HCLS KB and OWL

A Knowledgebase for Neuroscience

Built by the HCLS BioRDF task force.

Eric Prud'hommeaux

Groups/Sets/Classes

[Named] collections of things with similar attributes.

Groups/Sets/Classes

[Named] collections of things with similar attributes.

Groups/Sets/Classes

[Named] collections of things with similar attributes.

OWL Expressivity

Allows you to define classes.

courtesy: Fabien Gandon

Algabraic Properties

• transitiveProperty:
  • :Bob :worksFor :Sue .
  • :Sue :worksFor :Tom .
  • :worksFor a owl:TransitiveProperty .
  • ⇒ :Bob :worksFor :Tom .
• inverseProperty:
  • :hasChild owl:inverseOf :hasParent .
• reflexiveProperty:
  • :friendOf a owl:SymmetricProperty.

Uses

• Type inference.
  • :Bob a :MGHcharlesStOncologist .
• Identity inference.
  • merge the :Bob and :BobSmith nodes.
• Consitency rules.
  • An :MGHcharlstStPatient
    • is an :MGHpatient.
    • has a :physician of type (:MGHcharlesStOncologist or :MGHcharlesStOptician or ...).
    • has an MGH Charles Street consent form.

OWL type inference

• onProperty
  • :fluffy :hasChild :fluffyPrime .
  • :fluffyPrime a :kitten.
  • ⇒ :fluffy a :cat .

OWL identity inference

• functionalPropery
  • :Bob :hasChild :Sue .
  • :BobSmith :hasChild :sue .
  • :hasChild a owl:FunctionalProperty .
  • ⇒ :Bob is the same as :BobSmith
• InverseFunctionalPropery
  • :Bob foaf:mbox <mailto:bobS@foo.example> .
  • :BobSmith foaf:mbox <mailto:bobS@foo.example> .
  • foaf:mbox a owl:InverseFunctionalProperty .
  • ⇒ :Bob is the same as :BobSmith

Cardinality

cardinality constraints

• :patientEncounter5 :patient :Bob .
• :patientEncounter5 :patient :BobSmith .
• :patient owl:maxCardinality 1 .
• ⇒ :Bob is the same as :BobSmith

OWL consistency rules

• An :MGHcharlstStPatient
  • is an :MGHpatient.
  • has one :physician of type (:MGHcharlesStOncologist or :MGHcharlesStOptician or ...).
  • has an MGH Charles Street consent form.
• Avoid unstated assumptions.

"Validation" is tricky

• • _:patientX :physician _:physY
    _:physY a :MGHcharlesStOncologist
  • _:patientX :physician _:physZ
    _:physZ a :MGHcharlesStOpticiaMn
  • ⇒ :MGHcharlesStOncologist is the same as :MGHcharlesStOptician
• use disjointWith to assert that the class of :MGHcharlesStOncologists has different members than the the class :MGHcharlesStOpticians
• (use differentFrom to assert that :MGHcharlesStOncologist7 is not the same as :MGHcharlesStOptician3)

OWL expression

• An :MGHcharlstStPatient is an :MGHpatient who has one :physician of type (:MGHcharlesStOncologist or :MGHcharlesStOptician or ...)
• Manchester syntax:

    (:SubClassOf :MGHcharlstStPatient)
  AND
    (:physician ONLYSOME (
        :MGHcharlesStOncologist, 
        :MGHcharlesStOptician))

• ...

OWL expression

• ...
• Manchester syntax:

    (:SubClassOf :MGHcharlstStPatient)
  AND
    (:physician ONLYSOME (
        :MGHcharlesStOncologist, 
        :MGHcharlesStOptician))

• Abstract syntax

  Class(a:MGHcharlstStPatient partial a:MGHpatient)
  Class(a:MGHcharlstStPatient complete 
      restriction(a:physician
          allValuesFrom(unionOf(a:MGHcharlesStOncologist a:MGHcharlesStOptician))))

• ...

OWL expression

• ...
• Abstract syntax

  Class(a:MGHcharlstStPatient partial a:MGHpatient)
  Class(a:MGHcharlstStPatient complete 
      restriction(a:physician
          allValuesFrom(unionOf(a:MGHcharlesStOncologist a:MGHcharlesStOptician))))

• RDF syntax:

  _:MCSO rdfs:subClassOf :MGHpatient .
  _:MCSO rdfs:subClassOf _:physType .
  _:physType owl:onProperty :physician .
  _:physType owl:allValuesFrom ( :MGHcharlesStOncologist :MGHcharlesStOptician ).
  _:MCSO owl:equivalentClass :MGHcharlstStPatient .

• ...

OWL expression

• ...
• RDF syntax:

  _:MCSO rdfs:subClassOf :MGHpatient .
  _:MCSO rdfs:subClassOf _:physType .
  _:physType owl:onProperty :physician .
  _:physType owl:allValuesFrom _:list1 .
  _:list1 rdf:first :MGHcharlesStOncologist .
  _:list1 rdf:rest _:list2 .
  _:list2 rdf:first :MGHcharlesStOptician .
  _:list2 rdf:rest rdf:nil .
  _:MCSO owl:equivalentClass :MGHcharlstStPatient .

OWL restrictions

• _:physType a owl:Restriction .
• _:physType owl:onProperty :physician .
• _:physType owl:allValuesFrom _:anotherRestriction .

HCLS KB flagship query

An article with PubMed id 10698743 mentions ncbi_gene:1812 and that the corresponding PubMed record has a MeSH term mesh:D017966:

HCLS KB flagship query

A set of genes or gene products in human bodies are described by ncbi_gene:1812. Here, we call this set _:equiv1812.

HCLS KB flagship query

bySequence:ncbi_gene.1812 has the same members as the class _:equiv1812:

HCLS KB flagship query

Adenylate cyclase activation, go:GO_0007190, is part of signal transduction, go:GO_0007166.
_:activateAdenylCyclase is the class of functions that are realized_as adenylate cyclase activation:

@@OWL for Abox reasoning

_:molecularSignalers_1 is defined by the ability to activate adenyl cyclase:

HCLS KB flagship query

The class of proteins in the intersection of _:signalingParticipants_1 and bySequence:ncbi_gene.1812 is here abbreviated protein:p1812_7190_1, though the actual identifier is protein:product_of_ncbi_gene.1812_that_participates_in_
...GO_0007190_fbc49f20524727a24c7b7effa29bad4a:

HCLS KB flagship query

ncbi_gene:1812 and go:GO_0007190 have human-readable labels.

HCLS KB flagship query

try it (or try the tiny URL for the query)

prefix go: <http://purl.org/obo/owl/GO#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix mesh: <http://purl.org/commons/record/mesh/>
prefix sc: <http://purl.org/science/owl/sciencecommons/>
prefix ro: <http://www.obofoundry.org/ro/ro.owl#>
prefix senselab: <http://purl.org/ycmi/senselab/neuron_ontology.owl#>
prefix obo: <http://purl.org/obo/owl/obo#>

SELECT ?genename ?processname ?receptor_protein_name

WHERE {
  # PubMeSH includes ?gene_records mentioned in ?articles which are identified by pmid in ?pubmed_records .
GRAPH <http://purl.org/commons/hcls/pubmesh> {
  ?pubmed_record sc:has-as-minor-mesh mesh:D017966 .
  ?article sc:identified_by_pmid ?pubmed_record .
  ?gene_record sc:describes_gene_or_gene_product_mentioned_by ?article
}

  # The Gene Ontology asserts that foreach ?protein, ?protein ro:has_function [ ro:realized_as ?process ].
GRAPH <http://purl.org/commons/hcls/goa> {
  ?protein rdfs:subClassOf ?restriction1 .
  ?restriction1 owl:onProperty ro:has_function .
  ?restriction1 owl:someValuesFrom ?restriction2 .
  ?restriction2 owl:onProperty ro:realized_as .
  ?restriction2 owl:someValuesFrom ?process .
  # Also, foreach ?protein, ?protein has a parent class which is linked by some predicate to ?gene_record.
  ?protein rdfs:subClassOf ?protein_superclass .
  ?protein_superclass owl:equivalentClass ?restriction3 .
  ?restriction3 owl:onProperty sc:is_protein_gene_product_of_dna_described_by .
  ?restriction3 owl:hasValue ?gene_record .
  # Each ?process (that we are interested in) is a subclass of the signal transduction process.
  # @@ nested graph constraint
  GRAPH <http://purl.org/commons/hcls/20070416/classrelations> {
      { ?process obo:part_of go:GO_0007166 }
    UNION
      { ?process rdfs:subClassOf go:GO_0007166 }
  }
}

GRAPH <http://purl.org/commons/hcls/gene> {
  ?gene_record rdfs:label ?genename
}

GRAPH <http://purl.org/commons/hcls/20070416> {
  ?process rdfs:label ?processname
}}

OWL restriction expressivity

• PARTIAL — This restriction is a necessary condition for this class.
• COMPLETE — This restriction completely defines the extent of this class.
• AND — This restriction requires both things to be true.
• OR — This restriction requires either thing to be true.
• ALL — The values of some property must all be in some set.
• SOME — Some of the values of a property must be in some set.

OWL Resources

• W3C OWL Guide and Specifications
• Manchester OWL Syntax (PDF)
• OWL 1.1 Working Group - currently working on a new version of OWL
• OWL Reasoner List - community maintained list of open-source and commercial OWL tools

Wrap up

Is this a coherent picture?

• Does the Semantic Web meet our needs?
• Data sharing ...
• Data protection ...

Policy/Security

• SW data can be private data
• using interrop standards helps companies
  • communicate internall
  • communicate with partners
• web authentication for the simple access rules
• federated policy language for the complex interactions
• location-based policy languages during clinical acquisition
• n.b. PLING use cases @@and add one

Is this a coherent picture?

• Does the Semantic Web meet our needs?
• Data sharing ...
• Data protection ...
• Scalability

Semantic Web Scalability

• allows anyone can invent unambiguous terms
• provides tools to stitch together with rest of SW for best data re-use
• most data use requires no inference
• use inference when you need

Is this a coherent picture?

• Does the Semantic Web meet our needs?
• Data sharing ...
• Data protection ...
• Scalability
• Expressivity