SADI SWSIP '09 'cause you can't always GET what you want!

’cause you can’t always GET what you want!

Web Servicesvs.Semantic Web

Web Servicesare not “connected” to the Semantic WebWhy?

Web ServicesXML + XML SchemaSemantic WebRDF + OWL

Web ServicesPOST of SOAP-XMLSemantic WebGET of RDF-XML

Web ServicesNo (rigorous) semanticsSemantic WebRich, flexible semantics

Web Services&Semantic Web Fundamentally different technologies!

>1000 X more data in the Deep Web than in Web pagesIn bioinformatics this is primarily databases and analytical algorithms

Web Service output is criticalto success for the Semantic Web!!

Research Question

WITHOUT INVENTING A NEW
TECHNOLOGY OR STANDARD

Can we define frameworks and/or best practices
that make Web Services
“transparent” to the Semantic Web?

Semantic Web?
An information system where machines can receive information from one source, re-interpret it, and correctly use it for a purpose that the source had not anticipated.

Semantic Web?
If we cannot achieve those two things, then IMO we don’t have a “semantic web”, we only have a distributed (??), linked database… and that isn’t particularly exciting…

What do we need to do?
Make Web Services exhibit the same “behavior” as GET
Add rich Semantics to Web Services at every level of the WS “stack”

What do we have to work with?(Without inventing new technologies or standards…)
Data
Interface annotations

Semantic Automated Discovery and Integrationhttp://sadiframework.org
Founding partner

History of SADIBased on observations of the usage and behaviour of BioMoby Semantic Web Servicessince 2002

SADI Observation #1:
What does ‘GET’ really do? What “behaviour” of GET do we need to mimic in a Web Service?

GET guarantees the response relates to the input URI in a very precise and predictable way
POST does not…
Web Services have a fundamentally different semantic behaviour than the Semantic Web

We can fix that!
(without breaking any existing rules or standards!)

All Web Services in Bioinformatics create implicitbiologicalrelationships between their input and output

SADI: Core Proposition
Make the implicit explicit
Model all Web Services this way

SADI: Core Proposition
Web Service output must be Triples
SUBJECT URI of the output graph is the same URI as the SUBJECT URI of the input graphthat was POSTedto the Web Service
Define OWL classes that describe your input and output triples

Consequence(i.e. why SADI works!)
The Semantics of the triples
from a Web Service are now explicit and identical to the Semantics of GET

How do we exploit this?
Current Web Service definition systems such as WSDL, and OWL-S are missing a crucial annotation element…
…the semantic relationship between input and output

With SADI services, this relationship can be automatically derived by “diff-ing” the input and output OWL classes
…because the SUBJECT node of the input and output graphs is guaranteed to be the same!

We have constructed a simple prototype Web Services registry that provides discovery based on annotation of these biological relationships

Demo #1
a plug-in to the
IO-Informatics Knowledge Explorer

The Sentient Knowledge Explorerfrom IO InformaticsA Semantic Integration, Visualization and Search Tool

SADI Plug-in to the Sentient Knowledge Explorer
The Knowledge Explorer has a plug-ins API that we have utilized to pass data directly from SADI to the KE visualization and exploration system
Data elements in KE are queried for their “type” (rdf:type); this is used to discover additional data properties by querying the SADI Web Service registry

BACKGROUND of DATASET
NIST toxicity compendium study
8 toxicants
Liver
Serum
Urine
Genomic [Affymetrix MA]
Metabolomic [LC/MS] data
conducted under NIST Advanced Technology Program (ATP), Award # 70NANB2H3009 as a Joint Venture between Icoria / Cogenics (Division of CLDA) and IO Informatics.
Microarray studies were conducted under NIEHS contract # N01-ES-65406.
The Alcohol study was conducted under NIAAA contract # HHSN281200510008C in collaboration with Bowles Center for Alcohol Studies (CAS) at UNC.
This work was also made possible through contributions from members of IO Informatics’ Working Group on “Semantic Applications for Translational Research”.

DEMO
Knowledge ExplorerPlug-in
For more information about the Knowledge Explorer surf to:http://io-informatics.com

Call SADI to provide discovery of predicates based on data-type

SADI fills-in the “Encodes” property from the discovered Web Service(s)

Discover services that provide the hasGOTerm property for Protein Sequence datatype

DEMO
Knowledge ExplorerPlug-in
For more information about the Knowledge Explorer surf to:http://io-informatics.com

SADI Demo #2Imagine there is a “virtual graph” connecting every conceivable input for every conceivable Web Service to their respective outputs How do we query that graph?

“SHARE”Semantic Health And Research EnvironmentSADI client application

What pathways does UniProt protein P47989 belong to?
PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#>
PREFIX ont: <http://ontology.dumontierlab.com/>
PREFIX uniprot: <http://lsrn.org/UniProt:>
SELECT ?gene ?pathway
WHERE {
uniprot:P47989 pred:isEncodedBy ?gene .
?gene ont:isParticipantIn ?pathway .
}

Recapwhat we just saw
A standard SPARQL query was entered into SHARE – a SADI-based query engine
The query was interpreted to extract the properties being queried and these were passed to SADI for Web Service discovery
SADI searched-for, found, and accessed the databases and/or analytical tools capable of generating those properties

Recapwhat we just saw
We posed, and answered a complex database query
WITHOUT A DATABASE
(in fact, the data didn’t even have to exist...)

RDF graph browsing and querying is useful… …but where’s the semantics??Let’s bring in some ontologies!

My Definition of Ontology (for this talk)
Ontologies explicitly define the things that exist in “the world” based on what propertieseach kind of thing must have

Ontology Spectrum
Frames
(Properties)
Thesauri
“narrower
term”
relation
Selected
Logical
Constraints
(disjointness,
inverse, …)
Catalog/
ID
Formal
is-a
Informal
is-a
Formal
instance
General
Logical
constraints
Terms/
glossary
Value Restrs.

Semantic Web?

Dynamic Discovery DistributedInterpretationRe-interpretation

Powered by SADI
Prototype SADI-enabled SWS Client

Data exhibits “late binding”

Late binding:“purpose and meaning”
of the data isnot determined untilthe moment it is required

Benefit
of late binding
Data is amenable to
constant re-interpretation

How do we achieve this?
DO NOT
PRE-CLASSIFY DATA!
just hang properties on it

These are axioms that enable classification
Frames
(Properties)
Thesauri
“narrower
term”
relation
Selected
Logical
Constraints
(disjointness,
inverse, …)
Catalog/
ID
Formal
is-a
Informal
is-a
Formal
instance
General
Logical
constraints
Terms/
glossary
Value Restrs.
These are
indexing/annotation systems

Design OWL-DL ontologies describing cardiovascular concepts
Ontologies are in the “Frames+” area of the Ontology spectrum, and therefore can leverage SADI and be “executed” as workflows

What the…??? Did you just say “execute ontologies as workflows?!”

Another interesting consequence of the SADI architectureOntology = Query = Workflow

WORKFLOW

QUERY:
SELECT images of mutations from genes in organism XXX that share homology to this gene in organism YYY

Concept:
“Homologous Mutant Image”

As OWL AxiomsHomologousMutantImage is owl:equivalentTo {
Gene Q hasImage image P
Gene Q hasSequence Sequence Q
Gene R hasSequence Sequence R Sequence Q similarTo Sequence R
Gene R = “my gene of interest” }

Those axioms combine to create an
OWL Class:
homologous mutant images

QUERY:
Retrieve owl:homologous mutant images for gene XXX

Demo #3
Discover instances of OWL classes
from data that doesn’t exist…

Show me patients whose creatinine level is increasing over time, along with their latest BUN and creatinine levels.
PREFIX regress: <http://sadiframework.org/examples/regression.owl#>
PREFIX patients: <http://sadiframework.org/ontologies/patients.owl#>
SELECT ?patient ?bun ?creat
FROM <http://sadiframework.org/ontologies/patients.rdf>
WHERE {
?patient patients:creatinineLevels ?collection .
?collection regress:hasRegressionModel ?model .
?model regress:slope ?slope
FILTER (?slope > 0) .
?patient pred:latestBUN ?bun .
?patient pred:latestCreatinine ?creat .
}

Show me patients whose creatinine level is increasing over time, along with their latest BUN and creatininelevels(now as an OWL class  ElevatedCreatininePatient)
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX patients: <http://sadiframework.org/ontologies/patients.owl#>
SELECT ?patient ?bun ?creat
FROM <http://sadiframework.org/ontologies/patients.rdf>
WHERE {
?patient rdf:typepatients:ElevatedCreatininePatient .
?patient pred:latestBUN ?bun .
?patient pred:latestCreatinine ?creat .
}

Start burrowing through the OWL class  find that we need aregression model OWL class

Regression models have features like slopes and intercepts… and so onThe class is completely decomposed until a set of required Services are discoveredcapable of creating all these necessary properties

Successful decomposition of the OWL class to discover
the need for a LinearRegression Web Service, and so on

VOILA!

Demo #3
Discover instances of OWL classes
from data that doesn’t exist…

SADI and CardioSHARE
OWL Class restrictions converted into workflows
SPARQL queries converted into workflows
Reasoning happening at the same time as queries are being executed

(AFAIK)This is a completely novel behaviour!

Ontologies are reasonedWorkflows are executedQueries are resolvedso what do we call what this client does??

“Reckoning”Dynamic discovery of instances of OWL classes through synthesis and invocation of a Web Service workflow capable of generating data described by the OWL Class restrictions, followed by reasoning to classify the data into that ontology

But OWL Classes can be (and often are) completely “made-up”What does that mean in the context of SADI and CardioSHARE?

Current Research We believe that ontologies and hypothesesare, in some ways, the same “thing”……simply assertions about individuals that may or may not existIf an instance of a class exists, then the hypothesis is “validated”

Current Research Constructing OWL classes that represent patient categories mimicking clinical outcomes research experiments done on the BC Cardiac RegistryThe original experiments have already been published, and therefore act as a gold-standardWe attempt to use “Reckoning” to automatically discover instances of these patient Classes and compare our results with those of the clinical researchers

Hypothesis
Ischemia
SADI
Web
“agents”
Hypertension
Blood Pressure
CardioSHARE architecture: Increasingly complex ontological layers organize data into richer concepts, even hypotheses
Database 1
Database 2
AnalysisAlgorithmXX

Recap
SADI Semantic Web Services generate triples; the predicates of those triples are indexed... Period!!
For a given query, determine which properties are available, and which need to be discovered/generated
Discovery of services through index queries + on-the-fly “classification” of local data against the service interface OWL Classes

Semantic Web

What SADI + SHARE supports
Re-interpretation :
The SADI data-store simply collects properties, and matches them up with OWL Classes in a SPARQL query and/or from individual service provider’s Web Service interface

What SADI + SHARE supports
Novel re-use:
Because we don’t pre-classify, there is no way for the provider to dictate how their data should be used. They simply add their properties into the “cloud” and those properties are used in whatever way is appropriate for me.

Important “wins”
Data remains distributed – no warehouse!
Data is not “exposed” as a SPARQL endpoint  greater provider-control over computational resources
Yet data appears to be a SPARQL endpoint… no modification of SPARQL or reasoner required.

And all this because we simply require
that the input URI
is the same as the output URI

Join us!
SADI and CardioSHARE are Open-Source projects
Come join us – we’re having a lot of fun!!
http://sadiframework.org

Credits
Benjamin VanderValk (SADI & CardioSHARE)
Luke McCarthy (SADI & CardioSHARE)
SoroushSamadian (CardioSHARE)
IO Informatics (Knowledge Explorer API)
microsoftResearch
Fin

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SADI SWSIP '09 'cause you can't always GET what you want!

by Mark Wilkinson on Dec 06, 2009

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SADI SWSIP ’09 ’cause you can’t always GET what you want! — Presentation Transcript