Semantic Web, an introduction for bioscientists

Applied Semantic WebTimely. Practical. Reliable.http://applied-semantic-web.org

Semantic WebAn IntroductionEmanuele Della [email protected]://emanueledellavalle.org

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

Share, Remix, Reuse — Legally

This work is licensed under the Creative Commons Attribution 3.0 Unported License.

Your are free:

• to Share — to copy, distribute and transmit the work

• to Remix — to adapt the work

Under the following conditions

• Attribution — You must attribute the work by inserting– “© applied-semantic-web.org” at the end of each reused slide– a credits slide stating “These slides are partially based on

“Semantic Web An Introduction” by Emanuele Della Valle http://applied-semantic-web.org/slides/2010/03/01_intro.ppt

To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/

2


Agenda

Dal Web delle origini al Semantic Web

Introduzione al Semantic Web

Applicazioni del Semantic Web

Conclusione

3

Emanuele Della Valle - http://applied-semantic-web.org 4

Il Web delle origini 1988 (CERN)


Il Web delle origini (1990)

[source: http://ww

w.w

3.org/DesignIssues/diagram

s/history/proposal-fig1.gif ]

[source: http://ww

w.w

3.org/DesignIssues/diagram

s/history/Architecture_crop.png ]


The Web today

Let’s browse together 2009 Maphttp://www.zoomorama.com/01-2477f0e8b447bb6570493cdac464c41f


Introduction

Computer should understand more

Large number of integrations - ad hoc - pair-wise

Too much information to browse, need for searching and mashing up automatically

Each site is “understandable” for us

Computers don’t “understand” much

?

Search & Mash-up Engine

010 0 1 1 0

01101

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

Millions of Applications


Introduction

What does “understand” mean?

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 to achive tasks for us

[ source http://www.thefarside.com/ ]


Introduction

What does Google “understand”?

Understanding that• [page1] links [page2] 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/

9


Introduction

Two ways for computer to “understand”

Smarter machines• Such as

– Natural Langue processing (NLP)– Audio Processing– Image Processing (IP)– Video Processing– … many many more

• They all work fine alone, the problem is combining them– E.g., NLP meets IP

- NLP: What does your eye see?- IP: I see a sea- NLP: You see a “c”?- IP: Yes, what else could it be?

• Not the Semantic Web approach

Smarter Data• Make data easier for machines to publish, share, find and

understand– E.g. http://wordnet.rkbexplorer.com/description/word-sea vs.

http://wordnet.rkbexplorer.com/description/word-c • The Semantic Web approach

Some NLP Related Entertainment http://www.cl.cam.ac.uk/Research/ NL/amusement.html

10


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.– Both for computers and people

11



“The Semantic Web is not a separate Web, but an extension of the current one […] ”

Web 1.0 The Web Today

12



“The Semantic Web […] , in which information is given well-defined meaning […]”

Human understandable but “only” machine-

readable

Human and machine

“understandable”

?

Web 1.0 Semantic Web

13



Semantic Web

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 &Search


Introduction Bio2RDF project - http://bio2rdf.org/

15


Introduction 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• http://bio2rdf.org/searchns/ns/searchedTerm

16


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?• http://bio2rdf.org/image/genbank:AB037513

17


Introduction 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

• […]

18

Bio2RDF


<div id="event-info-where" class="info-wh-info vcard"> <h2><a rel="bookmark" class="fn org location" href="/venues/V0-001-000693919-2"> Circus Krone Munich</a></h2> <div class="adr"> <span class="street-address">1</span><br> <span class="locality">Munich</span>, <span class="region">Bayern</span> <br> <span class="country-name">Germany</span>

Introduction Light Example: Publishing Semantic Mark-up

A firefox plug-in such as Operator can extract those semantic mark-up from the page and offers actions such as “add the event to your calendar” https://addons.mozilla.org/en-US/firefox/addon/4106

19


Introduction Example: BBC’s Artist as Linked Data

<?xml version="1.0" encoding="utf-8"?> <rdf:RDF xmlns:rdf = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs = "http://www.w3.org/2000/01/rdf-schema#" xmlns:owl = "http://www.w3.org/2002/07/owl#" xmlns:dc = "http://purl.org/dc/elements/1.1/" xmlns:foaf = "http://xmlns.com/foaf/0.1/" xmlns:rel = "http://www.perceive.net/schemas/relationship/" xmlns:mo = "http://purl.org/ontology/mo/" xmlns:rev = "http://purl.org/stuff/rev#" > <rdf:Description rdf:about="/music/artists/a3cb23fc-acd3-4ce0-

8f36-1e5aa6a18432.rdf"> <rdfs:label>Description of the artist U2</rdfs:label> <foaf:primaryTopic rdf:resource="/music/artists/a3cb23fc-acd3-

4ce0-8f36-1e5aa6a18432#artist"/> </rdf:Description> <mo:MusicGroup rdf:about="/music/artists/a3cb23fc-acd3-4ce0-

8f36-1e5aa6a18432#artist"> <foaf:name>U2</foaf:name> <owl:sameAs rdf:resource="http://dbpedia.org/resource/U2" /> <foaf:page rdf:resource="/music/artists/a3cb23fc-acd3-4ce0-8f36-

1e5aa6a18432.html" /> <mo:musicbrainz

rdf:resource="http://musicbrainz.org/artist/a3cb23fc-acd3-4ce0-8f36-1e5aa6a18432.html" />

<mo:homepage rdf:resource="http://www.u2.com/" /> <mo:fanpage rdf:resource="http://www.atu2.com/" /> <mo:wikipedia rdf:resource="http://en.wikipedia.org/wiki/U2" /> <mo:imdb

rdf:resource="http://www.imdb.com/name/nm1277752/" /> <mo:myspace rdf:resource="http://www.myspace.com/u2" /> <mo:member rdf:resource="/music/artists/7f347782-eb14-40c3-

98e2-17b6e1bfe56c#artist" /> <mo:member rdf:resource="/music/artists/1f52af22-0207-40ac-

9a15-e5052bb670c2#artist" />

HTML: http://www.bbc.co.uk/music/artists/a3cb23fc-acd3-4ce0-8f36-1e5aa6a18432

RDF : http://www.bbc.co.uk/music/artists/a3cb23fc-acd3-4ce0-8f36-1e5aa6a18432.rdf


Introduction New York Times Thesaurus

For more than 150 years, The New York Times has meticulously indexed its archives. Through this process, we have developed an enormous collection of subject headings […].

Unfortunately, our list of subject headings is an island. For example, even though we can show you every article written about “Colbert, Stephen,” our databases can’t tell you that he was born on May 13, 1964, or that he lost the 2008 Grammy for best spoken word album to Al Gore. To do this we would need to map our subject headings onto other Web databases such as Freebase and DBPedia.

So that’s exactly what we did. Over the last several months we have manually mapped more than 5,000 person name subject headings onto Freebase and DBPedia. […]

So now you can visit http://data.nytimes.com/N66220017142656459133 and see that our “Colbert, Stephen” is equivalent to DBPedia’s http://dbpedia.org/resource/Stephen_Colbert and Freebase’s http://rdf.freebase.com/rdf/en.stephen_colbert. Even more importantly, your computer can visit http://data.nytimes.com/N66220017142656459133.rdf and get all of this information in a computer-readable (RDF) document.

October 29, 2009, 4:07 pmFirst 5,000 Tags Released to the Linked Data Cloud

By EVAN SANDHAUS AND ROB LARSON


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

22

Try

it!

http

://s

ig.m

a/se

arch

?q=

Pro

pran

olol


Introduction The new era of Semantic Apps

One of the highlights of October's Web 2.0 Summit in San Francisco was the emergence of 'Semantic Apps' as a force.

The purpose of this post is to highlight 10 Semantic Apps. […] It reflects the nascent status of this sector, even though people like Hillis and Spivack have been working on their apps for years now.

Read out more at http://www.readwriteweb.com/archives/10_semantic_apps_to_watch.php


Introduction Semantic Web “layer cake”

Standardized

UnderInvestigation

Already Possible

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


Introduction Architectural view of the lower layers

[source http://www.w3.org/DesignIssues/diagrams/sw-double-bus.png ]


Credits

Introduction and RDF slides are partially based on “Fundamentals of the Semantic Web” by David Boothhttp://www.w3.org/2002/Talks/0813-semweb-dbooth/

26

Semantic Web, an introduction for bioscientists

Education

semantic web introduzione

semantic web applicazioni

semantic web conclusione

current web

separate web

web agents

id http

address http