CSHALS 2010 W3C Semanic Web Tutorial

The Semantic Web LandscapeA Practical Introduction
Lee Feigenbaum
VP Technology & Standards, Cambridge Semantics
Co-chair, W3C SPARQL Working Group
For CSHALS 2010 Tutorial Attendees
February 24, 2010

The W3C HCLS interest group set out to use Semantic Web technologies to receive precise answers to a complex question:
A Motivating Example: Drug Discovery
Find me genes involved in signal transduction that are related to pyramidal neurons.

General search
223,000 hits, 0 results

Domain-limited search
2,580 potential results

Specific databases
Too many silos!

A Semantic Web Approach
Integrate disparate databases…
MeSH
PubMed
Entrez Gene
Gene Ontology
…

A Semantic Web Approach (cont’d)
…so that onequery…

…(trivially) spans several databases…

…to deliver targeted results…

Agreement on common terms and relationships
Incremental, flexible data structure
Good-enough modeling
Query interface tailored to the data model
What’s the trick?

What is the semantic web?

Semantic Web
Web of Data
Giant Global Graph
Data Web
Web 3.0
Linked Data Web
Semantic Data Web
Branding

“The Semantic Web” a.k.a “Linked Open Data”
Augments the World Wide Web
Represents the Web’s information in a machine-readable fashion
Enables…
…targeted search
…data browsing
…automated agents
What is it & why do we care? (1)
World Wide Web : Web pages :: The Semantic Web : Data

“Semantic Web technologies”
A family of technology standards that ‘play nice together’, including:
Flexible data model
Expressive ontology language
Distributed query language
Drive Web sites, enterprise applications
What is it & why do we care? (2)
The technologies enable us to build applications and solutions that were not possible, practical, or feasible traditionally.

A common set of technologies:
...enables diverse uses
...encourages interoperability
A coherent set of technologies:
…encourage incremental application
…provide a substantial base for innovation
A standard set of technologies:
...reduces proprietary vendor lock-in
...encourages many choices for tool sets
A Common & Coherent Set of Technology Standards

The (In)Famous Layer Cake

Semantic Web Technology Timeline
2001
2004
2008
2010
2007
1999
RIF
HCLS

As technologies & tools have evolved, Semantic Web advocates have progressed through stages:
2010: Where we are

2010: Where we’re not
Image from Trey Ideker via Enoch Huang
Semantic Web technologies are not a ‘magic crank’ for discovering new drugs (or solving other problems, for that matter)!

2010: Where we’re not (cont’d)
XML vs. RDF?
“Ontology” vs. “ontology”?
Data integration vs. reasoning vs. KBs vs. search vs. app. development vs. …
Semantic Web vs. Linked Data?
The Semantic Web still suffers from confusing and conflicting messaging, each of which asserts it’s “correct”.

People with appropriate skill sets for designing & building Semantic Web solutions are not widely available.

We don’t yet have standard solutions for privacy, trust, probability, and other elements of the Semantic Web vision.

What do Semantic Web solutions look like?

RDF is…
Resource Description Framework

RDF is…
The data model of the Semantic Web.

RDF is…
A schema-less data model that features unambiguous identifiers and named relations between pairs of resources.

RDF is…
A labeled, directed graph of relations between resources and literal values.
RDF graphs are collections of triples
Triples are made up of a subject, a predicate, and an object
Resources and relationships are named with URIs
predicate
subject
object

“Lee Feigenbaum works for Cambridge Semantics”
“Lee Feigenbaum was born in 1978”
“Cambridge Semantics is headquartered in Massachusetts”
Example RDF triples
works for
born in
headquartered
Lee Feigenbaum
Cambridge Semantics
Lee Feigenbaum
Cambridge Semantics
1978
Massachusetts

Triples connect to form graphs
headquartered
lives in
Massachusetts
born in
capital
works for
Lee Feigenbaum
Cambridge Semantics
Boston
1978

The graph data structure makes merging datawith shared identifiers trivial
Triples act as a least common denominatorfor expressing data
URIs for naming remove ambiguity
…the same identifier means the same thing
Why RDF? What’s different here?

Why RDF? Incremental Integration
RelationalDatabase
RDF

RDF is the model, for which there are several concrete syntaxes:
RDF/XML – standard, complex XML syntax
Turtle – common, textual, triples-oriented syntax
N3 – more expressive superset of Turtle
N-Triples – textual, line-oriented, useful for streaming
What does RDF look like?
When writing RDF by hand and in many guides, examples, and discussions these days, you’ll see Turtle most often.

Write a triple by writing its parts separated by spaces (subject predicate object)
A Bit of Turtle
@prefix ex: <http://example.org/myvocab/> .
@prefix geo: <http://geonames.example/> .
ex:LeeFeigenbaumex:employerex:CambridgeSemantics .
ex:LeeFeigenbaumex:birthYear 1978 .
ex:CambridgeSemanticsex:headquartersgeo:BostonMA .
geo:BostonMAex:population 574000 .

SPARQL is…
SPARQL Protocol And RDF Query Language

SPARQL is…
The query language of the Semantic Web.

SPARQL is…
A SQL-like language for querying sets of RDF graphs.

SPARQL is…
A simple protocol for issuing queries and receiving results over HTTP. So…
Every SPARQL client works with every SPARQL server!

SPARQL lets us:
Pull information from structured and semi-structured data.
Explore data by discovering unknown relationships.
Query and search an integrated view of disparate data sources.
Glue separate software applications together by transforming data from one vocabulary to another.
Why SPARQL?

Dealer 1
Dealer 2
Dealer 3
Employee
Directory
ERP / Budget
System
Web
EPA Fuel Efficiency
Spreadsheet
SPARQL Query Engine
What automobiles get more than 25 miles per gallon, fit within my department’s budget, and can be purchased at a dealer located within 10 miles of one of my employees?
SELECT ?automobile
WHERE { ?automobile a ex:Car ; epa:mpg ?mpg ;
ex:dealer ?dealer .
?employee a ex:Employee ; geo:loc ?loc .
?dealer geo:loc ?dealerloc .
FILTER(?mpg > 25 &&
geo:dist(?loc, ?dealerloc) <= 10) .
}
Web dashboard
SPARQL query

bio2rdf.org – querying life sciences data

3 pieces of the Semantic Web technology stack are about describing a domain well enough to capture (some of) the meaning of resources and relationships in the domain
RDF Schema
OWL
RIF
From the explicit to the inferred
Apply knowledge to data to get more data.

RDFS is…
RDF Schema

Elements of:
Vocabulary (defining terms)
I define a relationship called “prescribed dose.”
Schema (defining types)
“prescribed dose” relates “treatments” to “dosages”
(my prescribed dose is 2mg; therefore 2mg is a dosage)
Taxonomy (defining hierarchies)
Any “doctor” is a “medical professional”
(therefore Dr. Brown is a medical professional)
RDF Schema is…

WOL OWL is…
Web Ontology Language

Elements of ontology
Same/different identity
“author” and “auteur” are the same relation
two resources with the same “ISBN” are the same “book”
More expressive type definitions
A “cycle” is a “vehicle” with at least one “wheel”
A “bicycle” is a “cycle” with exactly two “wheels”
More expressive relation definitions
“sibling” is a symmetric predicate
the value of the “favorite dwarf” relation must be one of “happy”, “sleepy”, “sneezy”, “grumpy”, “dopey”, “bashful”, “doc”
OWL is…

A class is a (named) collection of things with similar attributes
OWL: Rich Class Definitions

OWL: Rich Class Definitions

RIF is…
Rules Interchange Format

Standard representation for exchanging sets of logical and business rules
Logical rules
A buyer buys an item from a seller if the seller sells the item to the buyer
A customer becomes a "Gold" customer as soon as his cumulative purchases during the current year top $5000
Production rules
Customers that become "Gold" customers must be notified immediately, and a golden customer card will be printed and sent to them within one week
For shopping carts worth more than $1000, "Gold" customers receive an additional discount of 10% of the total amount
RIF is…

Fantasy Land Architecture
Ontology / Schema
+
Custom UI
Custom UI
Custom UI
Custom UI
Custom UI
Custom UI

Reality
Internet
DB2
XML
LDAP Directory
Oracle
RDB
Custom UI
Custom UI
Custom UI
Custom UI
Custom UI
Custom UI

GRDDL is…
Gleaning Resource Descriptions from Dialects of Language

GRDDL is…
A method for authoritatively getting RDF data from XML and XHTML documents.

GRDDL is…
A mechanism for authoritatively deriving RDF data from families of XML and XHTML documents.

RDB2RDF is…
Relational Database toRDF

RDB2RDF is…
A W3C Working Group to define a standard way to map from relational databases to RDF (and SPARQL).

A simple set of 4 guidelines for publishing RDF data on the Web (over HTTP)
Developed by Tim Berners-Lee in 2006
Use URIs as names for things
Globally unique identity
Use HTTP URIs
Everyone has a Web browser/client
When someone looks up a URI, provide useful information
…in the form of RDF data
Include links to other URIs
Foster discovery of additional information
Linked Data is…

The LOD “cloud”, March 2009

Application specific portions of the cloud
Notably, bio-related data sets (in light purple)
some by the W3C “Linking Open Drug Data” task force

RDFa is…
RDF in Attributes

RDFa is…
A collection of HTML attributes that allow RDF to be embedded directly in Web pages.

Don’t Repeat Yourself (DRY)
In-context metadata (copy & paste)
Authoritative (no screen scrapig)
Why RDFa?

RDFa in action

Semantic Web landscape today

Semantic Web Tools
In 2010, there are a wide variety of open-source and commercial Semantic Web tools available.

Triple stores
Built on relational database
Native RDF store
Development libraries
Full-featured application servers
Types of RDF Tools
Most RDF tools contain some elements of each of these.

Community-maintained lists
http://esw.w3.org/topic/SemanticWebTools
Emphasis on large triple stores
http://esw.w3.org/topic/LargeTripleStores
Michael Bergman’s Sweet Tools searchable list:
http://www.mkbergman.com/?page_id=325
Finding RDF Tools

Query engines
Things that can run queries
Most RDF stores provide a SPARQL engine
Query rewriters
E.g. to query relational databases (more later)
Endpoints
Things that accept queries on the Web and return results
Client libraries
Things that make it easy to ask queries
Types of SPARQL Tools

Community-maintained list of query engines
http://esw.w3.org/topic/SparqlImplementations
Publicly accessible SPARQL endpoints
http://esw.w3.org/topic/SparqlEndpoints
Michael Bergman’s Sweet Tools searchable list:
http://www.mkbergman.com/?page_id=325
Finding SPARQL Tools

Editors/environments
Oiled, Protégé, Swoop, TopBraid, Ontotrack, …
Developing Tools and Infrastructure

Editors/environments
Oiled, Protégé, Swoop, TopBraid, Ontotrack, …
Reasoning systems
Cerebra, FaCT++, Kaon2, Pellet, Racer, CEL, …
Developing Tools and Infrastructure
Pellet
KAON2
CEL

Visualizing and Publishing Vocabularies

Reusable, public ontologies
FOAF
The Event Ontology
Measurement Units Ontology

Community-maintained list:
http://esw.w3.org/topic/GrddlImplementations
GRDDL tools
Most GRDDL tools are adapters to existing RDF stores or SPARQL engines to allow loading or querying data from XML and XHTML sources.

What about… everything else?
Standards don’t yet exist, but many tools exist to derive RDF and/or run SPARQL queries against other sources of data.

LDAP Directories
Squirrel RDF
http://jena.sourceforge.net/SquirrelRDF/

Excel spreadsheets
Anzo for Excel
http://www.cambridgesemantics.com/products/anzo_for_excel

Web-based data sources
Virtuoso Sponger Cartridges
http://virtuoso.openlinksw.com/dataspace/dav/wiki/Main/VirtSponger

Unstructured Text
Calais
http://www.opencalais.com/

Unstructured Text
Zemanta Web Service
http://developer.zemanta.com/

On the Web
Google, Yahoo!
Best Buy
NY Times
US Government
UK Government
Where is it being used?

Industries
Oil & Gas (integration, classification)
Finance (structured data, ontologies, XBRL)
Publishing (metadata)
Government (structured data, metadata, classification)
Libraries & museums (metadata, classification)
IT (rapid application development & evolution)

Health Care
Cleveland Clinic
Clinical research
Data integration, classification (= better search)
UT School of Health
Public health surveillance
SAPPHIRE—classification, ontology-driven development
Various
Clinical Decision Support
Agile, rule-driven, scalable in the face of change

Life Sciences
Agile knowledgebases at Pfizer
Target assessment at Eli Lilly
Integrated information links at Novartis
Astra Zeneca, J&J, UCB, …
CSHALS chronicles many of these uses and many more.

Take-away Advice

These are horizontal, enabling technologies.
But they apply particularly well to problems with these characteristics:
Heterogeneous data from multiple sources
Increasing reliance on connections within this data
Rapidly changing information needs
Significant early-mover advantage
Large amounts of data that would benefit from classification
Why are Semantic Web technologies appropriate for the life sciences?
Many tactical and strategic challenges in the life sciences industry feature these traits.

Getting Started with Semantic Web technologies
Don’t boil the ocean.

Getting Started with Semantic Web technologies
Goal: quick tactical wins on the path to large strategic value
Be sure to consider the operational ramifications
Who does what differently?
Ideal Semantic Web projects/applications have an incremental path towards broad deployment that generates demonstrable value along the way

Look beyond the core Semantic Web capabilities and consider:
integration with existing enterprise systems
development & extension models
deployment, logging, maintenance, backup
tooling
user experience
Choose practical, enterprise-ready tools
If you choose to build new components and assemble existing components together, it’s quite likely you’ll end up reinventing the wheel.

What level of expertise is necessary?
Technologies only?
Technologies + API?
Technologies + tooling?
Tooling only?
…
How will we acquire the expertise?
In-house (and if so, how?)
Vendor services
3rd-party services
Open-source community
Plan for Acquiring Expertise

I’m always happy to field questions & engage in discussion:
lee@cambridgesemantics.com
Thanks & Discussion

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CSHALS 2010 W3C Semanic Web Tutorial

by LeeFeigenbaum on Feb 24, 2010

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CSHALS 2010 W3C Semanic Web Tutorial — Presentation Transcript