  • Retrievs Field names and Datatypes from Votable
  • Extract columns from given Votable and to create a new Votable

• Cambridge Services Huapeng Yuan
  • InChIGoogle (Usage)
  • InChiServer (Usage)
  • CMLRSSServer (Usage)
  • Open Babel (Usage)
• ToxTree services Huapeng Yuan
  • ToxTreeServer (Usage)
• MACCS keys
  • DBUtil (Usage) -Note that these are located in the database web services due to the dependency on gNova. At one point these will be shifted to a more intuitive cheminformatics service
• CDK web services Rajarshi Guha You can access individual servces via PHP clients here. If there are algorithms or features you'd like to see or if you find bugs go to the Sourceforge page and submit a feature request or bug report
  • Molecular Similarity (Usage)
    • Pair wise 2D similarity
    • 2D similarity matrix
    • 3D similarity
    • Distance moments for use in 3D similarity calculations
  • Molecular Descriptors (Usage)
    • TPSA
    • XLogP
    • Surface area
    • Arbitrary descriptors
  • 2D Structure Diagrams (Usage)
  • Druglikeness Methods (Usage)
  • Cheminformatics Utility Methods (Usage)
    • Fingerprints
    • Molecular weight and formulae
    • SDF to PDB/CML conversion
    • 2D coordinate generation
    • General file format conversion using OpenBabel (this is a slightly restricted form of the OBserver service since it does not accept any arguments beyond the input and output format specifiers)

Statistics/Math Web Services

If there are algorithms or features you'd like to see or if you find bugs go to the Sourceforge page and submit a feature request or bug report. Rajarshi Guha.

• • Sampling distributions (Usage)
  • Linear Regression (Usage)
  • CNN Regression (Usage)
  • RF Regression (Usage)
  • LDA Classification (Usage)
  • K-means Clustering (Usage)
  • Feature Selection (Usage)
    • Stepwise and exhaustive feature selection for linear regression models
  • Model Generation (Usage)
    • Automatically generate linear and non-linear models for a dataset
  • t-Test (Usage)
  • XY Plots (Usage)
  • Histogram Plots (Usage)
• OSCAR3 Web service Huapeng Yuan invokes the OSCAR3 that extracts chemical information from text and produces an XML instance highlighting the chemical information
  • OSCAR3 Service (URL capable) (Usage)
• Other
  • Generic Similarity Search
  • Property Calculator
  • Hit Classifier

External chem/bio informatics web services

Running instances of the services below can also be used, although we have some local copies.

• Murray-Rust Group
  • InChI Google
  • InChI Server
  • Jumbo Converter
• NMRShiftDB services
  • NMRShiftDB Submission
  • NMRShiftDB Prediction
  • NMRShiftDB Spectrum Types
• VCC Laboratory
  • ALogPS
• NCI CSLS
  • NCI CSLS Lookup See here for example usage

Potential Services

The following are worth more investigation and are listed roughly in order of preference.

• CDK Candidate Services from Rajarshi Guha. These are command lines tools that should be easy to convert to services in Axis. Some of these have graphical components, so this will have to be decoupled.
  • Displaying highlighted substructures
  • Determining and displaying maxmimum common substructures
  • Batch generation of 2D diagrams
• PDB
• PubChem
• Blue Obelisk The following are member projects. I note many of them mention the Gnu Public License, so this is a area of future concern.
  • JChemPaintis a 2D molecular structure editor. Lots of visual components, so there may be some difficulty in making this into a service. This would make a an interesting chemistry equivalent to the "Web Map Server".
  • JMol is a 3D rendering tool for molecules. Could also build a Web Map Server equivalent around this, but probably it is better for building interactive applets.
  • [JOELib http://www-ra.informatik.uni-tuebingen.de/software/joelib/index.html] This looks like an alternative library to CDK. We need JOELib applications, not really JOELib itself.
  • Open Babel They use media wiki. This service is in development.

External general web services

• Google Web API - see Google APIs page