From da690ebf9d0bd63e799eceee54e4d9f0b09d8aac Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 15:25:27 -0500 Subject: [PATCH 1/4] VIVO-434 restoring "documentation for" --- rdf/tbox/filegraph/object-properties.owl | 62 +++++++++----------- rdf/tbox/filegraph/research-resource.owl | 13 ++++ rdf/tbox/firsttime/initialTBoxAnnotations.n3 | 5 ++ 3 files changed, 46 insertions(+), 34 deletions(-) diff --git a/rdf/tbox/filegraph/object-properties.owl b/rdf/tbox/filegraph/object-properties.owl index 4c95312e..1f06a387 100644 --- a/rdf/tbox/filegraph/object-properties.owl +++ b/rdf/tbox/filegraph/object-properties.owl @@ -201,7 +201,6 @@ - @@ -317,7 +316,6 @@ - @@ -497,7 +495,6 @@ - @@ -575,7 +572,6 @@ - @@ -593,8 +589,6 @@ PERSON: Melissa Haendel PERSON: Melissa Haendel used to study - - @@ -914,14 +908,7 @@ there is a measurement process p that has specified output m, a measurement datu http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) is_manufactured_by - - - - - - - - + @@ -1671,7 +1658,8 @@ there is a measurement process p that has specified output m, a measurement datu - + + @@ -1679,7 +1667,21 @@ there is a measurement process p that has specified output m, a measurement datu - + + + + + + + + + + + + + + + @@ -1687,7 +1689,16 @@ there is a measurement process p that has specified output m, a measurement datu - + + + + + + + + + + @@ -1704,7 +1715,6 @@ there is a measurement process p that has specified output m, a measurement datu - @@ -1717,22 +1727,6 @@ there is a measurement process p that has specified output m, a measurement datu - - - - - - - - - - - - - - - - diff --git a/rdf/tbox/filegraph/research-resource.owl b/rdf/tbox/filegraph/research-resource.owl index dccf8f43..795cdeb9 100644 --- a/rdf/tbox/filegraph/research-resource.owl +++ b/rdf/tbox/filegraph/research-resource.owl @@ -507,5 +507,18 @@ + + + + + OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) + PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice. + PlanAndPlannedProcess Branch + Protocol + a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. + protocol + + + diff --git a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 index cef6df9c..44a3d725 100644 --- a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 +++ b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 @@ -407,6 +407,9 @@ foaf:Person obo:OBI_0000643 rdfs:label "has grain"@en-US . +obo:OBI_0000272 + rdfs:label "protocol"@en-US . + vcard:Identification rdfs:label "Identification"@en-US . @@ -6173,6 +6176,8 @@ obo:ERO_0001716 vitro:prohibitedFromUpdateBelowRoleLevelAnnot ; vitro:selectFromExistingAnnot + "true"^^xsd:boolean ; + vitro:offerCreateNewOptionAnnot "true"^^xsd:boolean . vcard:hasRelated From 8d8df54219a76f8da3222ac91de6999c10beee4e Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 15:26:07 -0500 Subject: [PATCH 2/4] fixes a vcard bug --- .../update/sparqlConstructs/additions/vcard1-0c.sparql | 3 ++- .../update/sparqlConstructs/additions/vcard2d.sparql | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql index 03405d95..7443d28a 100644 --- a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql +++ b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql @@ -8,7 +8,8 @@ CONSTRUCT { _:vcard arg:ARG_2000029 ?s . _:vcard a v:Individual . } WHERE { - ?s vivo:middleName ?middleName + ?s vivo:middleName ?middleName . + ?s a foaf:Person FILTER NOT EXISTS { ?s arg:ARG_2000028 ?vcard } diff --git a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql index a065a9fe..cb32f1b9 100644 --- a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql +++ b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql @@ -8,6 +8,7 @@ CONSTRUCT { ?name vivo:middleName ?middleName . } WHERE { ?s vivo:middleName ?middleName . + ?s a foaf:Person . ?s arg:ARG_2000028 ?vcard . ?vcard v:hasName ?name } From 5adf4a587f6c7079a7013db34438fdf7d475c600 Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 15:50:11 -0500 Subject: [PATCH 3/4] object property cleanup --- rdf/tbox/filegraph/object-properties.owl | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/rdf/tbox/filegraph/object-properties.owl b/rdf/tbox/filegraph/object-properties.owl index 1f06a387..f61d226f 100644 --- a/rdf/tbox/filegraph/object-properties.owl +++ b/rdf/tbox/filegraph/object-properties.owl @@ -558,24 +558,6 @@ related technique - - - - - - - - - - - - - - - - - - From ef3ac5008d150351a503498fe70c881b9a5ca4bb Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 16:08:22 -0500 Subject: [PATCH 4/4] VIVO-494 hiding "realizes" --- rdf/tbox/firsttime/initialTBoxAnnotations.n3 | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 index 44a3d725..672d3388 100644 --- a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 +++ b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 @@ -5983,7 +5983,11 @@ vcard:Name rdfs:label "Name"@en-US . obo:BFO_0000055 - rdfs:label "realizes"@en-US . + rdfs:label "realizes"@en-US ; + vitro:hiddenFromDisplayBelowRoleLevelAnnot + ; + vitro:prohibitedFromUpdateBelowRoleLevelAnnot + . geo:nationalityAR rdfs:label "nationalityAR"@en-US ;