query update

dbmi-pitt · Oct 9, 2015 · 5fe6e65 · 5fe6e65
1 parent 6f5fc5b
commit 5fe6e65
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diff --git a/queries/AE-01.sparql b/queries/AE-01.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-08-13
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/STAT-05.sparql → queries/DO NOT USE/STAT-05.sparql b/queries/STAT-05.sparql → queries/DO NOT USE/STAT-05.sparql
diff --git a/queries/EP-04.sparql b/queries/EP-04.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-08-13
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -20,13 +20,13 @@ PREFIX swande: <http://purl.org/swan/1.2/discourse-elements#>
 
 
 # What other claims are supported by this evidence item?
-## using <http://www.ncbi.nlm.nih.gov/pubmed/10771452> as "this evidence item" and claim-154 as "other than this claim"
+## using <http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=165cff62-b284-4a27-a65d-9ec8a5bfcdd8> as "this evidence item" and claim-261 as "other than this claim"
 
 SELECT DISTINCT ?claim ?cLabel
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
-      ?aURN oa:hasSource <http://www.ncbi.nlm.nih.gov/pubmed/10771452>. 
+      ?aURN oa:hasSource <http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=165cff62-b284-4a27-a65d-9ec8a5bfcdd8>. 
 
       ?anItem oa:hasTarget ?aURN.
 
@@ -38,5 +38,5 @@ WHERE
 
       ?claim rdfs:label ?cLabel.
 
-      FILTER (!regex( ?claim, poc:ddi-spl-annotation-claim-154 ))
+      FILTER (!regex( ?claim, poc:ddi-spl-annotation-claim-261 ))
 }
diff --git a/queries/EP-05.sparql b/queries/EP-05.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-08-13
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -20,7 +20,7 @@ PREFIX swande: <http://purl.org/swan/1.2/discourse-elements#>
 
 
 # What other claims are challenged by this evidence item?
-## using <http://www.ncbi.nlm.nih.gov/pubmed/10771452> as "this evidence item" and claim-192 as "other than this claim"
+## using <http://www.ncbi.nlm.nih.gov/pubmed/10771452> as "this evidence item" and claim-96 as "other than this claim"
 
 SELECT DISTINCT ?claim ?cLabel
 FROM <inferred-graph-oa-mp.xml>
@@ -38,5 +38,5 @@ WHERE
 
       ?claim rdfs:label ?cLabel.
 
-      FILTER (!regex( ?claim, poc:ddi-spl-annotation-claim-192 ))
+      FILTER (!regex( ?claim, poc:ddi-spl-annotation-claim-96 ))
 }
diff --git a/queries/FA-01.sparql b/queries/FA-01.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-02.sparql b/queries/FA-02.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-03.sparql b/queries/FA-03.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-04.sparql b/queries/FA-04.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-05.sparql b/queries/FA-05.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-06.sparql b/queries/FA-06.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -26,7 +26,7 @@ SELECT ?claim ?claimlabel
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
-    ?druglabelstatement a dikbEvidence:Non_traceable_Drug_Label_Statement;
+    ?druglabelstatement a dikbEvidence:Non_traceable_Statement;
 	mp:supports ?claim.
 
     ?claim rdfs:label ?claimlabel.

diff --git a/queries/FA-07.sparql b/queries/FA-07.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-08.sparql b/queries/FA-08.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-09.sparql b/queries/FA-09.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-10.sparql b/queries/FA-10.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FA-11.sparql b/queries/FA-11.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FE-01.sparql b/queries/FE-01.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FE-02.sparql b/queries/FE-02.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -20,15 +20,15 @@ PREFIX swande: <http://purl.org/swan/1.2/discourse-elements#>
 
 
 # List all the evidence (supporting or challenging) for claim X from a specific evidence type?
-## The example claim here is claim-103, and the source is drug-label statements
+## The example claim here is claim-330, and the source is drug-label statements
 
 SELECT DISTINCT xsd:string(?source) as ?evidence_source ?modality
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
-      {?evidence mp:supports poc:ddi-spl-annotation-claim-103} UNION {?evidence mp:challenges poc:ddi-spl-annotation-claim-103} .
-      ?evidence rdf:type dikbEvidence:Non_traceable_Drug_Label_Statement.  
-      ?evidence ?modality poc:ddi-spl-annotation-claim-103.
+      {?evidence mp:supports poc:ddi-spl-annotation-claim-330} UNION {?evidence mp:challenges poc:ddi-spl-annotation-claim-330} .
+      ?evidence rdf:type dikbEvidence:Non_traceable_Statement.  
+      ?evidence ?modality poc:ddi-spl-annotation-claim-330.
 
       ?anItem oa:hasBody ?evidence;
 	     oa:hasTarget ?aURN.

diff --git a/queries/FE-03.sparql b/queries/FE-03.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -20,15 +20,15 @@ PREFIX swande: <http://purl.org/swan/1.2/discourse-elements#>
 
 
 # List all the in vitro (supporting or challenging) evidence for claim X? 
-## In this case, claim-86 is used as claim X 
+## In this case, claim-102 is used as claim X 
 
 SELECT DISTINCT xsd:string(?source) as ?evidence_source ?modality
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
-      {?evidence mp:supports poc:ddi-spl-annotation-claim-86} UNION {?evidence mp:challenges poc:ddi-spl-annotation-claim-86} .
+      {?evidence mp:supports poc:ddi-spl-annotation-claim-102} UNION {?evidence mp:challenges poc:ddi-spl-annotation-claim-102} .
 
-      ?evidence ?modality poc:ddi-spl-annotation-claim-86.
+      ?evidence ?modality poc:ddi-spl-annotation-claim-102.
 
       ?method mp:supports ?evidence;
               rdf:type ?type.

diff --git a/queries/FE-04.sparql b/queries/FE-04.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -20,15 +20,15 @@ PREFIX swande: <http://purl.org/swan/1.2/discourse-elements#>
 
 
 # List all the in vivo evidence(supporting or challenging) for claim X? 
-## In this case, claim-90 is used as claim X
+## In this case, claim-11 is used as claim X
 
 SELECT DISTINCT xsd:string(?source) as ?evidence_source ?modality
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
-      {?evidence mp:supports poc:ddi-spl-annotation-claim-90} UNION {?evidence mp:challenges poc:ddi-spl-annotation-claim-90} .
+      {?evidence mp:supports poc:ddi-spl-annotation-claim-11} UNION {?evidence mp:challenges poc:ddi-spl-annotation-claim-11} .
 
-      ?evidence ?modality poc:ddi-spl-annotation-claim-90.
+      ?evidence ?modality poc:ddi-spl-annotation-claim-11.
 
       ?method mp:supports ?evidence;
               rdf:type ?type.

diff --git a/queries/FE-06.sparql b/queries/FE-06.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-23
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FE-07.sparql b/queries/FE-07.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-23
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FE-08.sparql b/queries/FE-08.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-22
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FE-09.sparql b/queries/FE-09.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-22
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/FE-10.sparql b/queries/FE-10.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-22
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/PK-01.sparql b/queries/PK-01.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/PK-03.sparql b/queries/PK-03.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21 
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -19,13 +19,13 @@ PREFIX siocns: <http://rdfs.org/sioc/ns#>
 PREFIX swande: <http://purl.org/swan/1.2/discourse-elements#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
 
-# For a given pharmacokinetic property, ie ketoconazole_increases_auc_triazolam (claim-30)
+# For a given pharmacokinetic property, ie fluoxetine_increases_auc_despiramine (claim-34)
 # What is the average of the pharmacokinetic value?
 
 SELECT avg(xsd:decimal(?v)) as ?average_value
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
-    {?e mp:supports poc:ddi-spl-annotation-claim-30} UNION {?e mp:challenges poc:ddi-spl-annotation-claim-30} .
+    {?e mp:supports poc:ddi-spl-annotation-claim-34} UNION {?e mp:challenges poc:ddi-spl-annotation-claim-34} .
     ?e dikbD2R:increases_auc ?v.
 }
diff --git a/queries/STAT-01.sparql b/queries/STAT-01.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/STAT-02.sparql b/queries/STAT-02.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/STAT-03.sparql b/queries/STAT-03.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/STAT-04.sparql b/queries/STAT-04.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1 
-# DIKB MP/NP version: 2015-07-21
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -20,15 +20,13 @@ PREFIX swande: <http://purl.org/swan/1.2/discourse-elements#>
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 
 #### Show distribution of evidence types for all types of claims
-### LIMITATION OF THE CURRENT MODEL - have to query for count of label statements separately, see STAT-05
 
 SELECT ?cType as ?claim_type ?type as ?evidence_type count(?type) as ?evidence_count
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
      { ?data mp:supports ?claim } UNION { ?data mp:challenges ?claim }.
-     ?methods mp:supports ?data;
-	      rdf:type ?type.
+     ?data rdf:type ?type.
      {?claim mp:qualifiedBy obo:DIDEO_00000096} UNION {?claim mp:qualifiedBy obo:RO_0002449} UNION {?claim mp:qualifiedBy obo:DIDEO_00000000}.
      ?claim mp:qualifiedBy ?cType.
      FILTER (!regex ( ?cType, obo:CHEBI_ ) && !regex( ?cType, obo:PR_ ))

diff --git a/queries/STAT-06.sparql b/queries/STAT-06.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-08-07
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/STAT-07.sparql b/queries/STAT-07.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1
-# DIKB MP/NP version: 2015-08-12
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>

diff --git a/queries/STAT-08.sparql b/queries/STAT-08.sparql
@@ -1,5 +1,5 @@
 # SPARQL version: 1.1 
-# DIKB MP/NP version: 2015-08-13
+# DIKB MP/NP version: 2015-10-09
 
 PREFIX aoOld: <http://purl.org/ao/core/> # needed for AnnotationSet and item until the equivalent is in Open Data Annotation
 PREFIX cnt: <http://www.w3.org/2011/content#>
@@ -25,7 +25,6 @@ SELECT ?cType as ?claim_type COUNT(DISTINCT ?claim) as ?claim_count
 FROM <inferred-graph-oa-mp.xml>
 WHERE 
 {
-     { ?statement mp:supports ?claim } UNION { ?statement mp:challenges ?claim }.
      {?claim mp:qualifiedBy obo:DIDEO_00000096} UNION {?claim mp:qualifiedBy obo:RO_0002449} UNION {?claim mp:qualifiedBy obo:DIDEO_00000000}.
      ?claim mp:qualifiedBy ?cType.
      FILTER ( !regex(?cType, obo:CHEBI_) && !regex(?cType, obo:PR_) )

diff --git a/queries/use-cases.txt b/queries/use-cases.txt
@@ -64,7 +64,7 @@ different versions of product labeling for the same drug? **DEFERRED**
 2. Number of evidence items for each claim type **done**
 3. Number of evidence items against each claim type **done**
 4. Show the distribution of the evidence types for types of claims **done**
-5. Show the count of label statements for all types of claims **done**
+5. Show the count of label statements for all types of claims **no longer relevant, merged with 4**
 6. Show the count of drugs included in this version of the DIKB **done**
 7. Show the count of full nanopublications in the system **done**
 8. Show the count of claims by the type of claims