Syntactic Mediation in Grid and Web Service

Architectures

Martin Szomszor

Terry R. Payne

Luc Moreau

University of Southampton

myGrid [http://www.mygrid.org.uk]

Syntactic Mediation… Cambridge online dictionary defines mediation as: Verb [I or T]

“to talk to two separate people or groups involved in a disagreement to try to help them to agree or find a solution to their problem”

Syntax The structure and organisation of information

Syntactic mediation To mediate between two parties who not agree on

syntax

… in Grid and Web Services

Questions to be answered When is syntactic mediation required? What are the current solutions? How can they be improved?

Use Case Taken from a Bioinformatics Grid application

Our solution Intermediary representation of data in OWL Mappings between XML and OWL

Conclusions and further work

Grid and Web Services Grid

Coordinated resource access Service oriented view of resource access

Web Services Architecture Supporting the service oriented view Resources exposed through Web Service

interfaces This powerful model enables complex

collaboration of disparate resources, typically through the use of workflow

myGrid - Bioinformatics

In-silico experimentation myGrid is service orientated

Steps in the experimental process correspond to Web Service invocations

Taverna - The Virtual Workbench Compose Edit Execute Monitor View results

Taverna Workbench

A Bioinformatics Use Case

Get some sequence data and perform a sequence alignment Sequence alignment checks for similarities

between different sequences Many sequence data repositories

XEMBL DDBJ-XML

Many sequence alignment services NCBI Blast …

Bio Example - Workflow Two stages More than one service for some stages

AccessionNumber

Get Sequence

Data

Get Sequence

Data

SequenceData

AlignmentResult

SequenceAlignment

SequenceAlignment

XEMBLServiceXEMBLService

DDBJ-XMLService

DDBJ-XMLService NCBI BlastNCBI Blast

Bio Example - Workflow Two possible concrete workflows

Using XEMBL Service

Using DDBJ-XML Service

AccessionNumber

XEMBLService

XEMBLService

SequenceData

AlignmentResult

NCBI BlastService

NCBI BlastService

AccessionNumber

DDBJ-XMLService

DDBJ-XMLService

SequenceData

AlignmentResult

NCBI BlastService

NCBI BlastService

Syntactic Compatibility

Is the output from one service compatible with the input to another service?

XEMBLService

XEMBLService

SequenceData

NCBI BlastService

NCBI BlastService

XEMBLService

XEMBLService

BSML Sequence Record

NCBI BlastService

NCBI BlastService

FASTA FormattedSequence

Conceptually the same typeBut different syntactic types

Syntactic Mediation

When a syntactic miss-match occurs, some additional processing is required

We define this processing as syntactic mediation

Current solutions Explicitly defined transform (e.g. XSLT) Hard coded black-box components

Assisted Mediation

How can we achieve this? Use ontologies for a common conceptual model of

the data Describe how parts of the data schema (XML-

Schema) correspond to parts in the semantic schema (OWL)

Transform data sets into their corresponding conceptual representations

Use conceptual representation as a common model to mediate between services's data models

Syntactic Mediation

XEMBLServiceXEMBLService

NCBI BlastService

NCBI BlastService

BSMLSequenceRecord

AccessionNumber

FASTA Formatted Sequence

AlignmentResults

Conceptual representation of sequence dataTransform XML output

from XEMBL serviceto OWL concept instance

Serialise OWL conceptinstance to XML for input

to NCBI Blast Service

Bioinformatics Use Case: Sequence Data Ontology

Sequence_Data

descriptionaccession_idsequencehas_featurehas_reference

authorsjournaltitle

Reference

Sequence_Feature

location

Feature_Source

lab_hostisolatemol_typeorgansim

Feature_CDS

translationproductprotien_id

Sequence_Location

startend

BSML_Sequence_Data

date_createddate_last_updated

DDBJ_Sequence_Data

versiondivision

Key:Object property

Subconcept

Transformation of XML to OWL

<Sequence ic-acckey="AB000059"> <Feature-table> <Feature class="SOURCE"> <Qualifier value-type="isolate” value="Som1"/> <Qualifier value-type="organism” value="Feline …”/> <Interval-loc startpos="1" endpos="1755"/> </Feature> </Feature-table></Sequence>

Sequence Data

AB000059

Accession_IDFeature Source

Location

Som1 Feline …

1 1755has-Feature

isolate organism

has-location

start end

Transformation of OWL to XML

Sequence Data

AB000059

Accession_ID Feature Source

LocationSom1 Feline …

1 1755

has-Feature

isolate organism has-location

start end

<DDBJXML> <ACCESSION>AB000059</ACCESSION> <FEATURES> <source> <location>1..1755</location> <qualifiers name="isolate">Som1</qualifiers> <qualifiers name="organsim">Felis ...</qualifiers> </source> </FEATURES></DDBJXML>

Mapping Language We present a simple mapping language to

describe the transformation of data from XML to OWL

Mappings are bi-directional XML to OWL OWL to XML

Hierarchical view of both data models Template is applied to match source model and

create destination model Data values are mapped from source to

destination via variable assignment

Example Mapping 1

Mapping an attribute value

<Sequence ic-acckey="AB000059"> Sequence Data

AB000059

Accession_ID

{xml}Sequence[ic-acckey = $accession]<->{owl}Sequence_Data( Accession_id($accession))

$accession

Example Mapping 2

Mapping an element value

Sequence Data

aatagagtg…

sequence

{xml}Sequence( seq-data($sequence))<->{owl}Sequence_Data( sequence($sequence))

$sequence

<Sequence> <seq-data>aatagagtg…</seq-data></Sequence>

Example Mapping 3

Mapping an group of element values<Reference> <RefAuthors>Horiuchi M.</RefAuthors> <RefTitle>evolutionary…</RefTitle> <RefJournal>Unpublished</RefJournal></Reference>

Reference

Horiuchi, M.

author

{xml}Reference( RefAuthors($author), RefTitle($title), RefJournal($journal))<->{owl}Reference( author($author), title($title), journal($journal))

Evolutionary…

Unpublished

title

journal

Example Mapping 4

Split and join

<location>1:1755</location>

Sequence_Location

1

start

{xml}location( split($start, “:”, $end))<->{owl}Sequence_Location( start($start), end($end))

1755

end

Example Mapping 5 Mapping an sequence of elements

<feature-table> element contains a sequence of <Reference> elements

<feature-table> <Reference> <RefAuthors>Horiuchi M.</RefAuthors> <RefTitle>evolutionary…</RefTitle> <RefJournal>Unpublished</RefJournal> </Reference> <Reference> <RefAuthors>Horiuchi M.</RefAuthors> <RefJournal>EMBL/GenBank/DDBJ…</RefJournal> </Reference></feature-table>

Example Mapping 5

Reference

Horiuchi, M.

author

Evolutionary… Unpublished

title

journal

Reference

Horiuchi, M.

author

EMBL/GenBank/DDBJ…

journal

Sequence_Data

has-reference has-reference

Each <Reference> element corresponds to an instance of the ‘Reference’ concept

Example Mapping 5

{xml}feature-table( Reference( RefAuthors($author), RefTitle($title), RefJournal($journal) )…)<->{owl}Sequence_Data( Reference( author($authors), title($title), journal($journal) )…)

The ellipsis (…) construct is used to denote this behaviour

sequence

Mapping Language (BNF)

Mapping Language Engine

Java component built on Dom4J and Jena Input: Mapping and Data set (XML or OWL) Output: Data set (XML or OWL)

Transformation Process

Four stages Create data model for input

DOM4J for XML JENA for OWL

Parse mapping Apply source mapping to bind variables Apply destination mapping and create new

instance filling variables with their corresponding values from the source

Assisted data mediation for WS

XEMBLServiceXEMBLService

NCBI BlastService

NCBI BlastService

BSMLSequenceRecord

AccessionNumber

FASTA Formatted Sequence

AlignmentResults

Conceptual representation of sequence dataTransform XML output

from XEMBL serviceto OWL concept instance

Serialise OWL conceptinstance to XML for input

to NCBI Blast Service

Assisted data mediation for WS

XEMBLServiceXEMBLService

NCBI BlastService

NCBI BlastService

BSMLSequenceRecord

AccessionNumber

FASTA Formatted Sequence

AlignmentResults

Mapping Language

EngineMapping

Mapping Language

EngineMapping

OWL instance

Comparison of Approaches

Direct mappings between compatible data formats

Mappings from data format to common conceptual model

Number of Mappings 1 mapping for each pair of compatible data formats. For n compatible formats, n2

mappings required

1 mapping from each data format to its conceptual model. For n compatible data formats, n mappings required

Addition of Data Must create mappings to all other compatible formats

Create one mapping to conceptual model

Why OWL? Expressive Power

Complex concept specifications

Reasoning power Subsumption and concept classification

Classification of data Given an XML document and some mappings, it

would be possible to find which mappings are valid and therefore what are the possible conceptual models for the given document

Conclusions

By using mappings from XML documents to OWL instances, we can automatically transform a portion of data from one representation to another, providing both share a common conceptual model

This can be used to rectify data incompatibilities that occur in workflows with data flow between services - assisted mediation

Further Work Add regular expression support

More powerful than our existing split and join operators

Mapping Repository Current implementation assumes that mappings

are know We cannot assume that end users are able to

write mappings Ideally, a repository of mappings would be available to

users allowing them to find the appropriate mapping Domain experts could create mappings and upload them

to the repository Would allow us to support further automation

Suggest mappings to user

Questions and comments?