Semantic Web, an introduction for bioscientists
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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
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“Semantic Web An Introduction” by Emanuele Della Valle http://applied-semantic-web.org/slides/2010/03/01_intro.ppt
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Agenda
Dal Web delle origini al Semantic Web
Introduzione al Semantic Web
Applicazioni del Semantic Web
Conclusione
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Il Web delle origini 1988 (CERN)
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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 ]
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The Web today
Let’s browse together 2009 Maphttp://www.zoomorama.com/01-2477f0e8b447bb6570493cdac464c41f
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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
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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/ ]
Emanuele Della Valle - http://applied-semantic-web.org
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/
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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
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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.– Both for computers and people
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Emanuele Della Valle - http://applied-semantic-web.org
Introduction The Semantic Web 2/4
“The Semantic Web is not a separate Web, but an extension of the current one […] ”
Web 1.0 The Web Today
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Emanuele Della Valle - http://applied-semantic-web.org
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”
?
Web 1.0 Semantic Web
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Emanuele Della Valle - http://applied-semantic-web.org 14
Introduction The Semantic Web 4/4
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
Emanuele Della Valle - http://applied-semantic-web.org
Introduction Bio2RDF project - http://bio2rdf.org/
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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
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Emanuele Della Valle - http://applied-semantic-web.org
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
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Emanuele Della Valle - http://applied-semantic-web.org
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
• […]
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Bio2RDF
Emanuele Della Valle - http://applied-semantic-web.org
<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
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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
Emanuele Della Valle - http://applied-semantic-web.org
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
Emanuele Della Valle - http://applied-semantic-web.org 22
Introduction Browsing the LOD with http://sig.ma/
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Try
it!
http
://s
ig.m
a/se
arch
?q=
Pro
pran
olol
Emanuele Della Valle - http://applied-semantic-web.org 23
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
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Introduction Semantic Web “layer cake”
Standardized
UnderInvestigation
Already Possible
[ source http://www.w3.org/2007/03/layerCake.png ]
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Introduction Architectural view of the lower layers
[source http://www.w3.org/DesignIssues/diagrams/sw-double-bus.png ]
Emanuele Della Valle - http://applied-semantic-web.org
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/
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