SADI: Semantic Support for Automated Workflow Generation

The SADI Taverna plugin and SHARE

Presentation to Workflow trackISoLA 2010, Crete, October 2010

Web ServicesXML + XML Schema

Semantic WebRDF + OWL

Web ServicesPOST of SOAP-XML

Semantic WebGET of RDF-XML

Web ServicesNo (rigorous) semantics

Semantic WebRich, flexible semantics

Web Services&

Semantic Web

Fundamentally and deeply different Web technologies!

How can we make them work together?

Founding partner

Semantic Automated Discovery and Integrationhttp://sadiframework.org

MicrosoftResearch

SADI

“best-practices” for Semantic Web Service provision

standards-compliant

Lightweight(only 2 “rules”)

What [most] bioinformatics Web Services do

HTTP POST RESPONSE

Bioinformatics web services implicitly create RDF “triples”

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

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

Consequence

The “Semantics” of our interaction with the Web Service are now

explicit

Consequence

“Semantics” of HTTP POST are identical to the “Semantics” of HTTP GET

Therefore SADI Web Services behave like the Semantic Web

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

A workbench for designing and executingScientific Workflows

Taverna

Load-up your data and press “play”!

SADI PLUG-IN TO TAVERNA

KEGG_Pathway KEGG RecordhasPathwayGene

Initialize Semantic Search...

Connect your desired service to the workflow

Lather, Rinse, Repeat

And so on

Und so weiter

Because we’re generating RDFthe output data is often in the form of a URI

And these URIs are “Live”

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

SHARESemantic Health And Research Environment

SPARQL enhanced by SADI

A Novel SPARQL Query Engine

Uses SADI to automatically construct a workflow that creates a query-specific database

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 .

}

Likely Rejecter:

A patient who has creatinine levelsthat are increasing over time

- - Wilkinson MD

Likely Rejecter:

…but there is no “likely rejecter” column or table in our database…

only blood chemistry measurementsat various time-points

?

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”

The machine continues to burrow down through the definition and discovers that regression lines have things like slopes and intercepts, etc…

Then…

Two magical events occur…

The machine figures out

by itself

the need to do a Linear Regression analysis

in order to answer your question

The machine figures out

by itself

how and where that analysiscan be done

and does it automatically!

http://www.impactlab.net/2009/03/22/improve-your-brain-power/

The SHARE system utilizes SADI to discover analytical services on the Web that do linear regression analysis

VOILA!

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

Join us!

SADI and CardioSHARE are Open-Source projects

Come join us – we’re having a lot of fun!!

http://sadiframework.org

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 )

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

Microsoft Research

FinThis presentation available on SlideShare:

keywords ‘wilkinson’ ‘ISoLA2010’