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 $

This work is licensed under a Creative Commons Attribution 3.0 License, with attribution to W3C.

outline

what/who is LODD?
drug knowledge
Semantic Web advantages
confident interpretation
business view

LODD (who)

task force in W3C's
Semantic Web in Health Care and Life Sciences interest group
14 participants from 13 organizations
8 academia
Freie Universitat Berlin, University of Amsterdam, Carleton University, University of Toronto, DERI, University of Oxford, Uppsala University, Stony Brook University School of Medicine
2 industry
Johnson & Johnson, AZ
3 other orgs
W3C, NIST, National Research Council Canada

LODD (what)

8 million triples
370,000 links
10 datasets
DrugBank LinkedCT DailyMed DBpedia Diseasome RDF-TCM RxNorm SIDER STITCH Medicare ChEMBL
that we know of

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

schema discovery
scales like the web
familiar maintenance
confidence of interpretation

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)

RDF - graph model
RDFS - subClassOf, domain
OWL - sameAs
RIF - if foo then bar
SKOS - friend broaderThan gooodFriend

semantic ecosystem (layer cake)

RDF - graph model
RDFS - subClassOf, domain
OWL - sameAs
RIF - if foo then bar
SKOS - friend broaderThan gooodFriend

advantages of LOD

schema discovery
scales like the web
familiar maintenance
confidence of interpretation
data discovery (browsability)
maintenance/diagnostic tools
"mashups" as declarative queries
take advantage of the layer cake

advantages of LOD

schema discovery
scales like the web
familiar maintenance
confidence of interpretation
data discovery (browsability)
maintenance/diagnostic tools
"mashups" as declarative queries
take advantage of the layer cake

"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

data selection (use cases)
license evaluation
disambiguation
common identifiers
schema design

disambiguation

X is a drug. What's that mean?

compositional: active ingredient, compound
structural: delivery mechanism
naming: generic name, brand name (locality)

common identifiers

How do people talk about the same thing?

InChI
SMILES
DrugBank
ChEBI

schmema design

What entities do these identifiers identify?

What are the relationships between these entities?

?activity extractedFrom ?resource .
?resource pubmedID ?ID .
?activity onAssay ?assay .
?assay hasTarget ?protein .
?protein hasKeyword "blah" .
?activity forMolecule ?molecule .
?molecule smiles "COC(=O)..." .

timeline

how long does this take?

Oct 2008 examined candidate datasets
diseasome, drugbank, dailymed
March 2009 LODD paper
Sept 2009 won itriplification challenge
more databases...
best practices document
Oct 2010 - Allen Brain Atlas

business view

What capitol incentives are there for maintenance/improvement?

research: pharmaceuticals
safety/efficacy: govornment, clinics
Entogen built a business on LODD

Entogen

provides interface to LODD

awaiting Allen Brain Atlas

best practices

Best Practices: Mapping Experimental Data to RDF

low hanging fruit
tooling
ontology re-use
identifiers
exploitation

wrap-up

questions?

additional RDF slides:

LeeF's tutorial

LeeF's SPARQL tutorial on Semantic Universe

comprehensive tutorial
working examples
useful resources

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

SemWeb designed for inference.
Use sparingly.
Standards encourage semantic interoperability.

Rules

IF (X subClassOf Y && Y subClassOf Z) THEN (X subClassOf Z).
IF (X subClassOf Y && Y subClassOf Z) THEN (AC32E5B7C9963E).
Pattern expressivity:
- logical connectives: AND, OR, NOT
- quantifiers: forall, forsome
- restrictions: (FILTERs)
- term construction

Rules Interchange Format (RIF)

IF (X subClassOf Y && Y subClassOf Z) THEN (X subClassOf Z).
IF (X subClassOf Y && Y subClassOf Z) THEN (AC32E5B7C9963E).
XML format.

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>

Patient history
- Name
- Age
- Illnesses
Encounter details
- Reason for visit
- Vitals (e.g. BP)
- Tests
- Prescriptions
Facility details…

Mapped to RDF

Relational data …

… as a graph.

Using Existing Data(bases)

Global names.
http://someheathprovider.example/patientVisits/C1#info
Simple, declarative sentences.
Global links.
Typed values.

Using Existing Data(bases)

Global names.
http://someheathprovider.example/patientVisits/C1#info
Simple, declarative sentences.
Global links.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
provider:C1 role:patient provider:P1 .
Global links.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
provider:C1 role:patient provider:P1 .
Global links.
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
Global links.
http://someheathprovider.example/roles#patient
Typed values.

Using Existing Data(bases)

Global names.
Simple, declarative sentences.
Global links.
Typed values.
e.g. ISO 8601 datetimes
provider:P1 role:birthdate "1946-11-03"^^xsd:date .