Alan RuttenbergSchool ofDental Medicine

Technology of the Semantic Web

Alan RuttenbergOral Diagnostic Sciences

Clinical and Translational Data Exchange

Alan RuttenbergSchool ofDental Medicine

Goals of this section• Discuss a number of core standards and technologies related to

the Semantic Web– URIs– HTTP– RDF– OWL– SPARQL

• Discuss several practices I’ve found useful– Adopt a common set of principles. Work with others– Be relentless in reuse– MIREOT– Build and release ontologies like software

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Alan RuttenbergSchool ofDental Medicine

Universal Resource Identifiers

• Globally unique identifier• Namespace collision avoidance by mechanism

of domain name ownership• Many associated with network protocols (e.g.

http) but some note (e.g. urn: )• HTTP URIs favored for semantic web usage.• httpRange-14 an attempt to clarify that an HTTP

URI can refer to anything (not just web pages)

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Alan RuttenbergSchool ofDental Medicine

The case for using URIs as identifiers and the http URI scheme

• A global namespace promotes generic tools– Query, inference, cross-reference, data integration

• URIs coordinate with web standards– Created with and for the Web– IETF and W3C recommended for naming– HTTP, HTML, RDF, OWL, SPARQL

• http: URIs are universally understood– Most people will know what to do with an http: URI

• http: URIs can identify anything– Not only a web page, but any kind of entity

• http: URIs are as reliable as anything else– Durability doesn’t depend on protocol– http: URIs are not tied to the HTTP protocol

• It is easy to be helpful and give back documentation about an entity when the URI identifier is put into a web browser.

Alan RuttenbergSchool ofDental Medicine

Cool URIs don’t change

• To build a stable, predictable resources, we want people to be able to continue to access the same URI over time

• Changes in organizational structure, job, funding conspire to interfere with that

• Solution: Use two levels of indirection to a public redirection server (http://purl.org) to give us the option to fix things if it breaks.

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Alan RuttenbergSchool ofDental Medicine

OBO URI Strategycheap, relocatable = sustainable

http://purl.obofoundry.org/obo/OBI_0000225

http://purl.org/obo/OBI_0000225

Network protocol

Domain name we own. Currently synonym (CNAME) for purl.org

To coexist with other purls

* Redirect somewhere else if purl.org goes belly up.http://obofoundry.org/id-policy.shtml

Prefix/Numerical Accession

*

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Dance of the semantic web URI “dereference”

Alan RuttenbergSchool ofDental Medicine

Alan RuttenbergSchool ofDental Medicine

HTML for human, RDF for machines

Alan RuttenbergSchool ofDental Medicine

RDF

• An extremely simple language– No classes– All assertions are ‘triples’ subject predicate object.– Can’t be inconsistent (except in uninteresting case)– A well defined semantics (see http://www.w3.org/TR/rdf-mt/)

Though that doesn’t prevent it from being misunderstood– Introduces model-theoretic semantics, interpretation,

graphs– Provides a basis for semantic extensions

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Alan RuttenbergSchool ofDental Medicine

RDFS

• Extends RDF with – Classes– Domain, range of properties– Subclass relation– Subproperty relation– A few data structures (bag,list etc. though problems)– Some standard annotation properties such as

rdfs:label, rdfs:comment …– No more inconsistencies than RDF

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Alan RuttenbergSchool ofDental Medicine

OWL• OWL is the first Semweb language that allows for

inconsistencies. It allows work that is good enough to be wrong

• Some aspects of OWL 2– Fragment of first order logic– Profiles allow one to choose expressivity vs performance– Well documented conformance criteria– Maximum expressivity while still decidable– Allows metalogical statements (“think post-it notes”) about

anything in the language, even expressions.

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Alan RuttenbergSchool ofDental Medicine

Relentless Reuse• OBO Foundry aims at building orthogonal interoperating

resources

• Reuse is successfully achieved by using the identifier from the source ontology in your own ontology.

• See http://obofoundry.org/

OBI: cell CL: cell

Alan RuttenbergSchool ofDental Medicine

There are many existing ontologies (but make sure they are good)

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Alan RuttenbergSchool ofDental Medicine

MIREOT• Minimimum Information to Reference an External ontology

term• ~ copy/paste of terms into your own ontology• Terms in OBO Foundry ontologies stand on their own• If their meaning changes, they are deprecated

=> denotation of individual terms remain stable=> they can be seen as individual units of meaning

Alan RuttenbergSchool ofDental Medicine

MIREOT in practice

external.owlContains minimal information about mapped classes

externalDerived.owlContains additional information about mapped classes

xxx.owlMain ontology file, imports external andexternalDerived.owl files.

IMPORTS

SCRIPT

Alan RuttenbergSchool ofDental Medicine

Have a deliberate release processThe goal of a deliberate release process is to prepare a version that is aimed at users (which might be other developers or biologists) rather than the developers of this ontologyTypical activities

• Creation of dated release directory in repository• Copy project files to release directory• Update of MIREOT related files• Merge in one release file for ease of use• Run reasoner to add inferred axioms• OWL and OBO format• Quality checks• Create dated and "latest" PURLs as stable URIs for your ontology

Alan RuttenbergSchool ofDental Medicine

Adopt shared principlesfrom http://www.obofoundry.org/wiki/index.php/Category:Accepted

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Alan RuttenbergSchool ofDental Medicine

Links• http://www.w3.org/TR/webarch/ • http://www.w3.org/wiki/AwwswHome• http://www.ietf.org/rfc/rfc2396.txt to be superseded by

http://tools.ietf.org/html/rfc3986 • http://www.w3.org/TR/rdf-mt/• http://www.w3.org/TR/rdf-schema/ • http://www.w3.org/TR/owl2-overview/ • http://www.w3.org/wiki/AwwswHome

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