Keep the complexity. Simplify with SKOS.James Morris

Information Architect

• The Working Taxonomist and the need for reusing terms in a vocabulary network.

• The Semantic Web to the rescue!– SKOS: Yeah!– OWL: uh oh!

• The false either/or. – SKOS: too simple! – OWL: too complicated!

• The Semantic Web is designed to allow for both the sophistication of OWL and the practicality of SKOS to coexist.

• Here’s how.

Overview

Working Taxonomist

SNOMED-CT

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Working Taxonomist

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Preferred Name: Cisplatin

A drug used to treat many types of cancer. Cisplatin contains the metal platinum. It kills cancer cells by damaging their DNA and stopping them from dividing. Cisplatin is a type of alkylating agent.

AbiplatinBlastolemBriplatinCDDPCis-diammine-dichloroplatinumCis-platinumCis-platinum II Diamine DichlorideCismaplatCisplatinaCisplatinumCisplatylCitoplatinoCysplatynaDDPLederplatinMetaplatinNeoplatinPeyrone's ChloridePlacisPlastistilPlataminePlatiblastinPlatinexPlatinolPlatinol-AQ

Working Taxonomist

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Working Taxonomist

Cisplatin

A drug used to treat many types of cancer. Cisplatin contains the metal platinum. It kills cancer cells by damaging their DNA and stopping them from dividing. Cisplatin is a type of alkylating agent.

Cismaplat

Lederplatin

WHAT’S WRONG WITH THIS PICTURE?

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Working Taxonomist

SNOMED-CT

Dragging and Dropping!

Cutting and Pasting!

Copying! Duplicating!

Stop the insanity! Build!

Semantic Web—a solution?

SKOS…provides a means for representing knowledge organization systems (including controlled vocabularies, thesauri, taxonomies, and folksonomies) in a distributed and linkable way.

SKOS vocabularies provide a cornerstone for linking information on the web. … Publishing vocabularies in SKOS allows the concepts they define to be referenced on a global scale.”

“

Remember: The “S” is for Simple!

SKOS in a nutshell

skos:definition

skos:prefLabel

skos:altLabel

skos:broader

skos:broader

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SKOS in a nutshell

ncit:C2901 a skos:Concept .

ncit:C2901 skos:prefLabel “Bladder Neoplasm” .

ncit:C2901 skos:altLabel “Tumor of Bladder”, “Urinary Bladder Tumor” .

ncit:C2901 skos:definition “A benign or malignant…” .

ncit:C2901 skos:broader ncit:C2900 .

ncit:C2901 skos:broader ncit:C3431 .

Written in code, it would look like this

Simple. Not complicated.

Semantic Web—a solution?

PROBLEM SOLVED!!

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Linking Open Data cloud diagram 2014, by Max Schmachtenberg, Christian Bizer, Anja Jentzsch and Richard Cyganiak. http://lod-cloud.net/

Semantic Web—a solution?

Where are the biomedical SKOS vocabularies?

1. Semantic Web is about more than just Taxonomies.

2. Biomedical Ontologies are using the Semantic Web the model the processes of life and OWL provides that framework.

3. OWL allows you model anything. SKOS explicitly models taxonomies and thesauri.

4. To the Working Taxonomist trying to improve search, navigation, document management and build KM solutions, OWL is very complicated.

Semantic Web – what I learned

Semantic Web—too complicated?

ncit:C2901 a owl:Thing .

ncit:C2901 rdfs:label “Bladder Neoplasm” .

ncit:C2901 ncit:FULL_SYN “Tumor of Bladder”, “Urinary Bladder Tumor” .

ncit:C2901 ncit:DEFINITION “A benign or malignant…” .

ncit:C2901 owl:equivalentClass

[ rdf:type owl:Class ; owl:intersectionOf (ncit:C2900 ncit:C3431)] .

“Bladder Neoplasm” as represented in OWL.

What happened to the hierarchy?

Semantic Web—too complicated?

ncit:C2900

ncit:C2901

ncit:C3431

owl:equivalentClass

owl:intersectionOf

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“Bladder Neoplasm”

“Bladder Disorder”“Urinary System Neoplasm”

ncit:C2901 owl:equivalentClass

[ rdf:type owl:Class ; owl:intersectionOf (ncit:C2900 ncit:C3431)] .

Semantic Web—too complicated?

ncit:C2901 owl:equivalentClass

[ rdf:type owl:Class ; owl:intersectionOf (ncit:C2900 ncit:C3431)] .

This is the challenge. The NCI OWL file represents the “hierarchy” like this:

ncit:C2901 skos:broader ncit:C2900 .

ncit:C2901 skos:broader ncit:C3431 .

When, as a Working Taxonomist, all I need to represent is this:

• Biomedical ontologies are modeled to describe scientific entities with enough detail so that machines can make accurate inferences.

• OWL is needed for that level of sophistication. How OWL is used can vary greatly, even within the same knowledge domain.

• SKOS is only modeling terminology for the practical application in knowledge management systems (the way taxonomies have always been used). SKOS vocabularies can be used interchangeably.

• OWL helps machines understand information. SKOS helps humans interact with information.

OWL vs SKOS – either/or?

OWL and SKOS – both/and

Q: Can we use the Semantic Web to allow the sophisticated OWL modeling of the NCI Thesaurus, but still have our hierarchy of terms and term properties in SKOS?

A: Yes! It’s built into the fundamentals of the Semantic Web.

Build!

ncit:C2901 owl:equivalentClass

[ rdf:type owl:Class ; owl:intersectionOf (ncit:C2900 ncit:C3431)] .

ncit:C2901 skos:broader ncit:C2900 .

ncit:C2901 skos:broader ncit:C3431 .

OWL and SKOS – both/and

CONSTRUCT {?concept skos:broader ?parent .}WHERE {?concept owl:equivalentClass [a owl:Class ;

owl:intersectionOf [rdf:rest*/rdf:first

?parent]]}

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This:

Takes OWL:

Creates SKOS:

OWL and SKOS – both/and

ncit:C2900

ncit:C2901

ncit:C3431

owl:equivalentClass

owl:intersectionOf

Build!

this OWL:

Graphically, our code will take…

“Bladder Neoplasm”

“Bladder Disorder”“Urinary System Neoplasm”

OWL and SKOS – both/and

ncit:C2900

ncit:C2901

ncit:C3431

Build!

skos:broaderskos:broader

this SKOS:

…and create

“Bladder Neoplasm”

“Bladder Disorder”“Urinary System Neoplasm”

• Sophisticated ontologies that use OWL are necessary for certain disciplines and applications.

• We can leverage the basics from these ontologies to create SKOS properties. – The capability to built into the Semantic Web.– It does not have to change, convert, or otherwise

manipulate the original ontology.– Publishers of ontologies can do this, too.

• We’re just making them more useful to the Working Taxonomist.

Bottom line

SMARTLOGIC – AMERICAS560 S. WINCHESTER BLVD, SUITE 500SAN JOSE, CALIFORNIA, 95128TEL: 408 213 9500FAX: 408 572 5601 SMARTLOGIC – EUROPE, MIDDLE-EAST AND AFRICA14 GREVILLE STREETLONDON, EC1N 8SBTEL: +44 (0)203 176 4500FAX: +44 (0)207 785 7014

WWW.SMARTLOGIC.COMINFO@SMARTLOGIC.COM © 2014 SMARTLOGIC SEMAPHORE LIMITED 

Thank you! James Morris

james.morris@smartlogic.com

@jamesraymorris

Acknowledgements:

• My SmartLogic colleagues, especially Matthieu Jonglez, Anne Lapkin, Evelyn Kent, and Stuart Laurie.

• My early Semantic Web mentors: Dean Allemang, Bob Ducharme, Tom Plasterer, and Kerstin Forsberg.

• The Special Libraries Association Taxonomy Community of Practice.

• The American Library Association’s Linked Library Data Interest Group, especially Theodore Gerontakos and Sarah Quimby.

Thank you!

Extra Slides…

SKOS in a nutshell

“Bladder Neoplasm” “Tumor of Bladder”

ncit:C2900

ncit:C2901

ncit:C2900

skos:definition

“ A benign or malignant, primary or metastatic neoplasm of the bladder.”

skos:prefLabel

“Bladder Disorder”“Urinary System Neoplasm”

skos:prefLabel

skos:altLabelskos:prefLabel

skos:broaderskos:broader

“Urinary Bladder Tumor”

Build!

Semantic Web—too complicated?

ncit:C2900

ncit:C2901

ncit:C3431

rdfs:label

“Bladder Neoplasm”

ncit:FULL_SYN

“Urinary Bladder Tumor”

ncit:DEFINITION

“ A benign or malignant, primary or metastatic neoplasm of the bladder.”

“Tumor of Bladder”

owl:equivalentClass

owl:intersectionOf

rdfs:label

“Bladder Disorder”“Urinary SystemNeoplasm”

rdfs:label

Build!