Controlled vocabularies definition method for bridging formal ontologies development

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Controlled vocabularies definition method for
bridging formal ontologies development

• Paolo Ciccarese, PhD
• Mass General Hospital / Harvard Medical School

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Background
time

• AlzForum http//www.alzforum.org/
• Semantic Web Applications in Neuromedicine SWAN
  http//swan.mindinformatics.org/ SWAN
  Alzheimer http//hypothesis.alzforum.org/
• Science Collaboration Framework SCF
  http//www.sciencecollaboration.org/ StemBook
  http//www.stembook.org/
• HCLSIG Scientific Discourse Task Force
  http//esw.w3.org/topic/HCLSIG/SWANSIOC

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SWAN Ontology Ecosystem
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An example of SWAN content curation
Seeding neuritic plaques from the distance a
possible role for brainstem neurons in the
development of Alzheimer's disease pathology.
Muresan Z, Muresan V
Journal Article
SWAN Curator Gwen Wong, PhD
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Kim hypothesis
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Graph view
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An example of Research Statement
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Relationships between discourse elements
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Life Science Entities - 1
Research Statement
refersTo
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Life Science Entities - 2
Research Statement
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But

• Creating ontologies takes time long time
• Creating ontologies requires skilled knowledge
  engineers and skilled domain experts
• The time needed for developing ontologies is
  influencing the application development
• Is creating ontologies always the optimal
  solution?

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SWAN Additional Annotation - 1
Mechanisms Taxonomy
Research Statement
qualifiedBy
qualifiedBy
Hypothesis
Claim
qualifiedBy
Pathogenic Narrative
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Other Additional Annotation - 2
Nature Reports - Stem Cells Cheat Sheet Nature
Publishing Group
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Need for controlled vocabularies

• Using terms coming from controlled vocabularies
  is a good compromise in the case of high quality
  human curated scientific content
• Maybe we can use controlled vocabularies as an
  easy and incremental method to get to formal
  ontologies

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Requirements

• Controlled vocabularies
• Controlled vocabularies should be easy and fast
  to be defined by not ontologists
• Link the terms to existing (or future) ontologies
  and keep track of provenance/authoring
• OWL-DL but without impacting the reasoning
• Share the vocabularies in RDF format

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Agile definition and mapping

• We dont want users not ontologists to deal
  with classes, properties and restrictions
• Taxonomies are often enough for simple
  classifications and can be defined easily (terms
  definitions)
• We want trained ontologists to figure out how to
  map the terms to existing ontologies (if we have
  resources to do so)

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Possible solution SKOS
The Simple Knowledge Organization System provides
a model for expressing the basic structure and
content of concept schemes such as thesauri,
classification schemes, subject heading lists,
taxonomies, folksonomies, and other similar types
of controlled vocabulary.
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How to refer to formal ontologies?
?
?
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An example
er
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Mapping to formal ontology
ltskosConcept rdfabout"stemcellcheatsheethsc"gt
ltskosprefLabelgtHSClt/skosprefLabelgt
ltskosdefinitiongtHaematopoietic stem cells
(blood-forming stem cells that reside in bone
marrow)lt/skosdefinitiongt ltskosbroader
rdfresource"stemcellcheatsheetcell"/gt
lt!-- Mapping --gt ltqualifiersexactMeaninggt
ltqualifiersMeaninggt
ltqualifiersmeaningURI
rdfresource"http//purl.org/obo/owl/CLCL_000003
7"/gt lt!-- hematopoietic stem cell --gt
ltdctermspublisher rdfresource"http//swan.
mindinformatics.org/"/gt
ltdctermscreated rdfdatatype"xsddateTime"gt2009
-01-28T0000000500lt/dctermscreatedgt
ltdctermsissuedgt2009-01-29T1000000500lt/d
ctermsissuedgt ltpavcuratedBy
rdfresource"http//swan.mindinformatics.org/peop
le/tim-clark/"/gt
ltdctermscreatorgt
ltfoafPerson rdfabout"http//www.hcklab.org/peop
le/pc/"gt ltfoafnamegtPaolo
Ciccareselt/foafnamegt
lt/foafPersongt lt/dctermscreatorgt
ltqualifiersMeaninggt
lt/qualifiersexactMeaninggt lt/skosConceptgt
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Meaning Of A Tag (MOAT) - 1
ltmoatTag rdfabout"http//tags.moat-project.org/
tag/apple"gt ltmoatnamegtlt!CDATAapplegtlt/moat
namegt ltmoathasMeaninggt
ltmoatMeaninggt ltmoatmeaningURI
rdfresource"http//dbpedia.org/resource/Apple_Re
cords"/gt ltfoafmaker
rdfresource"http//apassant.net/alex"/gt
ltfoafmaker rdfresource"http//example.org/u
ser/foaf/1"/gt lt/moatMeaninggt
lt/moathasMeaninggt ltmoathasMeaninggt
ltmoatMeaninggt ltmoatmeaningURI
rdfresource"http//dbpedia.org/resource/Apple"/gt
ltfoafmaker rdfresource"http//exam
ple.org/user/foaf/1"/gt lt/moatMeaninggt
lt/moathasMeaninggt ltmoathasMeaninggt
ltmoatMeaninggt ltmoatmeaningURI
rdfresource"http//dbpedia.org/resource/Apple_In
c."/gt ltfoafmaker rdfresource"http/
/apassant.net/alex"/gt lt/moatMeaninggt
lt/moathasMeaninggt lt/moatTaggt
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Meaning Of A Tag (MOAT) - 2
lttagRestrictedTagginggt lttagtaggedResource
rdfresource"http//example.org/post/1"/gt
ltfoafmaker rdfresource"http//apassant.net/alex
"/gt lttagassociatedTag rdfresource"http//tags
.moat-project.org/tag/apple"/gt ltmoattagMeaning
rdfresource"http//dbpedia.org/resource/Apple_Re
cords"/gt lt/tagRestrictedTagginggt
http//moat-project.org/
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Alignment with MOAT
Meaning
moatMeaning
qualifiersMeaning
range
hasMeaning
domain
moathasMeaning
qualifiershasExactMeaning
meaningURI
moatmeaningURI
qualifiersmeaningURI
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Conclusions

• Easy to implement (also at application level)
• OWL-DL (with OWL2 - punning)
• Provenance
• Mapping to existing ontologies
• Doesnt change reasoning (unless we post-process
  the annotation)
• Aligned with MOAT

• Introduces a level of complexity (but we can
  always post-process the annotation)