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rename and synonyms #17

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rename and synonyms #17

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acbcc77
Merge branch 'main' into Import-CHEBI-dependencies
StroemPhi Feb 21, 2024
5e560ed
import NMR solvents
StroemPhi Mar 7, 2024
88a4faa
Merge branch 'main' into Import-CHEBI-dependencies
StroemPhi Mar 7, 2024
280d05a
update CHEBI module using `./run.sh make refresh-chebi`
StroemPhi Mar 7, 2024
0006702
import NMR references
NRayya Mar 13, 2024
49e84aa
Merge pull request #13 from nmrML/defs-references
StroemPhi Mar 18, 2024
530fd10
Move chebi:'chemical entity' under bfo:'material entity'
StroemPhi Mar 18, 2024
1300c13
Don't make the CHEBI module a base module
StroemPhi Mar 18, 2024
f318d8c
Refresh CHEBI import module
StroemPhi Mar 18, 2024
9900fb0
Merge branch 'main' into Import-CHEBI-dependencies
StroemPhi Mar 18, 2024
0546207
Merge branch 'main' into Import-CHEBI-dependencies
StroemPhi Mar 18, 2024
4c6f9bf
Ignore IAO, CHMO, OBI & PATO for now
StroemPhi Mar 18, 2024
b9a749c
Ignore IAO, CHMO, OBI & PATO for now (pt.2)
StroemPhi Mar 18, 2024
102a12d
Make CHEBI:role equivalent with BFO:role
StroemPhi Mar 18, 2024
856c365
Move NMR buffer and aquisition nucleus under BFO:material entity
StroemPhi Mar 18, 2024
bd96327
Add equivalence axiom to NMR solvent
StroemPhi Mar 18, 2024
dbde30f
Materialize inferred SubClassOf axioms using ROBOT reason:
StroemPhi Mar 18, 2024
c963fa7
Obsolete Chloroform-d in favor of imported CHEBI equivalent
StroemPhi Mar 19, 2024
28df8f4
Obsolete Hexafluorobenzene in favour of imported CHEBI equivalent
StroemPhi Mar 19, 2024
6dcf40b
Obsolete heavy water in favor of imported CHEBI equivalent
StroemPhi Mar 19, 2024
35d403c
Add textual definition to NMR solvent
StroemPhi Mar 19, 2024
79e9d84
Infer CHEBI_38589 (hexafluorobenzene) to be an NMR solvent
StroemPhi Mar 19, 2024
b95e94d
Move NMR:1400032> "calibration compound" under molecular entity
StroemPhi Mar 19, 2024
a8fd02f
Add logical definition to NMR:1400033 "chemical shift standard"
StroemPhi Mar 19, 2024
90c24b6
Add general class axiom to define subclasses of 'chemical shift stand…
StroemPhi Mar 19, 2024
e829279
Infer subclassOf 'chemical shift standard' axioms for those CHEBI mol…
StroemPhi Mar 19, 2024
712572f
rename calibration compound and remove synonyms
NRayya Mar 20, 2024
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5 changes: 1 addition & 4 deletions docs/odk-workflows/RepositoryFileStructure.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,7 @@ These are the current imports in NMRCV
| bfo | http://purl.obolibrary.org/obo/bfo.owl | mirror |
| ro | http://purl.obolibrary.org/obo/ro.owl | None |
| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
| iao | http://purl.obolibrary.org/obo/iao.owl | None |
| chmo | http://purl.obolibrary.org/obo/chmo.owl | None |
| pato | http://purl.obolibrary.org/obo/pato.owl | None |
| obi | http://purl.obolibrary.org/obo/obi.owl | None |
| chebi | http://purl.obolibrary.org/obo/chebi.owl | None |

## Components
Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases:
Expand Down
52 changes: 20 additions & 32 deletions src/ontology/Makefile
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Expand Up @@ -10,7 +10,7 @@
# More information: https://github.com/INCATools/ontology-development-kit/

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= 048e86b877413691096fdaf760046bfa1f9cc76be28e57b283a8dd03e21e3213
CONFIG_HASH= a4c0ac9d9d7ac7b03403ce94c3d1d76c44d412b433490d312ed763a12e8e19f6


# ----------------------------------------
Expand Down Expand Up @@ -159,7 +159,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = bfo ro omo iao chmo pato obi
IMPORTS = bfo ro omo chebi

IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -376,6 +376,13 @@ $(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combine
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi

## Module for ontology: chebi

$(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_combined.txt
if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/chebi_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
$(ANNOTATE_CONVERT_FILE); fi


.PHONY: refresh-imports
refresh-imports:
Expand Down Expand Up @@ -432,36 +439,17 @@ mirror-omo: | $(TMPDIR)
$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/[email protected]


## ONTOLOGY: iao
.PHONY: mirror-iao
.PRECIOUS: $(MIRRORDIR)/iao.owl
mirror-iao: | $(TMPDIR)
curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/[email protected]


## ONTOLOGY: chmo
.PHONY: mirror-chmo
.PRECIOUS: $(MIRRORDIR)/chmo.owl
mirror-chmo: | $(TMPDIR)
curl -L $(OBOBASE)/chmo.owl --create-dirs -o $(TMPDIR)/chmo-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/chmo-download.owl -o $(TMPDIR)/[email protected]


## ONTOLOGY: pato
.PHONY: mirror-pato
.PRECIOUS: $(MIRRORDIR)/pato.owl
mirror-pato: | $(TMPDIR)
curl -L $(OBOBASE)/pato.owl --create-dirs -o $(TMPDIR)/pato-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/pato-download.owl -o $(TMPDIR)/[email protected]


## ONTOLOGY: obi
.PHONY: mirror-obi
.PRECIOUS: $(MIRRORDIR)/obi.owl
mirror-obi: | $(TMPDIR)
curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/[email protected]
## ONTOLOGY: chebi
.PHONY: mirror-chebi
.PRECIOUS: $(MIRRORDIR)/chebi.owl
ifeq ($(strip $(IMP_LARGE)),true)
mirror-chebi: | $(TMPDIR)
curl -L $(OBOBASE)/chebi.owl.gz --create-dirs -o $(MIRRORDIR)/chebi.owl.gz --retry 4 --max-time 200 && \
$(ROBOT) convert -i $(MIRRORDIR)/chebi.owl.gz -o $(TMPDIR)/[email protected]
else
mirror-chebi:
@echo "Not refreshing chebi because refreshing large imports is disabled (IMP_LARGE=$(IMP_LARGE))."
endif


$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
Expand Down
23 changes: 1 addition & 22 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -2,31 +2,10 @@
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">


<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://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://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://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://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://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://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"/>




<uri name="http://nmrML.org/nmrCV/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>

</group>
</catalog>
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