Personalizing medical research using Semantics

Mark Wilkinson, PI Bioinformatics, Heart + Lung Institute @ St. Paul’s HospitalVancouver, BC, Canada

Web Services

vs.

Semantic Web

Web Servicesare not “connected” to

the Semantic Web

Why?

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!

>1000 X more data in the “Deep Web”

than in Web pages

Primarily databases and analytical algorithms

Accessing these databases and

analytical algorithms “transparently”,

based on individual researcher’s

ideas, beliefs, preferences

will help us personalize

medical research

Mark Butler (2003) Is the semantic web hype? Hewlett Packard laboratories presentation at MMU, 2003-03-12

Semantic Web?(my definition)

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.

Re-interpretation

Correct re-use

Both are critical to

the personalization

of research

Building a

personalized Semantic Web…

Step-by-step…

Founding partner

Semantic Automated Discovery and Integrationhttp://sadiframework.org

SADI

“best-practices” for Semantic Web Service provision

standards-compliant

Lightweight(only 2 “rules”)

Rules come from observations:

SADI Observation #1:

Web Services in Bioinformatics create implicit biological relationships

between their input and output

SADI Observation #1:

SADI Best Practice #1

Make the implicit explicit…

A Web Service should create triples linking the input data to the output data, thus explicitly describing the semantic

relationship between them

SADI Best Practice #1

This is what bioinformatics Web Services implicitly do anyway!

Easy to implement this as a best-practice

SADI Observation #2:GET and POST

GET guarantees the response relates to the request URI

in a very precise and predictable way

POST does not…

SADI Observation #2:GET and POST

That’s why Web Services have a fundamentally different behaviour than the Semantic Web

SADI Observation #2:GET and POST

We can fix that!

(without breaking any existing rules or standards!)

SADI Best Practice #2

SUBJECT URI of the output graph (triples) is the same

as the SUBJECT URI of the input graph (triples)

(the output is “about” the input... Now explicitly!)

Consequence

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

explicit and identical to the “Semantics” of GET

SADI Web Service Interfaces

Service Interfaces defined by two OWL classes:

SADI Web Service Interfaces

OWL Class #1: My Input Class

SADI Web Service Interfaces

OWL Class #2: My Output Class

SADI Web Service Interfaces

My Service consumes OWL Individuals of Class #1

and returns OWL Individuals of Class #2

…but the URI of those two individuals is the same!(see best practice #2)

How do we discover services?

Since input and output are about the same “thing”,

we can automatically determine what a service

does by comparing the Input and Output OWL

classes

How do we find services?

Automatically index services in a registry based

on what properties (predicates) Services add to

their respective input data-types

EXAMPLE

Input Data: BRCA1 rdf:type Gene ID

Output Data: BRCA1 hasDNASequence AGCTTAGCCA…

Registry Index: Service provides “hasDNASequence” property to Gene IDs

Now we can answer questions like

“what is the DNA sequence of BRCA1?”

Discover a service that creates the

DNA Sequence property of gene identifiers

Okay, enough tech gobbledygook

What will this do for ME?

Demo #1

Imagine there is a “virtual database” containing all of the data from all of the databases,together with the output of

every conceivable analysis

How do we query that database?

“SHARE”

Semantic Health And Research Environment

SADI 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-aware query engine

Recapwhat we just saw

The query was interpreted to extract the properties being queried and these were passed to SADI for Web Service discovery

Recapwhat we just saw

SADI searched-for, found, and accessed all 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...)

Cool!

…but I’m supposed to be personalizing research…

Let’s make this a little more personal by bringing in Ontologies

My Definition of Ontology (for this talk)

Ontologies explicitly define the things that exist in “the world”

based on what properties each kind of thing must have

Ontology Spectrum

Catalog/ID

SelectedLogical

Constraints(disjointness,

inverse, …)

Terms/glossary

Thesauri“narrowerterm”relation

Formalis-a

Frames(Properties)

Informalis-a

Formalinstance

Value Restrs.

GeneralLogical

constraints

Demo #2Discover instances of OWL classes

from data that doesn’t exist…

Show me patients with elevated creatinine along with their latest BUN and creatinine levels

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX patients: <http://sadiframework.org/ontologies/patients.owl#> PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#> SELECT ?patient ?bun ?creatFROM <http://sadiframework.org/ontologies/patients.rdf>WHERE {

?patient rdf:type patients: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!

OWL Class restrictions converted into workflows

SPARQL queries converted into workflows

Reasoning happening in parallel with query execution

Data fulfilling OWL models is discovered,

or generated through running analytical tools

SADI and CardioSHARE

This SADI/SHARE behaviour is

completely novel

I still don’t seewhy this is“Personal”

??

Show me patients whose creatinine level is increasing over time, along with their latest BUN and creatinine

SELECT ?patient ?bun ?creatFROM <http://sadiframework.org/ontologies/patients.rdf>WHERE {

?patient rdf:type patients:ElevatedCreatininePatient .?patient pred:latestBUN ?bun . ?patient pred:latestCreatinine ?creat .

}

I created a small ontologydescribing my definition of

an Elevated Creatinine Patient

… it was MY ontology!

I can re-use it

I can modify it as I change my world-view

I can publish it for others to use

Others can modify it to fit THEIR world-view

My personal world-view is being dynamically resolved against

global data and knowledge

…but it’s bigger than that…

“Elevated Creatinine Patient”

I made that up! It came out of my head!

What’s a fancy word for a world-view that you make-up?

Hypothesis

Current Research

We believe that ontologies and hypotheses are, in some ways, the same “thing”…

…simply assertions about individuals that may or may not exist

If an instance of a class exists, then the hypothesis is “validated”

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

Find services that generate the properties we need

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.

My Purpose!!

What SADI + SHARE supports

Re-interpretation

We constantly compare the collection of properties, gathered from third-parties worldwide, to whatever world-model (query/ontology) we wish to view it

through.

MY world model

Novel re-use

There is no way for the provider to dictate how their data should be used, or how it should be interpreted. They simply add

their properties into the “cloud” and those properties are used in whatever

way is appropriate for me.

What SADI + SHARE supports

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.

Important “wins”

And all this because SADI simply requires

that the input URI

is the same as the output URI

Join us!

We have recently received funding from CANARIEto assist and train service providers

in deploying their own SADI Semantic Web Services

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

http://sadiframework.org

Fin

This presentation available on SlideShare: keywords ‘wilkinson’ ‘BioIT-2010’

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 A D I & C a r d i o S H A R E )

L u k e M c C a r t h y ( S A D I & 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 )

Microsoft Research