An Introduction to the Semantic Web for Life Science Practitioners

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Timely. Practical. Reliable.

http://applied-semantic-web.org

An Introduction to the Semantic Web

for Life Science Practitioners

Emanuele Della Valle

[email protected]

http://emanueledellavalle.org

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a credits slide stating These slides are partially based on

An Introduction to the Semantic Web for Life Science Practitioners

by Emanuele Della Valle

http://applied-semantic-web.org/slides/2011/01/1a-intro-4bio.ppt

§

To view a copy of this license, visit

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Emanuele Della Valle - http://applied-semantic-web.org

§

Motivation

§

The Semantic Web

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Introduction

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Emanuele Della Valle - http://applied-semantic-web.org

Web-based Knowledge Discovery Today

Large number of integrations

-

ad hoc

-

pair-wise

Possible, but a very

painful process

-- Carole Globe

Search &

Mash-up

Engine

Millions of Applications

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Introduction

Computer don t understand much

…

Large number of integrations

-

ad hoc

-

pair-wise

Possible, but a very

painful process

-- Carole Globe

Each site is understandable for us

Computers don t understand much

?

Search &

Mash-up

Engine

010 0 1 1 0 0 1101 10100 10 0010 01 101 101 01 110 1 10 1 10 0 1 1 0 1 0 1 0 0 1 1 0 1 1 1 10 0 1 101 0 1

Millions of Applications

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Emanuele Della Valle - http://applied-semantic-web.org

The Problem: Semantic Gap

Sensor Data

Semantic Gap

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Introduction

Understanding Means Bridging the Gap

Sensor Data

understanding

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Emanuele Della Valle - http://applied-semantic-web.org

Do We Really Know What Understanding means?

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Introduction

Two ways for computer to “understand”

§

Smart Machine

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Emanuele Della Valle - http://applied-semantic-web.org

Smart Machines

§

Working examples found on the Web

• 

Image Processing

–

retrievr: find by sketching

http://labs.systemone.at/retrievr/

• 

Audio Processing

–

midomi: find by singing

http://www.midomi.com/

• 

[…]

• 

Natural Language Processing

–

semantic proxy:

http://semanticproxy.opencalais.com/

about.html

Sensor Data

Symbolic Description

Ima

ge

Pro

ce

ssi

ng

Au

di

o

Pro

ce

ssi

ng

N

at

ura

l L

an

gu

ag

e

Pro

ce

ssi

ng

[

…

]

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Introduction

Smart Machines alone cannot bridge the gap

…

Natural Language Processing (NLP)

meets Image Processing (IP)

NLP

: What does your eye see?

IP

: I see a sea

NLP

: You see a c ?

IP

: Yes, what else could it be?

[Source NLP Related Entertainment

http://www.cl.cam.ac.uk/Research/NL/amusement.html]

Sensor Data

Ima

ge

Pro

ce

ssi

ng

N

at

ura

l

Language

Pro

ce

ssi

ng

sea

c

Semantic Gap

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Emanuele Della Valle - http://applied-semantic-web.org

…

smart data are need

Sensor Data

Ima

ge

Pro

ce

ssi

ng

N

at

ura

l

Language

Pro

ce

ssi

ng

sea

c

smart data

Natural Language Processing (NLP)

meets Image Processing (IP)

NLP

: What does your eye see?

IP

: I see a

wordnet:word-sea

NLP

:

mmm, I

see a

wordnet:word-c

IP

:

I believe we have different

understanding of the world …

NLP

:

So do I

The

Semantic Web

offers a

set of

standards

that lowers

the barriers to emplo

y

smart

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Introduction

What a machine understands of the Web

§

What we say to Web agents

§

" For more information visit

<a

href= http://www.ex.org >

my company </a>

Web

site. . .

§

What they hear

§

" blah blah blah blah blah

<a

href= http://www.ex.org >

blah blah blah </a>

blah

blah. . .

§

Jet this is enought to train them

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Emanuele Della Valle - http://applied-semantic-web.org

What Google understands

§

Understanding that

•

[page1] links [page2]

à

page2 is interesting

§

Google is able to rank results!

•

The heart of our software is PageRank™, a system for

ranking web pages […] (that)

relies on the uniquely

democratic nature of the web by using its vast link

structure as an indicator of an individual page's value

.

http://www.google.com/technology/

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Introduction

The Semantic Web 1/4

§

The Semantic Web is not a separate Web, but an

extension of the current one, in which information is given

well-defined meaning, better enabling computers and

people to work in cooperation.

The Semantic Web , Scientific American Magazine, Maggio 2001

http://www.sciam.com/article.cfm?articleID=00048144-10D2-1C70-84A9809EC588EF21

§

Key concepts

•

an extension

of the current Web

•

in which

information is given well-defined meaning

•

better enabling

computers

and

people

to work in

cooperation.

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Emanuele Della Valle - http://applied-semantic-web.org

The Semantic Web 2/4

§

The Semantic Web is not a separate Web,

but

an extension

of the current one […]

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Introduction

The Semantic Web 3/4

§

The Semantic Web […] ,

in which information is given

well-defined meaning

[…]

Human

understandable

but

“only”

machine-readable

Human and machine

“

understandable

”

?

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Emanuele Della Valle - http://applied-semantic-web.org

The Semantic Web 4/4

Semantic Web

META META META META META META META META META META

Fewer Integration

-

standard

-

multi-lateral

[…] better enabling

computers and

people to work in

cooperation.

Even More Applications

Easier to understand for people

More “understandable” for computers

Semantic

Mash-ups

&

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Introduction

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Emanuele Della Valle - http://applied-semantic-web.org

Bio2RDF REST services

§

Describe a resource by a dereferencable URI

•

http://bio2rdf.org/ns

:id

§

Global services over federated endpoints

•

http://bio2rdf.org/links/

ns:id

•

http://bio2rdf.org/search/

searchedTerm

§

Targeted services to a specific endpoint

•

http://bio2rdf.org/linksns/

ns2/ns1:id

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Introduction

Example of questions Bio2RDF can answer

§

What is known about human

BRCA

genes?

•

http://bio2rdf.org/search/BRCA1

§

What is known about human

BRCA

genes in Entrez Gene

databank (i.e., the Bio2RDF data source whose namespace is

geneid)?

•

http://bio2rdf.org/searchns/geneid/BRCA1

§

What can you tell me which fact are known about the human

tumor suppressor gene

BRCA1

(Gene ID:

672

)?

•

http://bio2rdf.org/geneid:672

§

What information is linked to geneid:672?

•

http://bio2rdf.org/links/geneid:672

§

Which is the FASTA sequence of the human

5-hydroxytryptamine

receptor 2A

(whose accession number is

AB037513

) in NCBI

GeneBank databank (i.e., the Bio2RDF data source whose

namespace is genbank).

•

http://bio2rdf.org/fasta/genbank:AB03751

§

And the image?

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Emanuele Della Valle - http://applied-semantic-web.org

Complex Example: Linking Open Data Project

§

Goal: extend the Web with data commons by publishing

open data sets using Semantic Web techs

Visit

http://esw.w3.org/topic/SweoIG/TaskForces/CommunityProjects/LinkingOpenData

!

Project Chartres

•

RDFizers

and

ConverterToRdf

•

Publishing Tools

•

Semantic Web

Browsers and

Client Libraries

•

Semantic Web

Search Engines

•

Applications

•

[

…

]

Bio2RDF

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Introduction

Browsing the LOD with http://sig.ma/

ry

it!

ht

tp

://

si

g.

ma

/se

arch

?q

=Pro

pra

no

lo

l

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Emanuele Della Valle - http://applied-semantic-web.org

Semantic Web layer cake

Standardized

Under

Investigation

Already

Possible

[ source http://www.w3.org/2007/03/layerCake.png ]

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Introduction

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Emanuele Della Valle - http://applied-semantic-web.org

§

Introduction and RDF slides are partially based on

Fundamentals of the Semantic Web by David Booth