Agenda

Intro: Information management in Biology

Information management engineering

Formats and standards

XML

MAGE example

Perspectives: the Semantic Web

The semantic web

Semantic Web and Biology

Service Integration: web services

Conclusions

Where do we are?

We have good technologies for data management

applications

We have XML for data exchange

But it's not enough...

What about semantics in XML?

How to exchange XML?

How to interface the applications?

Is it possible without IT specialists?

Ontologies

Ontologies

Examples of queries with ontologies

● “nails is-part-of elephant”? yes, because:

– “has-legs” and “has-nails” are particular “has-parts”

transitive relation

– “is-part-of” is the inverse

of “has-parts”

Ontologies

Examples of queries with ontologies

● “giraffe is-eaten-by lion”? yes, because:

– giraffe is-a herbivore => is-a animal

lion is-a carnivore =>

lion eats animal =>

lion eats giraffe

“is-eaten” is the

inverse of “eats”

ArrayExpres

s

MIAMExpress

RADMAGE-ML data exchange

Ontology instances propagated to

submission/annotation web forms

Curation of

user defined

terms, before

inclusion in

the ontology

User defined terms

collected via forms

MGED OntologyBiomaterialDescriptio

nSexC

C

C

C Gender

documentation: Subclass of sex applicable to heterogametic species (i.e., those in which the sexes produce gametes of markedly different size). Males produce small numerous gametes. Females produce small numbers of large gametes. Hermaphrodites are individuals with both male and female characteristics. Mixed refers to a population of individuals with more than one type of gender.

used in individuals: female, hermaphrodite,male,mixed_sex,unknown_sex

MAGE and Ontologies

THE “ontology”: Gene Ontology

Semantic Web The Web is a huge repository of information

Information is unstructured and without associated structured

semantics

We need to semantically structure the information

We need to share semantic representations

We need to “reason” over knowledge (inference)

Ontologies and other semantic-aware formalisms + XML

+ standards + semantic-web engines + applications

=

Semantic Web

Semantic Web examples

Semantic Web: Annonzilla

Semantic Web: Annonzilla

Semantic Web examples

Semantic Web examples

Friend of a Friend (FOAF), see also LinkedIn

RSS, possible future of PubMed and alike

RSSOwl, try with feeds from:Nature, Bioinformatics, etc.RSSOwl, try with feeds from:Nature, Bioinformatics, etc.

Semantic Web, RDF, Bioinformatics

Semantic Web, RDF, Bioinformatics

Semantic Web, RDF, Bioinformatics

Semantic Web, RDF, Bioinformatics

You may handle statements

Subject/Property(or verb)/Object may reference public resources,

identified by URIs (like Web pages)

A given resource may flexibly be annotated by many statements

Meaning of statements may be defined by other statements and

higher languages (which still are RDF representable)

Semantic Web, RDF, Bioinformatics

Semantic Web, RDF, Bioinformatics

Semantic Web, RDF, Bioinformatics

Refer to the same resource

The second doc extendsthe first one

Semantic Web, RDF, Bioinformatics

Semantic Web layered cake

Semantic Web layered cake

URI: how to address thing on internet

Unicode: the “alphabet”

RDF-S, OWL: ontologies, define the semantics of things

SPARQ-L: to make semantic-aware queries

Logic, proof, trust: deductions, logical “reasoning”,

inference

Unfortunately all this complexity is needed for...

...this!

MetabolicPathways

MolecularInteractionNetworks

SignalingPathways

Main categories:

Bioinformatics Semantic Web: BioPAX

Bioinformatics Semantic Web: BioPAX

species

reaction modifier

BioPAX Motivation

Before BioPAX With BioPAX

Common format will make data more accessible, promoting data sharing and distributed curation efforts

>150 DBs and tools

Database

Application

User

BioPAX in action

BioPAX in action

Bioinformatics Semantic Web

Several other in-progress examples

GandrKB

Flymine

Microarrays annotations (my PhD...)

FUGE (MAGE 2)

YeastHUB (simple integration by means of RDF)

...

Services Integration

User

Amazon Web site

3rd parties catalogs

PurchaseService

CC service

VISA

Mastercard

...

3

4

5

1 2,2b

6

7

89

Services IntegrationHow to realize such services integration?

Call remote code (RPC, J2EE)

Code mobility (Java Applets, Agents)

Exchange messages, use XML => SOAP and Web services

How to discover services?

Handily or Registers

How to know that a service is about “book purchasing”?

Up to user

Ontologies!

How to compose services?

Up to user

Reasoning!

Services IntegrationBank Trading Agent Stock Exch

Service

<SOAP-ENV:Envelope><SOAP-ENV:Body>

<xmlns:m=http://www.stock.org/stock />

<m:GetStockPrice><StockName>IBM</StockName>

</m:GetStockPrice></SOAP-ENV:Body>

</SOAP-ENV:Envelope>

<SOAP-ENV:Envelope><SOAP-ENV:Body>

<xmlns:m=http://www.stock.org/stock />

<m:GetStockPriceResponse><Price>34.5</Price>

</m:GetStockPriceResponse></SOAP-ENV:Body>

</SOAP-ENV:Envelope>

Web services in Biology

Web services in Biology

myGRID and Taverna

myGRID and Taverna

myGRID and Taverna

Future of Web services?Give me the directions from A to B...

Future of Web services?

Agenda

Intro: Information management in Biology

Information management engineering

Formats and standards

XML

MAGE example

Perspectives: the Semantic Web

The semantic web

Semantic Web and Biology

Service Integration: web services

Conclusions

ConclusionsWhat should a biologist know?

Bioinformatics integration is a complex task

Must be done by informaticians and biologists, together

As user, should have notion of general concepts:

Models and architectures

Object and relational models

n-tiers systems

Distributed systems, web services etc.

As user/curator should be aware of knowledge representation issues

The idea of standards, some standards

The idea of ontology, some ontologies

Should know about tools existence, try to use!

Thanks!

Find this slides at:

http://bioguest.btbs.unimib.it/~brandizi/master05