Web Services as Web Services as Integrators of Public Integrators of Public

Chemistry DatabasesChemistry Databases

Gary WigginsGary WigginsSchool of InformaticsSchool of Informatics

Indiana UniversityIndiana Universitywiggins@indiana.eduwiggins@indiana.edu

Interdisciplinary ScienceInterdisciplinary Science

““The boundary between the known and The boundary between the known and the unknown is where science flourishes.”the unknown is where science flourishes.”--Michael Shermer--Michael Shermer

““There are known knowns… There are There are known knowns… There are known unknowns… There are unknown known unknowns… There are unknown unknowns…”unknowns…”--Donald Rumsfeld--Donald Rumsfeld

BUT….BUT…. What about What about UNKNOWNUNKNOWN knowns? knowns?

zzzzzCASzzzzzCAS

““In an industry first, Chemical Abstracts In an industry first, Chemical Abstracts Service (CAS) has unveiled a Service (CAS) has unveiled a revolutionary new literature searching tool revolutionary new literature searching tool which will permit scientists to search and which will permit scientists to search and retrieve the world’s chemical literature—retrieve the world’s chemical literature—including patents and obscure technical including patents and obscure technical reports—in their sleep.”reports—in their sleep.”--Author unknown--Author unknown

Overview of the TalkOverview of the Talk

Introduction to Web ServicesIntroduction to Web Services Public Databases and Data Repositories Public Databases and Data Repositories

for Chemistryfor Chemistry Projects Underway or Planned at Indiana Projects Underway or Planned at Indiana

UniversityUniversity

Web Services IntroductionWeb Services Introduction

What are “Web Services”?What are “Web Services”? A distributed invocation system built on Grid A distributed invocation system built on Grid

computingcomputing• Independent of platform and programming Independent of platform and programming

languagelanguage• Built on existing Web standardsBuilt on existing Web standards

A service oriented architecture withA service oriented architecture with• Interfaces based on Internet protocolsInterfaces based on Internet protocols• Messages in XML (except for binary data Messages in XML (except for binary data

attachments)attachments)

Service Oriented Architecture Service Oriented Architecture (SOA)(SOA)

Goal is to achieve loose coupling among Goal is to achieve loose coupling among interacting software agentsinteracting software agents

Define Define serviceservice: a unit of work done by a : a unit of work done by a service provider to achieve desired end service provider to achieve desired end results for a service consumerresults for a service consumer

Both provider and consumer are roles Both provider and consumer are roles played by software agents on behalf of played by software agents on behalf of their owners.their owners.

Web Services ArchitecturesWeb Services Architectures

Individual services are registered globallyIndividual services are registered globally Broken down into individual services with Broken down into individual services with

inputs and outputs specifiedinputs and outputs specified Services are publishedServices are published Services are requestedServices are requested Open registry, publishing, and requestingOpen registry, publishing, and requesting

Service-Oriented ArchitectureService-Oriented Architecture

From Curcin et al. From Curcin et al. DDT, 2005, DDT, 2005, 10(12),86710(12),867

Web Services for ScienceWeb Services for Science

Invisible Services, Semantic Web, and Invisible Services, Semantic Web, and GridGrid

Easy-to-use tools for any scientistEasy-to-use tools for any scientist High throughput, resource intensive High throughput, resource intensive

computing done for low cost/resourcescomputing done for low cost/resources Shared communityShared community

Collaborations between labs and fieldsCollaborations between labs and fields Shared dataShared data Shared toolsShared tools

e-Science and the Grid 1e-Science and the Grid 1

e-Sciencee-Science:: Major UK ProgramMajor UK Program global collaborationglobal collaboration in key areas of science and the in key areas of science and the

next generation of infrastructure that will enable itnext generation of infrastructure that will enable it• reflects growing importance of international reflects growing importance of international

laboratories, satellites and sensors and their laboratories, satellites and sensors and their integrated analysis by distributed teamsintegrated analysis by distributed teams

• total investment of some £200M over the five-year total investment of some £200M over the five-year period from 2001 to 2006period from 2001 to 2006

CyberInfrastructureCyberInfrastructure: : the analogous US initiativethe analogous US initiative Grid TechnologyGrid Technology: supports e-Science & : supports e-Science &

CyberinfrastructureCyberinfrastructure

e-Science and the Grid 2e-Science and the Grid 2

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IMAGING INSTRUMENTS

COMPUTATIONALRESOURCES

LARGE-SCALE DATABASES

DATA ACQUISITION ,ANALYSIS

ADVANCEDVISUALIZATION

Basic Architectures:Basic Architectures:Servlets/CGI and Web ServicesServlets/CGI and Web Services

Browser

WebServer

HTTP GET/POST

DB or MPIAppl.

JDBC

WebServer

DBor MPIAppl.

JDBC

Browser

WebServer

SOAP

GUIClient

SOAPWSDL

WSDL

WSD

LWSD

L

When To Use Web Services?When To Use Web Services? Applications do not have severe restrictions on Applications do not have severe restrictions on

reliabilityreliability andand speedspeed.. Two or more organizations need to Two or more organizations need to cooperatecooperate..

One needs to write an application that uses another’s service.One needs to write an application that uses another’s service.

Services can be Services can be upgraded independentlyupgraded independently of of clients.clients.

Services can be easily expressed with Services can be easily expressed with simple simple request/responserequest/response semantics and semantics and simple statesimple state..

Web Services BenefitsWeb Services Benefits

Web services provide a clean separation Web services provide a clean separation between a capability and its user interface.between a capability and its user interface.

Increase in productivityIncrease in productivity Increase in flexibilityIncrease in flexibility Rapid return on investmentRapid return on investment Integration across multiple applicationsIntegration across multiple applications

Web Services AdvantagesWeb Services Advantages

Output in human- and computer-readable Output in human- and computer-readable formatsformats

I/O formats based on standard Internet I/O formats based on standard Internet protocolsprotocols

Resources accessible server to server Resources accessible server to server allow automated I/Oallow automated I/O

Integration based on specific services: you Integration based on specific services: you select services or data needed without select services or data needed without downloading the entire data setdownloading the entire data set

Web Services AdvantagesWeb Services Advantages

Description protocols provide details of Description protocols provide details of service provided and interface service provided and interface componentscomponents

Semantic Web standards increase Semantic Web standards increase efficiencyefficiency

Use a central registry and standardized Use a central registry and standardized description of servicesdescription of services

Quality and status of the information is Quality and status of the information is dynamically availabledynamically available

Web Services DrawbacksWeb Services Drawbacks

Based on new technologiesBased on new technologies Time and commitment required to learnTime and commitment required to learn Standards still in a state of fluxStandards still in a state of flux Issues with quality of data, (and for Issues with quality of data, (and for

chemistry, quantity of chemistry, quantity of open dataopen data), security, ), security, and privacyand privacy

Components of Web ServicesComponents of Web Services

ProtocolsProtocols WSDLWSDL SOAPSOAP UDDIUDDI

XML as a basis for the protocolsXML as a basis for the protocols OntologiesOntologies

OWL: Ontology Web LanguageOWL: Ontology Web Language Semantic WebSemantic Web

WSDL: Web Service Definition WSDL: Web Service Definition LanguageLanguage

Describes a service’s interface to clientsDescribes a service’s interface to clients Services register themselves with Web Services register themselves with Web

ServicesServices WSDL describes how to contact and WSDL describes how to contact and

interact with servicesinteract with services I/O, operations and messages to aid I/O, operations and messages to aid

interaction with clientinteraction with client

SOAP: Simple Object Access SOAP: Simple Object Access ProtocolProtocol

Maps abstract WSDL service descriptions Maps abstract WSDL service descriptions to concrete implementationsto concrete implementations

Flexible protocol to communicate Flexible protocol to communicate information between server and server or information between server and server or client and server using XMLclient and server using XML

Supports Remote Procedure CallsSupports Remote Procedure Calls Allows layers (security, authentication, Allows layers (security, authentication,

transactions) over the basic SOAP transactions) over the basic SOAP elementselements

UDDI: Universal Description, UDDI: Universal Description, Discovery, and IntegrationDiscovery, and Integration

Provides ways for clients and services to interact Provides ways for clients and services to interact with other serviceswith other services

Uses XMLUses XML Defines the means of access, e.g.,Defines the means of access, e.g.,

URLURL E-MailE-Mail

Defines services hosted by an entityDefines services hosted by an entity Business-oriented tagsBusiness-oriented tags Uses SOAP for communicatingUses SOAP for communicating

XML and Web servicesXML and Web services XML lends itself to distributed computing:XML lends itself to distributed computing:

It’s just a data description.It’s just a data description. Platform, programming language independentPlatform, programming language independent

Web Services Description Language Web Services Description Language (WSDL)(WSDL) Describes how to invoke a serviceDescribes how to invoke a service Can bind to SOAP, other protocols for actual Can bind to SOAP, other protocols for actual

invocationinvocation Simple Object Access Protocol (SOAP)Simple Object Access Protocol (SOAP)

Wire protocol extension for conveying RPC callsWire protocol extension for conveying RPC calls Can be carried over HTTP, SMTPCan be carried over HTTP, SMTP

RDF: Resource Description RDF: Resource Description FrameworkFramework

A standard for statements describing resourcesA standard for statements describing resources RDF statements consist of aRDF statements consist of a

Subject: the resource being describedSubject: the resource being described Predicate: the property ascribed to the resourcePredicate: the property ascribed to the resource Object: the entity to which the resource bears that Object: the entity to which the resource bears that

propertyproperty

An alternative to UDDI: said to more flexible and An alternative to UDDI: said to more flexible and extensible than UDDIextensible than UDDI

RDFS: Resource Description RDFS: Resource Description Framework SchemaFramework Schema

RDF statements ascribe properties to resources, RDF statements ascribe properties to resources, but RDF provides no means for describing those but RDF provides no means for describing those properties.properties.

RDFS defines classes and properties that are RDFS defines classes and properties that are used to describe classes, properties, and other used to describe classes, properties, and other resources.resources.

RDFS vocabulary descriptions are written in RDFS vocabulary descriptions are written in RDF.RDF.

RDFS provides a means of specifying a RDFS provides a means of specifying a vocabulary for a particular domain.vocabulary for a particular domain.

OWL: Web Ontology LanguageOWL: Web Ontology Language

Builds on RDF and RDFS and adds a Builds on RDF and RDFS and adds a means for richer descriptions of properties means for richer descriptions of properties and classesand classes Disjoint classesDisjoint classes Cardinality of classesCardinality of classes Characteristics of relations, like symmetryCharacteristics of relations, like symmetry

Standards for Web ServicesStandards for Web Services

Business Process Execution Language for Business Process Execution Language for Web Services (BPEL4WS)Web Services (BPEL4WS)

Ontology Web Language Semantics Ontology Web Language Semantics (OWL-S)(OWL-S)

Web Service Modeling Ontology (WSMO)Web Service Modeling Ontology (WSMO)

Standards Setting Bodies: OASISStandards Setting Bodies: OASIS

OASIS: Organization for Advancement of OASIS: Organization for Advancement of Structured Information StandardsStructured Information Standards ebXML: e-business XMLebXML: e-business XML UDDI: Universal Description, Discovery and UDDI: Universal Description, Discovery and

IntegrationIntegration Global Grid ForumGlobal Grid Forum

community of users, developers, and vendors community of users, developers, and vendors leading the global standardization effort for leading the global standardization effort for grid computinggrid computing

Standards Setting Bodies: W3CStandards Setting Bodies: W3C

W3C: World Wide Web ConsortiumW3C: World Wide Web Consortium OWL: Ontology Web LanguageOWL: Ontology Web Language RDF/RDFS: Resource Description RDF/RDFS: Resource Description

Framework/SchemaFramework/Schema SOAP: Simple Object Access ProtocolSOAP: Simple Object Access Protocol URI/URL/URN: Universal Resource URI/URL/URN: Universal Resource

Identifier/Locator/NameIdentifier/Locator/Name WSDL: Web Service Definition LanguageWSDL: Web Service Definition Language XML: eXtensible Markup LanguageXML: eXtensible Markup Language

Web Services Integration Projects: Web Services Integration Projects: BiosciencesBiosciences

myGridmyGrid http://www.mygrid.org.uk/http://www.mygrid.org.uk/

BIOPIPEBIOPIPE http://biopipe.org/http://biopipe.org/

BioMOBYBioMOBY http://biomoby.org/http://biomoby.org/

Web Services for Chemistry: Web Services for Chemistry: ProblemsProblems

Performance and scalabilityPerformance and scalability Proprietary dataProprietary data Competition from high-performance desktop Competition from high-performance desktop

applicationsapplications-- Geoff Hutchison, it’s a puzzle blog, 2005-01-05-- Geoff Hutchison, it’s a puzzle blog, 2005-01-05

ALSO: ALSO: Lack of a substantial body of trustworthy Open Lack of a substantial body of trustworthy Open

Access databasesAccess databases Non-standard chemical data formats (over 40 in Non-standard chemical data formats (over 40 in

regular use and requiring normalization to one regular use and requiring normalization to one another)another)

Necessary Ingredients in ChemistryNecessary Ingredients in Chemistry

Chemical communities to assemble Open Chemical communities to assemble Open Access databasesAccess databases Well-defined quality assurance procedures Well-defined quality assurance procedures

performed by distributed peer-review systemsperformed by distributed peer-review systems Software underlying the databases needs to Software underlying the databases needs to

be open source.be open source.

BlueObelisk.orgBlueObelisk.org A group of chemists, programmers, and A group of chemists, programmers, and

informaticians working collaboratively on informaticians working collaboratively on projects such as:projects such as: Chemistry Development Kit (CDK)Chemistry Development Kit (CDK) JChemPaintJChemPaint JmolJmol JUMBOJUMBO NMRShiftDBNMRShiftDB OctetOctet Open BabelOpen Babel QSARQSAR World Wide Molecular Matrix (WWMM)World Wide Molecular Matrix (WWMM)

Components of the Semantic Web Components of the Semantic Web for Chemistryfor Chemistry

XML – eXtensible Markup LanguageXML – eXtensible Markup Language RDF – Resource Description FrameworkRDF – Resource Description Framework RSS – Rich Site SummaryRSS – Rich Site Summary Dublin Core – allows metadata-based Dublin Core – allows metadata-based

newsfeedsnewsfeeds OWL – for ontologiesOWL – for ontologies BPEL4WS – for workflow and web servicesBPEL4WS – for workflow and web services

Murray-Rust et al. Org. Biomol. Chem. 2004, 2, 3192-Murray-Rust et al. Org. Biomol. Chem. 2004, 2, 3192-3203. 3203.

Chemistry Databases on the WebChemistry Databases on the Web

Marc Nicklaus lists 37 databases as of Marc Nicklaus lists 37 databases as of October 2001October 2001 Must have structure searching and at least Must have structure searching and at least

100 molecules100 molecules http://cactus.nci.nih.gov/ncidb2/chem_www.htmlhttp://cactus.nci.nih.gov/ncidb2/chem_www.html

SoaringBear’s List has 15 databasesSoaringBear’s List has 15 databases http://geocities.com/soaringbear/biomed/chem.htmlhttp://geocities.com/soaringbear/biomed/chem.html

Institutional RepositoriesInstitutional Repositories

NARSTO Quality Systems Science CenterNARSTO Quality Systems Science Center http://cdiac.esd.ornl.gov/programs/NARSTO/http://cdiac.esd.ornl.gov/programs/NARSTO/ Pollutant species in the troposphere over Pollutant species in the troposphere over

North AmericaNorth America Part of the Carbon Dioxide Information Part of the Carbon Dioxide Information

Analysis Center at ORNLAnalysis Center at ORNL NARSTO Data and Information Sharing ToolNARSTO Data and Information Sharing Tool

• http://mercury.ornl.gov/narsto/http://mercury.ornl.gov/narsto/

Public DatabasesPublic Databases

Developmental Therapeutics Program/NCIDevelopmental Therapeutics Program/NCI Some assay data for downloadSome assay data for download Structures for over 200,000 compoundsStructures for over 200,000 compounds

• http://http://dtp.nci.nih.gov/docs/dtp_search.htmldtp.nci.nih.gov/docs/dtp_search.html

Zinc and other screening databasesZinc and other screening databases NIST computational chemistry databaseNIST computational chemistry database Environmental fate and exposure Environmental fate and exposure

databasesdatabases

Other Public Databases 1Other Public Databases 1 ChemExper Chemical DirectoryChemExper Chemical Directory

> 200,000 substances; > 10,000 IR spectra> 200,000 substances; > 10,000 IR spectra http://chemexper.com/http://chemexper.com/

HIC-Up; Hetero-Compound Identification Centre HIC-Up; Hetero-Compound Identification Centre – Uppsala– Uppsala 5384 substances as of 1/15/055384 substances as of 1/15/05 http://http://xray.bmc.uu.se/hicupxray.bmc.uu.se/hicup//

Chemicals with Pharmaceutical Activity; a 3D Chemicals with Pharmaceutical Activity; a 3D Structural DatabaseStructural Database 400 3D structures400 3D structures http://http://www.chem.ox.ac.ukwww.chem.ox.ac.uk/mom/chemical-database//mom/chemical-database/

Isatin in ChemExperIsatin in ChemExper

Isatin ChemExper IR SpectrumIsatin ChemExper IR Spectrum

Isatin from HIC-UpIsatin from HIC-Up

Other Public Databases 2Other Public Databases 2

Cheminformatics.orgCheminformatics.org 41 data sets in 9 categories as of 8/18/0541 data sets in 9 categories as of 8/18/05 http://http://www.cheminformatics.orgwww.cheminformatics.org//

WebReactionsWebReactions http://webreactions.net/http://webreactions.net/

Other Public Databases 3Other Public Databases 3

MolTableMolTable http://www.moltable.org/http://www.moltable.org/

MatWeb Materials Property DataMatWeb Materials Property Data http://www.matweb.com/index.asp?ckck=1http://www.matweb.com/index.asp?ckck=1

Spectral Database for Organic Compounds (SDBS)Spectral Database for Organic Compounds (SDBS) Over 32,000 compoundsOver 32,000 compounds Has EI-MS, FT-IR, Has EI-MS, FT-IR, 11H NMR, H NMR, 1313C NMR, Raman, ESRC NMR, Raman, ESR http://www.aist.go.jp/RIODB/SDBS/cgi-bin/cre_index.cgihttp://www.aist.go.jp/RIODB/SDBS/cgi-bin/cre_index.cgi

NMRShiftDB (Christoph Steinbeck)NMRShiftDB (Christoph Steinbeck) 14,753 structures as of 8/19/0514,753 structures as of 8/19/05 Features peer-reviewed submission of data setsFeatures peer-reviewed submission of data sets http://www.nmrshiftdb.org/http://www.nmrshiftdb.org/

Comment on Link to PubChemComment on Link to PubChem

““It is great to know that - with PubChem - It is great to know that - with PubChem - there will be something like a single point there will be something like a single point of entry for people interested in structures of entry for people interested in structures and their properties. We are looking and their properties. We are looking forward to link our datasets to PubChem forward to link our datasets to PubChem structures.”structures.”--Christoph Steinbeck, commenting on the --Christoph Steinbeck, commenting on the

NMRShiftDB, CHMINF-L, 19 April 2005NMRShiftDB, CHMINF-L, 19 April 2005

Other Public Databases:Other Public Databases:Commercial TeasersCommercial Teasers

FTIRsearch.com (Thermo Electron)FTIRsearch.com (Thermo Electron) Demo file of 575 spectra from 87,000 in the full databaseDemo file of 575 spectra from 87,000 in the full database https://ftirsearch.com/default3.htmhttps://ftirsearch.com/default3.htm

ChemACXChemACX 30 of >350 suppliers catalog data30 of >350 suppliers catalog data http://chemacx.cambridgesoft.com/chemacx/index.asphttp://chemacx.cambridgesoft.com/chemacx/index.asp

Sunset Molecular Discovery, LLCSunset Molecular Discovery, LLC Wombat (World of Molecular BioAcTivity)Wombat (World of Molecular BioAcTivity)

• 117,007 entries with over 230,000 biological activities117,007 entries with over 230,000 biological activities Wombat PKWombat PK

• Database for Clinical Pharmacokinetics: 643 substances with 4668 Database for Clinical Pharmacokinetics: 643 substances with 4668 measurementsmeasurements

Three sample files from Wombat containing 341 Histamine-1 receptor Three sample files from Wombat containing 341 Histamine-1 receptor antagonistsantagonists

http://www.sunsetmolecular.com/http://www.sunsetmolecular.com/

Indiana University Existing ProjectsIndiana University Existing Projects

System for the Integration of System for the Integration of Bioinformatics Services (SIBIOS)Bioinformatics Services (SIBIOS) http://sibios.engr.iupui.eduhttp://sibios.engr.iupui.edu

PlatCom: A Platform for Computational PlatCom: A Platform for Computational Comparative GenomicsComparative Genomics http://bio.informatics.indiana.edu/sunkim/Platcom/http://bio.informatics.indiana.edu/sunkim/Platcom/

Reciprocal NetReciprocal Net http://www.reciprocalnet.org/index.htmlhttp://www.reciprocalnet.org/index.html

Indiana University Planned ProjectsIndiana University Planned Projects

Design of a Grid-based distributed data Design of a Grid-based distributed data architecturearchitecture

Development of tools for HTS data analysis and Development of tools for HTS data analysis and virtual screeningvirtual screening

Database for quantum mechanical simulation Database for quantum mechanical simulation datadata

Chemical prototype projectsChemical prototype projects Novel routes to enzymatic reaction mechanismsNovel routes to enzymatic reaction mechanisms Mechanism-based drug designMechanism-based drug design Data-inquiry-based development of new methods in Data-inquiry-based development of new methods in

natural product synthesisnatural product synthesis

Community Grids LabCommunity Grids Lab

Open Systems LabOpen Systems Lab

Web Services FutureWeb Services Future

Depends onDepends on Adoption of Adoption of standardsstandards IncorporationIncorporation of WS in current and newly of WS in current and newly

developed applicationsdeveloped applications Security, privacy, quality of dataSecurity, privacy, quality of data issues issues Development of WS tools and resourcesDevelopment of WS tools and resources for e- for e-

ScienceScience

““Tripos Embraces Web Services”Tripos Embraces Web Services”

Goal: to make it easier to incorporate Goal: to make it easier to incorporate Tripos’ high-throughput workflowsTripos’ high-throughput workflows Tripos’ Service-Oriented Informatics (SOI)Tripos’ Service-Oriented Informatics (SOI)

In partnership with SciTegic: Web services In partnership with SciTegic: Web services ensure software compatibility between the ensure software compatibility between the companies’ products.companies’ products.

Provocative ThoughtProvocative Thought

““While much bioscience is published with While much bioscience is published with the knowledge that machines will be the knowledge that machines will be expected to understand at least part of it, expected to understand at least part of it, almost all chemistry is published purely for almost all chemistry is published purely for humans to read.”humans to read.” Murray-Rust et al. Org. Biomol. Chem. 2004, Murray-Rust et al. Org. Biomol. Chem. 2004,

2, 3201.2, 3201.

Closing quoteClosing quote

““The future of chemistry depends on the The future of chemistry depends on the automated analysis of chemical automated analysis of chemical knowledge, combining disparate data knowledge, combining disparate data sources in a single resource, such as the sources in a single resource, such as the World-Wide Molecular Matrix, which can World-Wide Molecular Matrix, which can be analysed using computational be analysed using computational techniques to assess and build on these techniques to assess and build on these data.”data.” Townsend et al. Org. Biomol. Chem. 2004, 2, Townsend et al. Org. Biomol. Chem. 2004, 2,

3299.3299.

AcknowledgementsAcknowledgements

Christoph SteinbeckChristoph Steinbeck Geoffrey Fox, Marlon PierceGeoffrey Fox, Marlon Pierce Peter Murray-RustPeter Murray-Rust Michael D. Jensen, Timothy B. Patrick, Michael D. Jensen, Timothy B. Patrick,

Joyce A. MitchellJoyce A. Mitchell ElsevierElsevier

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