Slide 1

Semantically Resolving Type Mismatches in Scientific Workflows

Derouiche Kheiredine
kd05r@ecs.soton.ac.uk
School of Electronics and Computer Science
University of Southampton
November 2007

Scientific Workflows

Scientific workflows describe structured activitiesarising in scientific problem-solving.

Conducting experiments involve complex andstructured computations.

Semantic mismatches among resources involve muchhuman intervention.

Participating services are owned by differentorganizations, defining compensations is critical to asuccessful recovery from failures.

Semantically Resolving Type Mismatches in Scientific Workflows

Semantically Resolving Type Mismatches in Scientific Workflows

Workflows in Bioinformatics

Integrating different tools to solve biological problems

Usually involves:

Manual data transfer between applications

Understanding data formats

Converting file formats where appropriate

Manual workflows involve a large number of steps.Manual execution is time-consuming and error-prone

User is required to possess a deep knowledge andunderstanding of disparate application environments

Semantically Resolving Type Mismatches in Scientific Workflows

WSWUBlast Service Operation

WSWUBlast Service Operation

Using tools in Bioinformatics

blastn

(query, database, email)

blastn

(query, database, email)

BlastService

Specification of an in silico experimental design: Sequence Similarity Search

DNASequenceSimilaritySearch

Semantically Resolving Type Mismatches in Scientific Workflows

Automated Workflows

Make the task of creating a workflow a simple “dragand drop” process

Make the resulting workflow diagram selfdocumenting, showing exactly how to performbioinformatics experiment

Automatic execution of steps specified in workflow

Monitoring workflow execution to help debugging andintervention

Reduces complexity for scientific users, as well assupport sharing and allow repeatability

Semantically Resolving Type Mismatches in Scientific Workflows

Bioinformatics Workflow Systems

Specialized workflow systems designed to develop workflows inbioinformatics

Different workflow standards and systems:

BPEL: Business workflow standard adapted for scientific workflows

UNICORE: a Grid middleware, it provides a GUI for workflowdevcelopment

Globus: an open source toolkit implementing many Grid relatedstandards

Kepler: graph based modelling language to develop workflows

Taverna Workbench: choreography tool for bioinformatics WebServices

Triana: develop component based workflow and provide couplingwith Grid middleware tools

Windows Workflow Foundation (1)

Part of .NET Framework 3.0

Workflows are a collection of activities.

Components

Base Activity Library: Out-of-box activities and base forcustom activities.

Runtime Engine: Workflow execution and statemanagement.

Runtime Services: e.g. RDBMS, persistence, transactions

Visual Designer: Graphical and code-based constructionin Visual Studio or standalone

Semantically Resolving Type Mismatches in Scientific Workflows

Windows Workflow Foundation (2)

Semantically Resolving Type Mismatches in Scientific Workflows

Semantic Web Services

The augmentation of Web service descriptions withSemantic annotations.

Aims to automate Web service discovery, composition,invocation, and monitoring.

Two different approaches:

Revolutionary: OWL-S, and WSMO.

Evolutionary: WSDL-S, and SAWSDL.

The SAWSDL approach builds on existing Web servicestandards and is agnostic to ontology representation.

Semantically Resolving Type Mismatches in Scientific Workflows

Semantic Annotations for WebServices Description Language

SAWDL is an extension of WSDL using theextensibility elements.

Two basic types of annotations:

Model reference, associates selected WSDL componentswith Semantic concepts.

Schema mapping, deals with data heterogeneity bytransforming one data representation into another.

Annotations for WSDL 1.1 and WSDL 2.0.

API and tool support including: SWASDL4J,Woden4SAWSDL, Radiant...

Semantically Resolving Type Mismatches in Scientific Workflows

SAWSDL Scope

definition

import

types

message

part

portType

operation

input

output

fault

binding

operation

input

output

fault

service

port

Annotated usingmodelReference

Annotated usingmodelReference withschemaMapping

Note:

- All elements may have<documentation> as first child

Semantically Resolving Type Mismatches in Scientific Workflows

SAWSDL Example

<wsdl:definitions targetNamespace="http://www.w3.org/2002/ws/sawsdl/spec/wsdl/order#"

xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"

xmlns:xs="http://www.w3.org/2001/XMLSchema"

xmlns:sawsdl="http://www.w3.org/ns/sawsdl">

<wsdl:types>

<xs:element name=“purchaseOrderResponse“ type=“xs:string”

sawsdl:modelReference="http://www.w3.org/2002/ws/sawsdl/spec/ontology/purchaseorder#PurchaseOrderResponse"

sawsdl:liftingSchemaMapping="http://www.w3.org/2002/ws/sawsdl/spec/mapping/Response2Ont.xslt">

……

</xs:element>

</wsdl:types>

<wsdl:portType name=“PurchaseOrder">

<wsdl:operation name="order">

<sawsdl:attrExtensionssawsdl:modelReference="http://www.w3.org/2002/ws/sawsdl/spec/ontology/purchaseorder#RequestPurchaseOrder"/>

<wsdl:input

messageLabel="OrderRequestMessage"

element=“purchaseOrderRequest"/>

<wsdl:output

messageLabel="OrderResponseMessage"

element=“tns:purchaseOrderResponse"/>

</wsdl:operation>

</wsdl:portType>

</wsdl:definitions>

Semantically Resolving Type Mismatches in Scientific Workflows

Leveraging existing Java for .NET

A C# implementation of the SAWSDL specification.

Support of Model Reference annotations, OWL/RDFdefinitions.

Lifting/Lowering schema support, XSLT/SPARQLmapping definitions.

Allows the creation of SAWSDL based applications.

Extends the .NET API for WSDL1.1.

Support for WSDL2.0 through XSLT.

Semantically Resolving Type Mismatches in Scientific Workflows

Implementation

Development of a custom activity that extends thebase Web Service activity shipped with WF.

Enables a semi-automatic composition of SemanticWeb Services, and the execution of the workflow.

Can be composed with Web Services described usingWSDL files.

A C# implementation of the activity.

Semantic capabilities are provided by the Jena library,integration with C# is enabled via IKVM.

Semantically Resolving Type Mismatches in Scientific Workflows

Semantic Reasoning

Model reference annotations describe thefunctionalities a Web service provides.

Use ontologies as semantic models for the semanticannotations.

Reasoning capabilities are provided by using:

Jena, an open source Semantic Web framework for Java.

Pellet, an open source Java OWL-DL reasoner.

Currently support schema type and message partannotations to achieve automatic parameter binding.

Semantically Resolving Type Mismatches in Scientific Workflows

Schema Type Mapping

Provide mappings between XML and semantic models.

Lifting Schema Mapping specifies mapping betweenWSDL Type Definitions in XML and semantic data.

Used XSTL and XQuery as mapping languages.

Lowering Schema Mapping specifies mapping betweensemantic data and WSDL Type Definitions in XML.

Used SPARQL to query ontology, followed by XSTL andXQuery.

Semantic data is queried through SPARQL, it is supportedby Jena through its query engine.

Semantically Resolving Type Mismatches in Scientific Workflows

IKVM .NET

An implementation of Java for the Microsoft .NETFramework.

It includes the following components:

A Java Virtual Machine implemented in .NET.

A .NET implementation of the Java class libraries.

Tools that enable Java and .NET interoperability.

Used to compile Jena and Pellet JAR libraries into .NETDLL assemblies, Java bytecode is translated toCommon Intermediate Language (CIL).

Allowed using Jena’s capabilities in theimplementation of the Semantic Web service activity.

Semantically Resolving Type Mismatches in Scientific Workflows

Semantic Web Service Activity (1)

Activity bindings are the key feature that enablesproperty binding between activities, or on theworkflow itself.

This mechanism allows data propagation betweencomposed activities.

WF rely on syntactic approaches when bindingproperties between activities.

The SWS activity implements a basic semanticmatching engine to better support semanticallycompatible properties.

Semantically Resolving Type Mismatches in Scientific Workflows

Semantic Web Service Activity (2)

Automatically bind SWS parameters to composedworkflow activities using the semantic approach.

The semantic model annotation of an activity’s inputhas to be equivalent or a subclass of the composedactivity’s output one.

Values are mapped to the appropriate datarepresentation at design time.

Missing activity bindings can be manually added usingthe WF visual designer.

Semantically Resolving Type Mismatches in Scientific Workflows

Semantically Resolving Type Mismatches in Scientific Workflows

Bioinformatics Workflow Example

X14298

kd05r@ecs.soton.ac.uk

embl

GetEntry

getFASTA_DDBJEntry

WSWUBlast

M7WEXBN7013

Atgagtgatggagcagttcaaccagacggtggtcaacctgctgtcagaaatgaaagagctcaggatctgggaacgggtctggaggcggg

blastn

accession

sequence

database

jobID

Semantically Resolving Type Mismatches in Scientific Workflows

WSWUBlast

Automatic Binding inBioinformatics Workflow

blastn

SemanticReasoner

Output

Input

SAWSDL

Semantic Concept

Degrees of Match:

-Exact

-Subclass

Degrees of Match:

-Exact

-Subclass

Bind Parameters,Carry out necessarytranslations

Sequence

DNA Sequence

GetEntry

getFASTA_DDBJEntry

SAWSDL

Conclusion & Future Work

API implementations that enable the development ofsemantically annotated Web services.

Semantic Web service activity integration to WF,facilitating workflow building and manipulation.

Future Work:

Improve the SWS activity by processing more SAWSDLannotations, e.g. operation and portType.

Semantically annotate Bioinformatics Web services, then useWF to build a workflow composed of SWS activities in orderto test the implementation.

Implement an approach to semantically guide and verifycompensations and exceptions.

Semantically Resolving Type Mismatches in Scientific Workflows