From d096f4e17aa02b2d27d678d1b7f333a06b523ed5 Mon Sep 17 00:00:00 2001
From: patrick-lloyd-ray <67486986+patrick-lloyd-ray@users.noreply.github.com>
Date: Tue, 19 Sep 2023 10:14:42 -0700
Subject: [PATCH 1/4] updating repo
---
src/ontology/Makefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index cce9efb..2a097d8 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for bicano
# Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.4.2
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use bicano.Makefile instead
@@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS =
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by
SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
-ODK_VERSION_MAKEFILE = v1.4
+ODK_VERSION_MAKEFILE = v1.4.2
TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
From 1c857fa760ff55189f3e2e21847a2c5eda616b45 Mon Sep 17 00:00:00 2001
From: patrick-lloyd-ray <67486986+patrick-lloyd-ray@users.noreply.github.com>
Date: Tue, 19 Sep 2023 20:53:07 -0700
Subject: [PATCH 2/4] /
---
src/metadata/bicano.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/metadata/bicano.yml b/src/metadata/bicano.yml
index c8b5e46..8c1d849 100644
--- a/src/metadata/bicano.yml
+++ b/src/metadata/bicano.yml
@@ -1,7 +1,7 @@
# PURL configuration for http://purl.obolibrary.org/obo/bicano
idspace: BICANO
-base_url: /obo/bicano
+base_url: /bicano
products:
- bicano.owl: https://raw.githubusercontent.com/brain-bican/bican_application_ontology/main/bicano.owl
From cdebfb4d5fe65ceae25ba3bae20c1a3591a1417c Mon Sep 17 00:00:00 2001
From: patrick-lloyd-ray <67486986+patrick-lloyd-ray@users.noreply.github.com>
Date: Tue, 19 Sep 2023 20:55:40 -0700
Subject: [PATCH 3/4] updating yml
---
src/metadata/bicano.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/metadata/bicano.yml b/src/metadata/bicano.yml
index 8c1d849..ec7646b 100644
--- a/src/metadata/bicano.yml
+++ b/src/metadata/bicano.yml
@@ -1,4 +1,4 @@
-# PURL configuration for http://purl.obolibrary.org/obo/bicano
+# PURL configuration for http://purl.brain-bican.org/ontology/bicano
idspace: BICANO
base_url: /bicano
From 6718fb081c7c8ab84b2a717ef36704181c0fba90 Mon Sep 17 00:00:00 2001
From: patrick-lloyd-ray <67486986+patrick-lloyd-ray@users.noreply.github.com>
Date: Wed, 4 Oct 2023 15:39:15 -0700
Subject: [PATCH 4/4] release files
---
bicano-base.json | 34 +-
bicano-base.obo | 13 +-
bicano-base.owl | 61 +-
bicano-full.json | 34 +-
bicano-full.obo | 13 +-
bicano-full.owl | 72 +-
bicano-simple.json | 34 +-
bicano-simple.obo | 13 +-
bicano-simple.owl | 72 +-
bicano.json | 34 +-
bicano.obo | 13 +-
bicano.owl | 72 +-
src/ontology/Makefile | 12 +-
src/ontology/bicano-odk.yaml | 7 +
src/ontology/imports/merged_import.owl | 156937 +--------------
.../reports/bicano-edit.owl-obo-report.tsv | 2 -
src/sparql/bicano_terms.sparql | 2 +-
src/sparql/inject-subset-declaration.ru | 2 +-
src/sparql/inject-synonymtype-declaration.ru | 2 +-
src/sparql/iri-range-violation.sparql | 2 +-
src/sparql/label-with-iri-violation.sparql | 2 +-
.../owldef-self-reference-violation.sparql | 2 +-
22 files changed, 5298 insertions(+), 152137 deletions(-)
diff --git a/bicano-base.json b/bicano-base.json
index fffe4b5..d615825 100644
--- a/bicano-base.json
+++ b/bicano-base.json
@@ -1,41 +1,15 @@
{
"graphs" : [ {
- "id" : "http://purl.obolibrary.org/obo/bicano/bicano-base.json",
+ "id" : "http://purl.brain-bican.org/ontology/bicano/bicano-base.json",
"meta" : {
"basicPropertyValues" : [ {
"pred" : "http://purl.org/dc/elements/1.1/type",
"val" : "http://purl.obolibrary.org/obo/IAO_8000001"
- }, {
- "pred" : "http://purl.org/dc/terms/description",
- "val" : "None"
- }, {
- "pred" : "http://purl.org/dc/terms/license",
- "val" : "https://creativecommons.org/licenses/unspecified"
- }, {
- "pred" : "http://purl.org/dc/terms/title",
- "val" : "BICAN Application Ontology"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
- "val" : "2023-02-27"
+ "val" : "2023-10-04"
} ],
- "version" : "http://purl.obolibrary.org/obo/bicano/releases/2023-02-27/bicano-base.json"
- },
- "nodes" : [ {
- "id" : "http://purl.obolibrary.org/obo/BICANO_0000000",
- "lbl" : "root node",
- "type" : "CLASS"
- }, {
- "id" : "http://purl.org/dc/terms/description",
- "lbl" : "description",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/license",
- "lbl" : "license",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/title",
- "lbl" : "title",
- "type" : "PROPERTY"
- } ]
+ "version" : "http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano-base.json"
+ }
} ]
}
\ No newline at end of file
diff --git a/bicano-base.obo b/bicano-base.obo
index 7d05aac..1315c9f 100644
--- a/bicano-base.obo
+++ b/bicano-base.obo
@@ -1,13 +1,6 @@
format-version: 1.2
-data-version: bicano/releases/2023-02-27/bicano-base.owl
-ontology: bicano/bicano-base
+data-version: http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano-base.owl
+ontology: http://purl.brain-bican.org/ontology/bicano/bicano-base.owl
property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
-property_value: http://purl.org/dc/terms/description "None" xsd:string
-property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
-property_value: http://purl.org/dc/terms/title "BICAN Application Ontology" xsd:string
-property_value: owl:versionInfo "2023-02-27" xsd:string
-
-[Term]
-id: BICANO:0000000
-name: root node
+property_value: owl:versionInfo "2023-10-04" xsd:string
diff --git a/bicano-base.owl b/bicano-base.owl
index d0c7713..066069c 100644
--- a/bicano-base.owl
+++ b/bicano-base.owl
@@ -1,20 +1,16 @@
-
-
-
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+
+
- None
-
- BICAN Application Ontology
- 2023-02-27
+ 2023-10-04
@@ -33,52 +29,9 @@
-
-
-
-
-
-
- description
-
-
-
-
-
-
-
- license
-
-
-
-
-
-
-
- title
-
-
-
-
-
-
-
-
-
-
-
-
- root node
-
-
+
diff --git a/bicano-full.json b/bicano-full.json
index bf0fb3f..15dc631 100644
--- a/bicano-full.json
+++ b/bicano-full.json
@@ -1,38 +1,12 @@
{
"graphs" : [ {
- "id" : "http://purl.obolibrary.org/obo/bicano/bicano-full.json",
+ "id" : "http://purl.brain-bican.org/ontology/bicano/bicano-full.json",
"meta" : {
"basicPropertyValues" : [ {
- "pred" : "http://purl.org/dc/terms/description",
- "val" : "None"
- }, {
- "pred" : "http://purl.org/dc/terms/license",
- "val" : "https://creativecommons.org/licenses/unspecified"
- }, {
- "pred" : "http://purl.org/dc/terms/title",
- "val" : "BICAN Application Ontology"
- }, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
- "val" : "2023-02-27"
+ "val" : "2023-10-04"
} ],
- "version" : "http://purl.obolibrary.org/obo/bicano/releases/2023-02-27/bicano-full.json"
- },
- "nodes" : [ {
- "id" : "http://purl.obolibrary.org/obo/BICANO_0000000",
- "lbl" : "root node",
- "type" : "CLASS"
- }, {
- "id" : "http://purl.org/dc/terms/description",
- "lbl" : "description",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/license",
- "lbl" : "license",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/title",
- "lbl" : "title",
- "type" : "PROPERTY"
- } ]
+ "version" : "http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano-full.json"
+ }
} ]
}
\ No newline at end of file
diff --git a/bicano-full.obo b/bicano-full.obo
index 0b4e223..e528826 100644
--- a/bicano-full.obo
+++ b/bicano-full.obo
@@ -1,12 +1,5 @@
format-version: 1.2
-data-version: bicano/releases/2023-02-27/bicano-full.owl
-ontology: bicano/bicano-full
-property_value: http://purl.org/dc/terms/description "None" xsd:string
-property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
-property_value: http://purl.org/dc/terms/title "BICAN Application Ontology" xsd:string
-property_value: owl:versionInfo "2023-02-27" xsd:string
-
-[Term]
-id: BICANO:0000000
-name: root node
+data-version: http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano-full.owl
+ontology: http://purl.brain-bican.org/ontology/bicano/bicano-full.owl
+property_value: owl:versionInfo "2023-10-04" xsd:string
diff --git a/bicano-full.owl b/bicano-full.owl
index 373bdde..f789a52 100644
--- a/bicano-full.owl
+++ b/bicano-full.owl
@@ -1,76 +1,18 @@
-
-
-
- None
-
- BICAN Application Ontology
- 2023-02-27
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+
+
+ 2023-10-04
-
-
-
-
-
-
-
-
-
-
-
- description
-
-
-
-
-
-
-
- license
-
-
-
-
-
-
-
- title
-
-
-
-
-
-
-
-
-
-
-
-
- root node
-
-
+
diff --git a/bicano-simple.json b/bicano-simple.json
index b332324..0fc4021 100644
--- a/bicano-simple.json
+++ b/bicano-simple.json
@@ -1,38 +1,12 @@
{
"graphs" : [ {
- "id" : "http://purl.obolibrary.org/obo/bicano/bicano-simple.json",
+ "id" : "http://purl.brain-bican.org/ontology/bicano/bicano-simple.json",
"meta" : {
"basicPropertyValues" : [ {
- "pred" : "http://purl.org/dc/terms/description",
- "val" : "None"
- }, {
- "pred" : "http://purl.org/dc/terms/license",
- "val" : "https://creativecommons.org/licenses/unspecified"
- }, {
- "pred" : "http://purl.org/dc/terms/title",
- "val" : "BICAN Application Ontology"
- }, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
- "val" : "2023-02-27"
+ "val" : "2023-10-04"
} ],
- "version" : "http://purl.obolibrary.org/obo/bicano/releases/2023-02-27/bicano-simple.json"
- },
- "nodes" : [ {
- "id" : "http://purl.obolibrary.org/obo/BICANO_0000000",
- "lbl" : "root node",
- "type" : "CLASS"
- }, {
- "id" : "http://purl.org/dc/terms/description",
- "lbl" : "description",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/license",
- "lbl" : "license",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/title",
- "lbl" : "title",
- "type" : "PROPERTY"
- } ]
+ "version" : "http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano-simple.json"
+ }
} ]
}
\ No newline at end of file
diff --git a/bicano-simple.obo b/bicano-simple.obo
index f2b914d..eed83b2 100644
--- a/bicano-simple.obo
+++ b/bicano-simple.obo
@@ -1,12 +1,5 @@
format-version: 1.2
-data-version: bicano/releases/2023-02-27/bicano-simple.owl
-ontology: bicano/bicano-simple
-property_value: http://purl.org/dc/terms/description "None" xsd:string
-property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
-property_value: http://purl.org/dc/terms/title "BICAN Application Ontology" xsd:string
-property_value: owl:versionInfo "2023-02-27" xsd:string
-
-[Term]
-id: BICANO:0000000
-name: root node
+data-version: http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano-simple.owl
+ontology: http://purl.brain-bican.org/ontology/bicano/bicano-simple.owl
+property_value: owl:versionInfo "2023-10-04" xsd:string
diff --git a/bicano-simple.owl b/bicano-simple.owl
index 14e19b2..f7d652e 100644
--- a/bicano-simple.owl
+++ b/bicano-simple.owl
@@ -1,76 +1,18 @@
-
-
-
- None
-
- BICAN Application Ontology
- 2023-02-27
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+
+
+ 2023-10-04
-
-
-
-
-
-
-
-
-
-
-
- description
-
-
-
-
-
-
-
- license
-
-
-
-
-
-
-
- title
-
-
-
-
-
-
-
-
-
-
-
-
- root node
-
-
+
diff --git a/bicano.json b/bicano.json
index 67780cb..5e3ea37 100644
--- a/bicano.json
+++ b/bicano.json
@@ -1,38 +1,12 @@
{
"graphs" : [ {
- "id" : "http://purl.obolibrary.org/obo/bicano.json",
+ "id" : "http://purl.brain-bican.org/ontology/bicano.json",
"meta" : {
"basicPropertyValues" : [ {
- "pred" : "http://purl.org/dc/terms/description",
- "val" : "None"
- }, {
- "pred" : "http://purl.org/dc/terms/license",
- "val" : "https://creativecommons.org/licenses/unspecified"
- }, {
- "pred" : "http://purl.org/dc/terms/title",
- "val" : "BICAN Application Ontology"
- }, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
- "val" : "2023-02-27"
+ "val" : "2023-10-04"
} ],
- "version" : "http://purl.obolibrary.org/obo/bicano/releases/2023-02-27/bicano.json"
- },
- "nodes" : [ {
- "id" : "http://purl.obolibrary.org/obo/BICANO_0000000",
- "lbl" : "root node",
- "type" : "CLASS"
- }, {
- "id" : "http://purl.org/dc/terms/description",
- "lbl" : "description",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/license",
- "lbl" : "license",
- "type" : "PROPERTY"
- }, {
- "id" : "http://purl.org/dc/terms/title",
- "lbl" : "title",
- "type" : "PROPERTY"
- } ]
+ "version" : "http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano.json"
+ }
} ]
}
\ No newline at end of file
diff --git a/bicano.obo b/bicano.obo
index 8d311de..d4e5ad5 100644
--- a/bicano.obo
+++ b/bicano.obo
@@ -1,12 +1,5 @@
format-version: 1.2
-data-version: releases/2023-02-27
-ontology: bicano
-property_value: http://purl.org/dc/terms/description "None" xsd:string
-property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified
-property_value: http://purl.org/dc/terms/title "BICAN Application Ontology" xsd:string
-property_value: owl:versionInfo "2023-02-27" xsd:string
-
-[Term]
-id: BICANO:0000000
-name: root node
+data-version: http://purl.brain-bican.org/ontology/bicano/releases/2023-10-04/bicano.owl
+ontology: http://purl.brain-bican.org/ontology/bicano.owl
+property_value: owl:versionInfo "2023-10-04" xsd:string
diff --git a/bicano.owl b/bicano.owl
index b4010ce..504ff2f 100644
--- a/bicano.owl
+++ b/bicano.owl
@@ -1,76 +1,18 @@
-
-
-
- None
-
- BICAN Application Ontology
- 2023-02-27
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+
+
+ 2023-10-04
-
-
-
-
-
-
-
-
-
-
-
- description
-
-
-
-
-
-
-
- license
-
-
-
-
-
-
-
- title
-
-
-
-
-
-
-
-
-
-
-
-
- root node
-
-
+
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index 2a097d8..ca8e6f6 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for bicano
# Generated using ontology-development-kit
-# ODK Version: v1.4.2
+# ODK Version: v1.4.3
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use bicano.Makefile instead
@@ -16,9 +16,9 @@
# these can be overwritten on the command line
OBOBASE= http://purl.obolibrary.org/obo
-URIBASE= http://purl.obolibrary.org/obo
+URIBASE= http://purl.brain-bican.org/ontology
ONT= bicano
-ONTBASE= http://purl.obolibrary.org/obo/bicano
+ONTBASE= http://purl.brain-bican.org/ontology/bicano
EDIT_FORMAT= owl
SRC = $(ONT)-edit.$(EDIT_FORMAT)
MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false
@@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS =
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by
SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
-ODK_VERSION_MAKEFILE = v1.4.2
+ODK_VERSION_MAKEFILE = v1.4.3
TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
@@ -314,7 +314,7 @@ $(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" remove --select "" \
- extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
+ extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi
@@ -323,7 +323,7 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_term
$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
- extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
+ extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi
diff --git a/src/ontology/bicano-odk.yaml b/src/ontology/bicano-odk.yaml
index 1d2db38..fb802b5 100644
--- a/src/ontology/bicano-odk.yaml
+++ b/src/ontology/bicano-odk.yaml
@@ -3,6 +3,12 @@ title: "BICAN Application Ontology"
github_org: brain-bican
git_main_branch: main
repo: bican_application_ontology
+report_fail_on: none
+uribase: http://purl.brain-bican.org/ontology
+export_formats:
+ - owl
+ - obo
+ - json
release_artefacts:
- base
- full
@@ -14,6 +20,7 @@ export_formats:
- json
import_group:
use_base_merging: TRUE
+ slme_individuals: exclude
exclude_iri_patterns:
-
-
diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl
index 8ab850b..82885f4 100644
--- a/src/ontology/imports/merged_import.owl
+++ b/src/ontology/imports/merged_import.owl
@@ -1,4 +1,4 @@
-Prefix(:=)
+Prefix(:=)
Prefix(owl:=)
Prefix(rdf:=)
Prefix(xml:=)
@@ -6,307 +6,10 @@ Prefix(xsd:=)
Prefix(rdfs:=)
-Ontology(
-
-Annotation(owl:versionInfo "2023-02-27")
-
-Declaration(Class())
-Declaration(Class())
-Declaration(Class())
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