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Overview of Linking Open Drug Data

practical drug knowledge in a semantic environment.


Eric Prud'hommeaux, Sanitation Engineer.
Last modified: $Date: 2010/08/23 14:05:45 $
Creative Commons License This work is licensed under a Creative Commons Attribution 3.0 License, with attribution to W3C.

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outline

LODD (who)

LODD (what)

drug knowledge

  @prefix : <http://rdf.farmbio.uu.se/chembl/onto/#> .
  act:a108377 :onAssay ass:a50464 . ass:a50464 :hasTarget p:t53 . p:t53 :hasKeyword "Isomerase" .
  act:a108377 :extractedFrom rsc:r6368 . rsc:r6368 bibo:pmid	pubmed:15125947 .
  act:a108377 :forMolecule mol:m258506 . mol:m258506 bo:smiles "COC(=O)[C@@H]1C[C@@H](CN1)NCc2n[nH]c3cccc(OCc4ccc(cc4)C(C)(C)C)c23" .
  act:a108377 :standardUnits "ug mL-1" .

Semantic Web advantages

extensibility

@prefix edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix galen: <http://www.co-ode.org/ontologies/galen#> .
@prefix snomed: <http://termhost.example/SNOMED/> .

<encounter7> edns:patient <patient3> ;
             edns:screeningBP <s20090714c> .
<patient3>   r:type galen:Patient ;
             foaf:family_name "Levin" ;
             foaf:firstName "Henry" .
<s20090714c> dc:date "2009-07-14T18:23"^^xsd:dateTime ;
             edns:systolic "132"^^edns:mmHg ;
             edns:diastolic "86"^^edns:mmHg .
             

extensibility example:

@prefix edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix galen: <http://www.co-ode.org/ontologies/galen#> .
@prefix snomed: <http://termhost.example/SNOMED/> .

<encounter7> edns:patient <patient3> ;
             edns:screeningBP <s20090714c> .
<patient3>   r:type galen:Patient ;
             foaf:family_name "Levin" ;
             foaf:firstName "Henry" .
<s20090714c> dc:date "2009-07-14T18:23"^^xsd:dateTime ;
             edns:systolic "132"^^edns:mmHg ;
             edns:diastolic "86"^^edns:mmHg ;
             edns:posture snomed:_163035008 . # SNOMED:sitting

semantic ecosystem (layer cake)

semantic ecosystem (layer cake)

advantages of LOD

advantages of LOD

"mashups" as declarative queries

SERVICE <http://uu3.org:8888/7tm_receptors>
  {
    ?iuphar  iface:family      ?family .
    ?iuphar  iface:code	       ?code .
    ?iuphar  iface:iupharName  ?iupharNm .
    ?human   iface:iuphar      ?iuphar .
    ?human   iface:geneName    "GABBR1" .
    ?human   iface:entrezGene  ?humanEntrez .
  }
SERVICE <http://dbpedia.org/sparql?default-graph-uri=http%3A%2F%2Fdbpedia.org&should-sponge=&>

  {
     _:gene  dbp:entrezgene    ?humanEntrez ;
             rdfs:label        ?label ;
    FILTER (lang(?label) = "en")
  }
GRAPH <http://hcls.deri.org/atag/data/gabab_example.html>
  {
     ?topic  rdfs:label        ?label .
     ?post   sioc:topic        ?topic
  }

confidence of interpretation

@prefix edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix galen: <http://www.co-ode.org/ontologies/galen#> .
@prefix snomed: <http://termhost.example/SNOMED/> .

<encounter7> edns:patient <patient3> ;
             edns:screeningBP <s20090714c> .
<patient3>   r:type galen:Patient ;
             foaf:family_name "Levin" ;
             foaf:firstName "Henry" .
<s20090714c> dc:date "2009-07-14T18:23"^^xsd:dateTime ;
             edns:systolic "132"^^edns:mmHg ;
             edns:diastolic "86"^^edns:mmHg ;
             edns:posture snomed:_163035008 . # SNOMED:sitting

emergency room blood pressure query

PREFIX edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX galen: <http://www.co-ode.org/ontologies/galen#>
PREFIX snomed: <http://termhost.example/SNOMED/>

SELECT ?date ?systolic ?diastolic WHERE {

?encounter edns:patient     ?patient ;
           edns:screeningBP ?screenBP .
?patient   foaf:family_name "Levin" ;
           foaf:firstName   "Henry" .
?screenBP  dc:date          ?date ;
           edns:systolic    ?systolic ;
           edns:diastolic   ?diastolic ;
} ORDER DESC BY ?date

clinical study blood pressure query (fussy)

PREFIX edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX galen: <http://www.co-ode.org/ontologies/galen#>
PREFIX snomed: <http://termhost.example/SNOMED/>

SELECT ?date ?systolic ?diastolic WHERE {

?encounter edns:patient     ?patient ;
           edns:screeningBP ?screenBP .
?patient   foaf:family_name "Levin" ;
           foaf:firstName   "Henry" .
?screenBP  dc:date          ?date ;
           edns:systolic    ?systolic ;
           edns:diastolic   ?diastolic ;
           edns:posture ?posture . 
FILTER (?posture = snomed:_163035008 || ?posture = snomed:_163035009)
} ORDER DESC BY ?date

clinical study blood pressure query (details)

PREFIX edns: <http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX galen: <http://www.co-ode.org/ontologies/galen#>
PREFIX snomed: <http://termhost.example/SNOMED/>

SELECT ?date ?systolic ?diastolic ?posture WHERE {

?encounter edns:patient     ?patient ;
           edns:screeningBP ?screenBP .
?patient   foaf:family_name "Levin" ;
           foaf:firstName   "Henry" .
?screenBP  dc:date          ?date ;
           edns:systolic    ?systolic ;
           edns:diastolic   ?diastolic .
  OPTIONAL {
    ?screenBP  edns:posture ?posture .
  }
} ORDER DESC BY ?date

process

disambiguation

X is a drug. What's that mean?

common identifiers

How do people talk about the same thing?

schmema design

What entities do these identifiers identify?

What are the relationships between these entities?

timeline

how long does this take?

business view

What capitol incentives are there for maintenance/improvement?

Entogen

provides interface to LODD

best practices

Best Practices: Mapping Experimental Data to RDF

wrap-up

questions?

additional RDF slides:

LeeF's tutorial

LeeF's SPARQL tutorial on Semantic Universe

Query #2: Multiple triple patterns: property retrieval

Find me all the people in Tim Berners-Lee's FOAF file that have names and email addresses. Return each person's URI, name, and email address.
PREFIX foaf:  <http://xmlns.com/foaf/0.1/>
SELECT *
WHERE {
    ?person foaf:name ?name .
    ?person foaf:mbox ?email .
}
        
  • We can use multiple triple patterns to retrieve multiple properties about a particular resource
  • Shortcut: SELECT * selects all variables mentioned in the query
  • Dataset: http://www.w3.org/People/Berners-Lee/card

Try it with HP's ARQ, OpenLink's Virtuoso, or Redland's Rasqal. (Expected results.)

Inference

Rules

Rules Interchange Format (RIF)

XML data

<?xml version="1.0"?>
<ClinicalDocument transformation="hl7-rim-to-pomr.xslt">
  <recordTarget>
    <patientRole>
      <patientPatient>
	<name>
	  <given>Henry</given>
	  <family>Levin</family>
	</name>
	<administrativeGenderCode code="M"/>
	<birthTime value="19320924"/>
      </patientPatient>
    </patientRole>
  </recordTarget>
  <component>
    <StructuredBody>
      <Observation>
	<code displayName="Cuff blood pressure"/>
	<effectiveTime value="200004071430"/>
	<targetSiteCode displayName="Left arm"/>
	<entryRelationship typeCode="COMP">
	  <Observation>
	    <effectiveTime value="200004071530"/>
	    <value value="132" unit="mm[Hg]"/>
	  </Observation>
	</entryRelationship>
      </Observation>
      <Observation>
	<code displayName="Cuff blood pressure"/>
	<effectiveTime value="200004071530"/>
	<targetSiteCode displayName="Left arm"/>
	<entryRelationship typeCode="COMP">
	  <Observation>
	    <code displayName="Systolic BP"/>
	    <effectiveTime value="200004071530"/>
	    <value value="135" unit="mm[Hg]"/>
	  </Observation>
	</entryRelationship>
	<entryRelationship typeCode="COMP">
	  <Observation>
	    <code displayName="Diastolic BP"/>
	    <effectiveTime value="200004071530"/>
	    <value value="88" unit="mm[Hg]"/>
	  </Observation>
	</entryRelationship>
      </Observation>
    </StructuredBody>
  </component>
</ClinicalDocument>

Mapped to RDF

[unrendered SVG image of HL7 data in RDF]

Relational data …

[unrendered SVG image of HL7 data in a relational database]

… as a graph.

[unrendered SVG image of HL7 data in RDF]

Using Existing Data(bases)

[unrendered SVG image of HL7 data in RDF]

[unrendered SVG image of HL7 data in RDF]

Using Existing Data(bases)

[unrendered SVG image of HL7 data in RDF]

[unrendered SVG image of HL7 data in RDF]

Using Existing Data(bases)

[unrendered SVG image of HL7 data in RDF]

[unrendered SVG image of HL7 data in RDF]

Using Existing Data(bases)

[unrendered SVG image of HL7 data in RDF]

[unrendered SVG image of HL7 data in RDF]

Using Existing Data(bases)

[unrendered SVG image of HL7 data in RDF]

[unrendered SVG image of HL7 data in RDF]

Using Existing Data(bases)

[unrendered SVG image of HL7 data in RDF]

[unrendered SVG image of HL7 data in RDF]