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Merged
StroemPhi merged 5 commits into from
Mar 5, 2024
Merged

Moving all classes from v1.1 to the edit file in this repo #8

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27122c7
Use current ontology IRI
StroemPhi Feb 20, 2024
37005e6
Copy nmrCV.owl 1.1. classes into nmrCV-edit.owl
StroemPhi Feb 20, 2024
bae89a0
Deactivate using base import modules for now
StroemPhi Feb 20, 2024
5a4cf0e
Update .gitignore
StroemPhi Feb 20, 2024
97d0f09
Merge branch 'main' into Complete-ODK-migration
StroemPhi Feb 21, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -45,3 +45,4 @@ src/patterns/all_pattern_terms.txt
.idea/inspectionProfiles/profiles_settings.xml
.idea/vcs.xml
.idea/workspace.xml
.idea/misc.xml
8 changes: 4 additions & 4 deletions docs/odk-workflows/RepoManagement.md
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Expand Up @@ -45,9 +45,9 @@ Note: our ODK file should only have one `import_group` which can contain multipl
1. Add an import statement to your `src/ontology/nmrCV-edit.owl` file. We suggest to do this using a text editor, by simply copying an existing import declaration and renaming it to the new ontology import, for example as follows:
```
...
Ontology(<http://purl.obolibrary.org/obo/nmrCV.owl>
Import(<http://purl.obolibrary.org/obo/nmrCV/imports/ro_import.owl>)
Import(<http://purl.obolibrary.org/obo/nmrCV/imports/go_import.owl>)
Ontology(<http://nmrML.org/nmrCV.owl>
Import(<http://nmrML.org/nmrCV/imports/ro_import.owl>)
Import(<http://nmrML.org/nmrCV/imports/go_import.owl>)
...
```
2. Add your imports redirect to your catalog file `src/ontology/catalog-v001.xml`, for example:
Expand All @@ -68,7 +68,7 @@ Import(<http://purl.obolibrary.org/obo/nmrCV/imports/go_import.owl>)
in your editors file (the ontology) and

```
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/go_import.owl" uri="imports/go_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/go_import.owl" uri="imports/go_import.owl"/>
```

in your catalog, tools like `robot` or Protégé will recognize the statement
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6 changes: 3 additions & 3 deletions docs/odk-workflows/components.md
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Expand Up @@ -17,20 +17,20 @@ components:
3) Add the component to your catalog file (src/ontology/catalog-v001.xml)

```
<uri name="http://purl.obolibrary.org/obo/nmrCV/components/your-component-name.owl" uri="components/your-component-name.owl"/>
<uri name="http://nmrML.org/nmrCV/components/your-component-name.owl" uri="components/your-component-name.owl"/>
```

4) Add the component to the edit file (src/ontology/nmrCV-edit.obo)
for .obo formats:

```
import: http://purl.obolibrary.org/obo/nmrCV/components/your-component-name.owl
import: http://nmrML.org/nmrCV/components/your-component-name.owl
```

for .owl formats:

```
Import(<http://purl.obolibrary.org/obo/nmrCV/components/your-component-name.owl>)
Import(<http://nmrML.org/nmrCV/components/your-component-name.owl>)
```

5) Refresh your repo by running `sh run.sh make update_repo` - this should create a new file in src/ontology/components.
Expand Down
21 changes: 9 additions & 12 deletions src/ontology/Makefile
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Expand Up @@ -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://nmrML.org
ONT= nmrCV
ONTBASE= http://purl.obolibrary.org/obo/nmrCV
ONTBASE= http://nmrML.org/nmrCV
EDIT_FORMAT= owl
SRC = $(ONT)-edit.$(EDIT_FORMAT)
MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false
Expand Down Expand Up @@ -365,8 +365,9 @@ mirror-bfo: | $(TMPDIR)
.PHONY: mirror-ro
.PRECIOUS: $(MIRRORDIR)/ro.owl
mirror-ro: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


## ONTOLOGY: omo
Expand All @@ -383,8 +384,7 @@ mirror-omo: | $(TMPDIR)
.PRECIOUS: $(MIRRORDIR)/iao.owl
mirror-iao: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/iao.owl --create-dirs -o $(MIRRORDIR)/iao.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/iao.owl -o $@.tmp.owl && \
$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/IAO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
$(ROBOT) convert -i $(MIRRORDIR)/iao.owl -o $@.tmp.owl &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


Expand All @@ -393,8 +393,7 @@ mirror-iao: | $(TMPDIR)
.PRECIOUS: $(MIRRORDIR)/chmo.owl
mirror-chmo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/chmo.owl --create-dirs -o $(MIRRORDIR)/chmo.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/chmo.owl -o $@.tmp.owl && \
$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CHMO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
$(ROBOT) convert -i $(MIRRORDIR)/chmo.owl -o $@.tmp.owl &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


Expand All @@ -403,8 +402,7 @@ mirror-chmo: | $(TMPDIR)
.PRECIOUS: $(MIRRORDIR)/pato.owl
mirror-pato: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl && \
$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PATO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
$(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


Expand All @@ -413,8 +411,7 @@ mirror-pato: | $(TMPDIR)
.PRECIOUS: $(MIRRORDIR)/obi.owl
mirror-obi: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && \
$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi


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28 changes: 14 additions & 14 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -3,26 +3,26 @@
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">


<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/bfo_import.owl" uri="imports/bfo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/bfo_import.obo" uri="imports/bfo_import.obo"/>
<uri name="http://nmrML.org/nmrCV/imports/bfo_import.owl" uri="imports/bfo_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/bfo_import.obo" uri="imports/bfo_import.obo"/>

<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/ro_import.owl" uri="imports/ro_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/ro_import.obo" uri="imports/ro_import.obo"/>
<uri name="http://nmrML.org/nmrCV/imports/ro_import.owl" uri="imports/ro_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/ro_import.obo" uri="imports/ro_import.obo"/>

<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/omo_import.owl" uri="imports/omo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/omo_import.obo" uri="imports/omo_import.obo"/>
<uri name="http://nmrML.org/nmrCV/imports/omo_import.owl" uri="imports/omo_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/omo_import.obo" uri="imports/omo_import.obo"/>

<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/iao_import.owl" uri="imports/iao_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/iao_import.obo" uri="imports/iao_import.obo"/>
<uri name="http://nmrML.org/nmrCV/imports/iao_import.owl" uri="imports/iao_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/iao_import.obo" uri="imports/iao_import.obo"/>

<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/chmo_import.owl" uri="imports/chmo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/chmo_import.obo" uri="imports/chmo_import.obo"/>
<uri name="http://nmrML.org/nmrCV/imports/chmo_import.owl" uri="imports/chmo_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/chmo_import.obo" uri="imports/chmo_import.obo"/>

<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/pato_import.owl" uri="imports/pato_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/pato_import.obo" uri="imports/pato_import.obo"/>
<uri name="http://nmrML.org/nmrCV/imports/pato_import.owl" uri="imports/pato_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/pato_import.obo" uri="imports/pato_import.obo"/>

<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/obi_import.owl" uri="imports/obi_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/nmrCV/imports/obi_import.obo" uri="imports/obi_import.obo"/>
<uri name="http://nmrML.org/nmrCV/imports/obi_import.owl" uri="imports/obi_import.owl"/>
<uri name="http://nmrML.org/nmrCV/imports/obi_import.obo" uri="imports/obi_import.obo"/>



Expand Down
8 changes: 4 additions & 4 deletions src/ontology/imports/bfo_import.owl
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@@ -1,15 +1,15 @@
Prefix(:=<http://purl.obolibrary.org/obo/nmrCV/imports/bfo_import.owl#>)
Prefix(:=<http://nmrML.org/nmrCV/imports/bfo_import.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/nmrCV/imports/bfo_import.owl>
<http://purl.obolibrary.org/obo/nmrCV/releases/2023-11-23/imports/bfo_import.owl>
Ontology(<http://nmrML.org/nmrCV/imports/bfo_import.owl>
<http://nmrML.org/nmrCV/releases/2024-02-20/imports/bfo_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl>)
Annotation(owl:versionInfo "2023-11-23")
Annotation(owl:versionInfo "2024-02-20")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Expand Down
82 changes: 78 additions & 4 deletions src/ontology/imports/chmo_import.owl
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@@ -1,22 +1,96 @@
Prefix(:=<http://purl.obolibrary.org/obo/nmrCV/imports/chmo_import.owl#>)
Prefix(:=<http://nmrML.org/nmrCV/imports/chmo_import.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/nmrCV/imports/chmo_import.owl>
<http://purl.obolibrary.org/obo/nmrCV/releases/2023-11-23/imports/chmo_import.owl>
Ontology(<http://nmrML.org/nmrCV/imports/chmo_import.owl>
<http://nmrML.org/nmrCV/releases/2024-02-20/imports/chmo_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/chmo/releases/2022-04-19/chmo.owl>)
Annotation(owl:versionInfo "2023-11-23")
Annotation(owl:versionInfo "2024-02-20")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000017>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000019>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000020>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000031>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000117>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000119>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/source>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
Declaration(AnnotationProperty(<http://purl.org/dc/terms/license>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#created_by>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#creation_date>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))
Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#saved-by>))
Declaration(AnnotationProperty(rdfs:label))
############################
# Annotation Properties
############################

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000115> (definition)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000115> "definition")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> (database_cross_reference)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasDbXref> "database_cross_reference")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> (has_exact_synonym)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> "has_exact_synonym")

# Annotation Property: <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> (has_obo_format_version)

AnnotationAssertion(rdfs:label <http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion> "has_obo_format_version")



############################
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/BFO_0000002> (continuant)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/BFO_0000002> "BFO:0000002")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000002> "continuant")

# Class: <http://purl.obolibrary.org/obo/BFO_0000015> (process)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/BFO_0000015> "BFO:0000015")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000015> "process")

# Class: <http://purl.obolibrary.org/obo/BFO_0000017> (realizable_entity)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/BFO_0000017> "BFO:0000017")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000017> "realizable_entity")
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000017> <http://purl.obolibrary.org/obo/BFO_0000020>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000019> (quality)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/BFO_0000019> "BFO:0000019")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000019> "quality")
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000019> <http://purl.obolibrary.org/obo/BFO_0000020>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000020> (specifically dependent continuant)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/BFO_0000020> "BFO:0000020")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000020> "specifically dependent continuant")
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000020> <http://purl.obolibrary.org/obo/BFO_0000002>)

# Class: <http://purl.obolibrary.org/obo/BFO_0000031> (generically dependent continuant)

AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/BFO_0000031> "BFO:0000031")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/BFO_0000031> "generically dependent continuant")
SubClassOf(<http://purl.obolibrary.org/obo/BFO_0000031> <http://purl.obolibrary.org/obo/BFO_0000002>)


)
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