Download - ISoLA 2010: SADI Taverna plug-in
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SADI: Semantic Support for Automated Workflow Generation
The SADI Taverna plugin and SHARE
Presentation to Workflow trackISoLA 2010, Crete, October 2010
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Web ServicesXML + XML Schema
Semantic WebRDF + OWL
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Web ServicesPOST of SOAP-XML
Semantic WebGET of RDF-XML
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Web ServicesNo (rigorous) semantics
Semantic WebRich, flexible semantics
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Web Services&
Semantic Web
Fundamentally and deeply different Web technologies!
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How can we make them work together?
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Founding partner
Semantic Automated Discovery and Integrationhttp://sadiframework.org
MicrosoftResearch
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SADI
“best-practices” for Semantic Web Service provision
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standards-compliant
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Lightweight(only 2 “rules”)
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What [most] bioinformatics Web Services do
HTTP POST RESPONSE
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Bioinformatics web services implicitly create RDF “triples”
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SADI “rule” #1
Make the implicit explicit…
A Web Service should create RDF “triples” linking input and output data, thus explicitly describing
the semantic relationship between them
Input and output structuresdescribed by OWL Classes
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SADI Rule #2
(Simple derivation from rule #1)
The URI of the input must be preserved in the output
Therefore, the output is explicitly about the input
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Consequence
The “Semantics” of our interaction with the Web Service are now
explicit
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Consequence
“Semantics” of HTTP POST are identical to the “Semantics” of HTTP GET
Therefore SADI Web Services behave like the Semantic Web
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IMPORTANT!!
SADI concerns itself ONLY with the way Web Services themselves are modeled
SADI is not competitive withnor incompatible with*
existing Web Service description standards(OWL-S, WSDL2, etc.)
* AFAIK
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A workbench for designing and executingScientific Workflows
Taverna
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Load-up your data and press “play”!
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SADI PLUG-IN TO TAVERNA
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KEGG_Pathway KEGG RecordhasPathwayGene
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Initialize Semantic Search...
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Connect your desired service to the workflow
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Lather, Rinse, Repeat
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And so on
Und so weiter
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Because we’re generating RDFthe output data is often in the form of a URI
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And these URIs are “Live”
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SADI-Taverna Summary
• Search for the property of the data you desire• Automatically adds the service
– correctly connected automatically• Unlike earlier BioMoby plugin, the SADI plugin
handles parsing into and out of RDF format automatically and transparently– Easy to connect SADI with non-SADI services
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SHARESemantic Health And Research Environment
SPARQL enhanced by SADI
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A Novel SPARQL Query Engine
Uses SADI to automatically construct a workflow that creates a query-specific database
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Show me the latest Blood Urea Nitrogen and Creatinine levelsof patients who appear to be rejecting their transplants
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#> PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#> SELECT ?patient ?bun ?creatFROM <http://sadiframework.org/ontologies/patients.rdf>WHERE {
?patient rdf:type patient:LikelyRejecter .?patient l:latestBUN ?bun . ?patient l:latestCreatinine ?creat .
}
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Likely Rejecter:
A patient who has creatinine levelsthat are increasing over time
- - Wilkinson MD
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Likely Rejecter:
…but there is no “likely rejecter” column or table in our database…
only blood chemistry measurementsat various time-points
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?
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The definition of a LikelyRejecter is encoded in a machine-readable document written in the OWL language (“Ontology”)
“the regression line over creatinine measurements should have an increasing slope”
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The machine continues to burrow down through the definition and discovers that regression lines have things like slopes and intercepts, etc…
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Then…
Two magical events occur…
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The machine figures out
by itself
the need to do a Linear Regression analysis
in order to answer your question
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The machine figures out
by itself
how and where that analysiscan be done
and does it automatically!
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http://www.impactlab.net/2009/03/22/improve-your-brain-power/
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The SHARE system utilizes SADI to discover analytical services on the Web that do linear regression analysis
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VOILA!
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SHARE Summary
SADI -enabled fully automated workflow generationin the context of creating a database capable of answering
A SPARQL query
Data absent from local data-store automatically determined to be needed
and the necessary workflow automatically constructed
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Join us!
SADI and CardioSHARE are Open-Source projects
Come join us – we’re having a lot of fun!!
http://sadiframework.org
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C r e d i t s
B e n j a m i n V a n d e r V a l k ( S H A R E & S A D I )
L u k e M c C a r t h y ( S A D I , S H A R E , T a v e r n a , C a r d i o S H A R E )
S o r o u s h S a m a d i a n ( C a r d i o S H A R E )
D a v i d W i t h e r s( T a v e r n a )
E d w a r d K a w a s ( S A D I S e r v i c e a u t o - g e n e r a t o r )
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U o f N e w B r u n s w i c k
D r. C h r i s B a k e rA l e x a n d r e R i a z a n o v
C a r l e t o n U n i v e r s i t yD r. M i c h e l D u m o n t i e rM a r c - A l e x a n d r e N o l i nL e o n i d C h e p e l e vS t e v e E t l i n g e rN i c h a e l l a K i e t hJ o s e C r u z
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Microsoft Research
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FinThis presentation available on SlideShare:
keywords ‘wilkinson’ ‘ISoLA2010’