Merge pull request #40 from nmrML/12_rework_NMR_instruments_and_manuf…

…acutrers_eqivalence_approach

Rework NMR instruments and manufacutrers

.gitignore

@@ -46,3 +46,4 @@ src/patterns/all_pattern_terms.txt
 .idea/vcs.xml
 .idea/workspace.xml
 .idea/misc.xml
+/.idea

docs/odk-workflows/RepositoryFileStructure.md

@@ -19,6 +19,8 @@ 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 |
+| obi | http://purl.obolibrary.org/obo/obi.owl | custom |
 | chebi | http://purl.obolibrary.org/obo/chebi.owl | None |
 
 ## Components

src/ontology/Makefile

@@ -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=                a4c0ac9d9d7ac7b03403ce94c3d1d76c44d412b433490d312ed763a12e8e19f6
+CONFIG_HASH=                1ba644404ead28f12b159a84d638daf10791c394ce2f9060998152d134df9dcc
 
 
 # ----------------------------------------
@@ -159,7 +159,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  bfo ro omo chebi
+IMPORTS =  bfo ro omo iao obi chebi
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -376,6 +376,10 @@ $(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: obi
+
+$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl
+	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in nmrCV.Makefile!" && false
 ## Module for ontology: chebi
 
 $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_combined.txt
@@ -427,7 +431,7 @@ mirror-bfo: | $(TMPDIR)
 .PHONY: mirror-ro
 .PRECIOUS: $(MIRRORDIR)/ro.owl
 mirror-ro: | $(TMPDIR)
-	curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \
+	curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \
 	$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl
 
 
@@ -439,6 +443,22 @@ mirror-omo: | $(TMPDIR)
 	$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl
 
 
+## 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) remove -i $(TMPDIR)/iao-download.owl --base-iri $(OBOBASE)/IAO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
+
+
+## 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) remove -i $(TMPDIR)/obi-download.owl --base-iri $(OBOBASE)/OBI --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
+
+
 ## ONTOLOGY: chebi
 .PHONY: mirror-chebi
 .PRECIOUS: $(MIRRORDIR)/chebi.owl

src/ontology/catalog-v001.xml

@@ -6,6 +6,8 @@
   <uri name="http://nmrML.org/nmrCV/imports/ro_import.owl" uri="imports/ro_import.owl"/>
   <uri name="http://nmrML.org/nmrCV/imports/omo_import.owl" uri="imports/omo_import.owl"/>
   <uri name="http://nmrML.org/nmrCV/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
+  <uri name="http://nmrML.org/nmrCV/imports/iao_import.owl" uri="imports/iao_import.owl"/>
+  <uri name="http://nmrML.org/nmrCV/imports/obi_import.owl" uri="imports/obi_import.owl"/>
 
 </group>
 </catalog>

src/ontology/imports/iao_terms.txt

@@ -0,0 +1,3 @@
+IAO:0000033 # 'directive information entity'
+    IAO:0000005 # 'objective specification'
+    IAO:0000104 # 'plan specification'

src/ontology/imports/obi_remove_list.txt

@@ -0,0 +1,34 @@
+OBI:0200000 # 'data transformation'
+OBI:0200166 # 'data transformation objective'
+OBI:0200111 # 'data visualization'
+OBI:0000659 # 'specimen collection process'
+OBI:0100051 # specimen
+OBI:0000953 # 'processed specimen'
+OBI:0000112 # 'specimen role'
+OBI:0002076 # 'collection of specimens'
+OBI:0000684 # 'specimen collection objective'
+OBI:0001933 # 'value specification'
+OBI:0000017 # 'regulatory role'
+OBI:0000947 # 'service provider role'
+OBI:0002989 # 'material supplier'
+OBI:0000450 # 'regulatory agency'
+IAO:0000009
+IAO:0000010
+IAO:0000027
+IAO:0000030
+IAO:0000037
+IAO:0000038
+IAO:0000064
+IAO:0000078
+IAO:0000098
+IAO:0000100
+IAO:0000101
+IAO:0000179
+IAO:0000180
+IAO:0000183
+IAO:0000184
+IAO:0000310
+NCBITaxon:10239
+NCBITaxon:2
+NCBITaxon:2157
+NCBITaxon:2759

src/ontology/imports/obi_terms.txt

@@ -0,0 +1,11 @@
+OBI:0000835 # manufacturer
+OBI:0100026 # organism
+NCBITaxon:9606 # Homo sapiens
+OBI:0000245 # organization
+OBI:0000571 # 'manufacturer role'
+OBI:0000011 # planned process
+OBI:0000457 # manufacturing
+OBI:0000832 # 'measurement device'
+OBI:0400107 # computer
+OBI:0000836 # test tube
+OBI:0000304 # is_manufactured_by