Resources: <SWObjects sparql binary> and <sample queries>
(contains <goProt.map> <goProt.rq>.
<goProt2.map> <goProt2.rq> <goProt2-bug.rq>.)
six task forces:
Other Projects: Clinical Decision Support...
We develop RDF tools, data and practices to help academia/industry use RDF.
Easy for us to extend schemas and feed back to project.
Easy for TMO's medical vocabs to become normative.
Effects:
@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 .
@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
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
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
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
Continuity of data ...
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 }
Category | User / Role | Interest |
---|---|---|
Research | Biologist (in vivo, in vitro, cellular & molecular) | Target identification, assay development, target validation |
Bioinformatician | Biological knowledge management, cellular modeling | |
Immunologist | Natural defense mechanisms | |
Cheminformatician | Predictive chemistry | |
Medicinal chemist | Drug efficacy | |
Systems physiologist | Tolerance, adverse events | |
Clinic | Clinical trial specialist | Trial formulation, recruitment |
Clinical decision support | Data Analysis, trend finding | |
Primary care physician | General, conventional care | |
Specialty medical provider | Specialized treatments | |
Business | Sales & marketing | Revenue generation |
Strategic/portfolio manager | Assessing market opportunities | |
Project manager | Prioritizing resources & activities | |
Health plan provider | Insurance coverage |
SELECT DISTINCT ?name ?patient WHERE { graph <pchr_new> { ?patient foaf:name ?name; trans:hasCondition [ trans:diagnosedWith trans:alzheimers_disease ] . FILTER ( !bif:exists (( SELECT ?result WHERE { ?encounter trans:patient ?patient ; trans:test [ a ?testname ; trans:result ?result ] . ?result trans:feature trans:variant_APOE4 ; trans:present true . } )) ) } }
@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" .
<?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>
http://someheathprovider.example/patientVisits/C1#info
http://someheathprovider.example/patientVisits/C1#info
provider:C1 role:patient provider:P1 .
provider:C1 role:patient provider:P1 .
http://someheathprovider.example/roles#patient
ISO 8601 datetimes
provider:P1 role:birthdate "1946-11-03"^^xsd:date .
<d2r:ClassMap d2r:type="eb:Customer" d2r:sql="SELECT Tab_K_Kunde.KundenNr, Tab_K_Kunde.FullName, Tab_K_Kunde.Anrede, Tab_K_Kunde_Kreditkarte.CCNo FROM Tab_K_Kunde_Kreditkarte INNER JOIN Tab_K_Kunde ON Tab_K_Kunde_Kreditkarte.KundenNr = Tab_K_Kunde.KundenNr;" d2r:groupBy="Tab_K_Kunde.KundenNr" d2r:uriPattern= “http://example.org/customers#@@Tab_K_Kunde.KundenNr@@“>
Re-uses OWL constructs:
<d2r:ObjectPropertyBridge d2r:property="rdf:type" d2r:pattern="iswc:@@Persons.Position@@"/>
Configuration consumable as RDF (SPARQL-able).
create iri class prd:product_iri using function OPLWEB.DBA.PRODUCT_URI (in id varchar) returns varchar, function OPLWEB.DBA.PRODUCT_URI_INVERSE (in id_iri varchar) returns varchar .
Uses hardened algorithms from SQL land.
PREFIX :mydb <http://cityhospital.example/dbs> CONSTRUCT { ?o a study:SubjectObservation . ?o study:subject ?p . ?o study:clinician ?d . ?d :foaf:name ?dName }
WHERE { ?o mydb:patient ?p . ?o mydb:doctor ?d . ?d mydb:name ?dName }
Intuitive (testable) semantics.
(a,b,c) set enumeration
union
disjunction
algebraics
intersection
complement
restriction
cardinality
equivalence
courtesy: Fabien Gandon