Coherence and Binding for Workflows and Service Compositions

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1 Coherence and Binding for Workflows and Service Compositions Item Type Presentation Authors Patrick, Timothy Citation Coherence and Binding for Workflows and Service Compositions , Download date 06/06/ :17:13 Link to Item

2 Coherence and Binding for Workflows and Service Compositions Timothy B. Patrick, PhD Health Administration and Informatics, College of Health Sciences University of Wisconsin-Milwaukee Collaborator: Michael Jensen, University of Missouri-Columbia

3 Overview Introduction to service compositions and workflows to support collaboration Example service composition/workflow system: Taverna The need for measures of coherence of service compositions Data-type ontology Example: BioMoby Possible worlds approach The need for workflow abstraction and binding

4 Service Composition Combine existing services to form higher level services Not a new idea, see Kalinichenko L.A. Emerging semantic-based interoperable inform, in Computers As Our Better Partners: Proceedings Of The IIsf-Acm Japan International Symposium, Tokyo, 7-9 March 1994.

5 work

6 Web Service Composition Web services have standard interface Increases opportunity for interoperability Taverna is workflow or service composition tool

9 Sharing and Reusing Workflows XML representation: Scufl

10 Overview Introduction to service compositions and workflows to support collaboration Example service composition/workflow system: Taverna The need for measures of coherence of service compositions Data-type ontology Example: BioMoby Possible worlds approach The need for workflow abstraction and binding

11 Data-types EMR Disease name Pubmed

12 Output and Input Data-types EMR Pubmed Output data-type: Disease name Input data-type: Disease name

13 Output and Input Data-types EMR Pubmed Output data-type: Input data-type: syntactic semantic syntactic semantic

14 Output and Input Data-types EMR Pubmed Output data-type: Input data-type: syntactic semantic syntactic semantic Underlying meaning Underlying meaning

15 Output and Input Data-types EMR Pubmed Output data-type: Input data-type: syntactic semantic syntactic semantic Representation Underlying meaning Representation Underlying meaning

16 BioMoby Project to support sharing of biological data and services Set of standards for using web services Focuses on users who are biological scientists with some computer training Not expert computer programmers

17 BioMoby Class Ontology Three relations Subclass HASA x HASA y x contains exactly one y HAS x HAS y x contains one or more y s

18 <rdfs:class rdf:about=" <rdfs:label xml:lang="en">genericsequence</rdfs:label> <rdfs:subclassof> <rdfs:class rdf:about=" Objects#VirtualSequence"/> </rdfs:subclassof> <moby:hasa> <mobyobject:string> <moby:articlename xml:lang="en">sequencestring</moby:articlename> </mobyobject:string> </moby:hasa> </rdfs:class>

19 <rdfs:class rdf:about=" <rdfs:label xml:lang="en">genericsequence</rdfs:label> <rdfs:subclassof> <rdfs:class rdf:about=" Objects#VirtualSequence"/> </rdfs:subclassof> <moby:hasa> <mobyobject:string> <moby:articlename xml:lang="en">sequencestring</moby:articlename> </mobyobject:string> </moby:hasa> </rdfs:class>

20 <rdfs:class rdf:about=" <rdfs:label xml:lang="en">genericsequence</rdfs:label> <rdfs:subclassof> <rdfs:class rdf:about=" Objects#VirtualSequence"/> </rdfs:subclassof> <moby:hasa> <mobyobject:string> <moby:articlename xml:lang="en">sequencestring</moby:articlename> </mobyobject:string> </moby:hasa> </rdfs:class>

21 <rdfs:class rdf:about=" <rdfs:label xml:lang="en">genericsequence</rdfs:label> <rdfs:subclassof> <rdfs:class rdf:about=" Objects#VirtualSequence"/> </rdfs:subclassof> <moby:hasa> <mobyobject:string> <moby:articlename xml:lang="en">sequencestring</moby:articlename> </mobyobject:string> </moby:hasa> </rdfs:class>

22 <rdf:property rdf:about=" <rdfs:isdefinedby rdf:resource=" <rdfs:label>articlename</rdfs:label> <rdfs:comment>uses a non-controlled vocabulary to describe the intended semantic relationship between the Subject node, and the node in which the Subject is associated through a HAS or HASA relationship. </rdfs:comment> <rdfs:range rdf:resource=" <rdfs:domain rdf:resource=" </rdf:property>

23 <rdfs:class rdf:about=" <rdfs:label xml:lang="en">genericsequence</rdfs:label> <rdfs:subclassof> <rdfs:class rdf:about=" Objects#VirtualSequence"/> </rdfs:subclassof> <moby:hasa> <mobyobject:string> <moby:articlename xml:lang="en">sequencestring</moby:articlename> </mobyobject:string> </moby:hasa> </rdfs:class>

24 Semantic Data-type Ontology Address problem of the articlename attribute in a systematic and controlled way Complement the syntactic approach

25 Data-type Ontology A given data-type may play different semantic roles Medical Subject Heading may play the role of patient descriptor in the output of one information service, while playing the role of dna sequence descriptor in the input of another. Possible Worlds approach Guarino, E. (1998). Formal Ontology and Information Systems. In N.Guarino (Ed.), (pp. 3-15). Amsterdam: IOS Press.

26 Possible Worlds A possible world in general is just a specific ordering or inter-relating of entities in some domain. Domain: a collection of services Entities: the data-types Possible worlds: the input and output interfaces of the services. Each possible world corresponds to an ontology.

27 EMR DNA sequence database Output data-type: Medical Subject Heading Input data-type: Medical Subject Heading

28 EMR Get DNA Sequence Output data-type: Medical Subject Heading Has role Patient descriptor Input data-type: Medical Subject Heading Has role Sequence descriptor

29 Coherent Service Compositions The problem is one of determining similarity of classes across different ontologies Is the class Medical Subject Heading in the output data-type ontology of the Electronic medical record system similar enough to the class Medical Subject Heading in the input data-type ontology of the DNA sequence database?

30 Overview Introduction to service compositions and workflows to support collaboration Example service composition/workflow system: Taverna The need for measures of coherence of service compositions Data-type ontology Example: BioMoby Possible worlds approach The need for workflow abstraction and binding

31 Need for Workflow Abstraction The focus on coherence of service compositions is somewhat misguided, however. A workflow tightly bound to a service composition, or worse to a composition of service instances, is very inflexible. Ries JE, Patrick TB, Springer GK. From Jobs to Work: Scheduling the Right Bioinformatics Tools. Proc AMIA Symp 2002, p

32 Need for Workflow Abstraction Get patient record Disease name Get Medical Literature

33 Coherence and Binding Get patient record Get Medical Literature provides Output data-type: Disease name Input data-type: Disease name provides Get patient record from Cerner system Pubmed Output data-type: ICD term Input data-type: ICD term

34 Coherence and Binding Get patient record Get Medical Literature provides Output data-type: Disease name Input data-type: Disease name provides Get patient record from Cerner system Pubmed Output data-type: ICD term Input data-type: ICD term

35 Coherence and Binding Get patient record Get Medical Literature provides Output data-type: Disease name Input data-type: Disease name provides Has role Has role Get patient record from Cerner system Pubmed Output data-type: ICD term Input data-type: ICD term

36 Conclusion Workflow abstraction language OWL-S Task ontology Web services Data-type ontology

37 Thanks.

Mustafa Jarrar: Lecture Notes on RDF Schema Birzeit University, Version 3. RDFS RDF Schema. Mustafa Jarrar. Birzeit University

Mustafa Jarrar: Lecture Notes on RDF Schema Birzeit University, 2018 Version 3 RDFS RDF Schema Mustafa Jarrar Birzeit University 1 Watch this lecture and download the slides Course Page: http://www.jarrar.info/courses/ai/