medicalcniformatisgroup i indexes, topic maps & the semantic net dr jeremy rogers mrcgp clinical...
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Indexes, Topic maps Indexes, Topic maps
& the semantic & the semantic netnetDr Jeremy Rogers MRCGPDr Jeremy Rogers MRCGP
Clinical Research FellowClinical Research Fellow
Medical Informatics GroupMedical Informatics Group
University of ManchesterUniversity of Manchester
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OutlineOutline
What’s an Index ?What’s a Topic Map ?
UsesStrengths & Weaknesses
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What’s in an index ?What’s in an index ?La Bohème, 10, 70, 197-198, 326 Cavalleria Rusticana, 71, 203-204 The Girl of the Golden West, see La fanciulla del West Leoncavallo, Ruggiero
I Pagliacci, 71-72, 122, 247-249, 326 Madama Butterfly, 70-71, 234-236, 326 Manon Lescaut, 294 Mascagni, Pietro
Cavalleria Rusticana, 71, 203-204 Puccini, Giacomo, 69-71
La Bohème, 10, 70, 197-198, 326 La fanciulla del West, 291
Madama Butterfly, 70-71, 234-236, 326 Manon Lescaut, 294 Tosca, 26, 70, 274-276, 326 Turandot, 70, 282-284, 326 Rustic Chivalry, see Cavalleria Rusticana singers, 39-52, See also individual names
baritone, 46 bass, 46-47 soprano, 41-42, 337 tenor, 44-45
soprano, 41-42, 337 tenors, 44-45 Tosca, 26, 70, 274-276, 326 Turandot, 70, 282-284, 326
different different typestypes of topic (the names of of topic (the names of operas are shown operas are shown in italicin italic))
different different typestypes of occurrence of occurrence (references to synopses are (references to synopses are in boldin bold))
synonyms for the same topicsynonyms for the same topic
links to associated topics (links to associated topics (see alsosee also))
associations between different topics associations between different topics (e.g. between a composer and his (e.g. between a composer and his works)works)
supertype and subtype informationsupertype and subtype information
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What’s a topic map ?What’s a topic map ?
• Very similar to an index except…• Implicit information made explicit
– Not represented in typographical conventions
• Consistent use of topics within indexes– Consistent use between indexes ?
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What is a topic map ?What is a topic map ?www.topicmaps.org
http://www.ontopia.net/topicmaps/materials/tao.html
• Means to convey knowledge about resources – Knowledge embodied in a superimposed
layer– A ‘map’ of the resources
• Captures – the subjects of which resources speak– the relationships between those subjects– implementation-independent
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What is a Topic Map ?What is a Topic Map ?
The central concepts in topic maps are:
Occurrences e.,g. a physical book, a web page= the page numbers
Associations e.g. ‘is-author-of’= ‘see also’ links
Topics e.g. ‘Shakespeare’, ‘Hamlet’= the list of subjects in an index
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History of Topic MapsHistory of Topic Maps• 1993 first description of topic maps• 2000 ISO/IEC standard 13250:2000
– Used HyTM
• 2001 minor update– To include XTM
• Main protagonists today – (a small but active community)– Ontopia (Oslo)– Techuila (Oxford)– InfoLoom (New York)– TopicMaps.Org
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An example:An example:Subjects OccurencesType
Shakespeare 1
Hamlet 2
Jonson 3
London 4
Stratford 5
Volpone 6
Play 7
Town 8
Associations
Person 9
Topics
An Example in XTM:An Example in XTM:<topic id=“2">
Shakespeare 1
Hamlet 2
Play 7
writtenBy
author
work
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf>
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf><baseName>
<baseNameString>Hamlet, Prince of Denmark</baseNameString>
<baseNameString>The Scottish Play</baseNameString></baseName>
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf><baseName>
<baseNameString>Hamlet, Prince of Denmark</baseNameString>
<baseNameString>The Scottish Play</baseNameString></baseName><occurrence>
<instanceOf><topicRef xlink:href=“#plain-text-format"/>
</instanceOf> <resourceRef xlink:href=“#mybook.hamlet.page101“/>
</occurrence></topic>
<association><instanceOf>
<topicRef xlink:href="#written-by"/></instanceOf>
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf><baseName>
<baseNameString>Hamlet, Prince of Denmark</baseNameString>
<baseNameString>The Scottish Play</baseNameString></baseName><occurrence>
<instanceOf><topicRef xlink:href=“#plain-text-format"/>
</instanceOf> <resourceRef xlink:href=“#mybook.hamlet.page101“/>
</occurrence></topic>
<association><instanceOf>
<topicRef xlink:href="#written-by"/></instanceOf><member>
<roleSpec><topicRef xlink:href="#author"/></roleSpec>
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf><baseName>
<baseNameString>Hamlet, Prince of Denmark</baseNameString>
<baseNameString>The Scottish Play</baseNameString></baseName><occurrence>
<instanceOf><topicRef xlink:href=“#plain-text-format"/>
</instanceOf> <resourceRef xlink:href=“#mybook.hamlet.page101“/>
</occurrence></topic>
<association><instanceOf>
<topicRef xlink:href="#written-by"/></instanceOf><member>
<roleSpec><topicRef xlink:href="#author"/></roleSpec><topicRef xlink:href="#1"/>
</member>
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf><baseName>
<baseNameString>Hamlet, Prince of Denmark</baseNameString>
<baseNameString>The Scottish Play</baseNameString></baseName><occurrence>
<instanceOf><topicRef xlink:href=“#plain-text-format"/>
</instanceOf> <resourceRef xlink:href=“#mybook.hamlet.page101“/>
</occurrence></topic>
<association><instanceOf>
<topicRef xlink:href="#written-by"/></instanceOf><member>
<roleSpec><topicRef xlink:href="#author"/></roleSpec><topicRef xlink:href="#1"/>
</member> <member>
<roleSpec><topicRef xlink:href="#work"/></roleSpec>
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf><baseName>
<baseNameString>Hamlet, Prince of Denmark</baseNameString>
<baseNameString>The Scottish Play</baseNameString></baseName><occurrence>
<instanceOf><topicRef xlink:href=“#plain-text-format"/>
</instanceOf> <resourceRef xlink:href=“#mybook.hamlet.page101“/>
</occurrence></topic>
<topic id=“2"> <instanceOf><topicRef xlink:href="#7"/></instanceOf><baseName>
<baseNameString>Hamlet, Prince of Denmark</baseNameString>
<baseNameString>The Scottish Play</baseNameString></baseName><occurrence>
<instanceOf><topicRef xlink:href=“#plain-text-format"/>
</instanceOf> <resourceRef xlink:href=“#mybook.hamlet.page101“/>
</occurrence></topic>
<association><instanceOf>
<topicRef xlink:href="#written-by"/></instanceOf><member>
<roleSpec><topicRef xlink:href="#author"/></roleSpec><topicRef xlink:href="#1"/>
</member> <member>
<roleSpec><topicRef xlink:href="#work"/></roleSpec><topicRef xlink:href="#2"/>
</member> </association>
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What are they for ?What are they for ?• Indexing large resources you can’t
write in directly– Original ‘back of book index’ motivation
• Organising web sites– Some elements on a web page generated
from topic map• E.g. www.ontopia.net/operamap/
• Expert systems• Way of storing information flows &
audit trails– Or any other network of info, really
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How do I make one ?How do I make one ?• By hand
– Very labour intensive, but usually highest quality– Some tools e.g. Ontopia, TMTab for Protégé,
TMDesigner
• Semi-automagically– If the original data is already well structured– Some language processing tools can help
• Automatic Transformation– Re-write other sources of the same information
• Useful websites– www.ontopia.net– www.techquila.com
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Strengths of Topic Maps…Strengths of Topic Maps…• Good for large or dynamic
information sources– E.g. ‘2001 Tax Products’
CDROM from US IRS– E.g. www.quid.fr
• Better querying than a static index– ‘Find all composers who have
written an opera that was not first performed in Italy but was based on a work originally written by Shakespeare’
• Making it possible/easier to merge knowledge resources– allegedly
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……and limitationsand limitations• Not so good for very large
information sources– E.g. The entire world wide web
(= ‘The Semantic Web’)– The ontology problem
• Different topics used differently • at different times & by different authors
• No inferencing (yet)– E.g. IF Aria sung-in Act I
AND Act I part-of ToscaTHEN Aria sung-in Tosca
• Limitations in what can be said– E.g. Child must have exactly one mother– E.g. Mother of a baby kangaroo must
also be a kangaroo
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Current DevelopmentsCurrent Developments
• Standardising the query language– ISO/IEC 18048 TMQL
• Standardising the constraint language– ISO/IEC 19756 TMCL (based on OWL
?)• “All persons must be born somewhere”• “A person may have died somewhere”
• Experiments with inferencing
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Topic maps vs. semantic Topic maps vs. semantic netsnets
A Semantic Net is any data structure network with nodes representing objects, classes or concepts, and the arcs representing relations between them (e.g.
is-a, part-of etc)
•Therefore, all topic maps are a kind of semantic net
•But not all semantic nets are topic maps– Because richer semantic nets may include e.g. cardinality– Not all semantic nets need external references
•Other kinds of semantic nets:– Mind maps– Entity Relation Diagrams & UML (databases)– Description Logics (ontologies)
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SummarySummary• Topic Maps formalise back of book
indexing– Especially useful for electronic age– Makes the index machine-readable
• Aspirations for more– Usual plans for global domination
• Relatively young– Details still being finalised– Low uptake so far– But key exemplars