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Rework roles #166

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merged 15 commits into from
Oct 24, 2022
Merged

Rework roles #166

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3576ca2
drop OMRSE import module #144
StroemPhi Oct 13, 2022
e9ee0cf
drop CRO import module
StroemPhi Oct 13, 2022
0580d32
check in forgotten code for dropping OMRSE import
StroemPhi Oct 13, 2022
c5a6982
update test instances
StroemPhi Oct 14, 2022
425772b
update AEON_0000006 (event organizer role)
StroemPhi Oct 14, 2022
5754acc
make AEON_0000008 (event committee chair role) also a subclass of OOS…
StroemPhi Oct 14, 2022
41310b5
sharpen definition of AEON_0000006 (event organizer role)
StroemPhi Oct 24, 2022
73cd49f
restrict AEON_0000009 (contact person role) to event context
StroemPhi Oct 24, 2022
c1e60c0
change genus to role instead of CRO_0000000 of AEON_0000010 (event at…
StroemPhi Oct 24, 2022
0e1c420
add 'realized in' some 'organized sociocultural event' axiom on AEON_…
StroemPhi Oct 24, 2022
b6c445d
revive AEON_0000012 (human reviewer role) due to issues with CRO equi…
StroemPhi Oct 24, 2022
23344af
make role genus for speaker roles and add event as realization contex…
StroemPhi Oct 24, 2022
2dbe6fb
delete duplicate definition of AEON_0000014 (keynote speaker role)
StroemPhi Oct 24, 2022
65f24bf
use role as genus in text def and add realized by organized event axiom
StroemPhi Oct 24, 2022
56c73ac
add term status annotations
StroemPhi Oct 24, 2022
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2 changes: 0 additions & 2 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -20,13 +20,11 @@ These are the current imports in AEON
| ro | http://purl.obolibrary.org/obo/ro.owl | custom |
| omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
| iao | http://purl.obolibrary.org/obo/iao.owl | custom |
| cro | http://purl.obolibrary.org/obo/cro.owl | custom |
| envo | http://purl.obolibrary.org/obo/envo.owl | custom |
| txpo | http://purl.obolibrary.org/obo/txpo.owl | custom |
| ico | http://purl.obolibrary.org/obo/ico.owl | custom |
| obi | http://purl.obolibrary.org/obo/obi.owl | custom |
| obib | http://purl.obolibrary.org/obo/obib.owl | custom |
| omrse | http://purl.obolibrary.org/obo/omrse.owl | custom |
| oostt | http://purl.obolibrary.org/obo/oostt.owl | custom |

## Components
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28 changes: 1 addition & 27 deletions src/ontology/Makefile
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Expand Up @@ -97,7 +97,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = bfo ro omo iao cro envo txpo ico obi obib omrse oostt
IMPORTS = bfo ro omo iao envo txpo ico obi obib oostt

IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -288,10 +288,6 @@ $(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combine

$(IMPORTDIR)/iao_import.owl: $(MIRRORDIR)/iao.owl
echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in aeon.Makefile!" && false
## Module for ontology: cro

$(IMPORTDIR)/cro_import.owl: $(MIRRORDIR)/cro.owl
echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in aeon.Makefile!" && false
## Module for ontology: envo

$(IMPORTDIR)/envo_import.owl: $(MIRRORDIR)/envo.owl
Expand All @@ -312,10 +308,6 @@ $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl

$(IMPORTDIR)/obib_import.owl: $(MIRRORDIR)/obib.owl
echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in aeon.Makefile!" && false
## Module for ontology: omrse

$(IMPORTDIR)/omrse_import.owl: $(MIRRORDIR)/omrse.owl
echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in aeon.Makefile!" && false
## Module for ontology: oostt

$(IMPORTDIR)/oostt_import.owl: $(MIRRORDIR)/oostt.owl
Expand Down Expand Up @@ -387,15 +379,6 @@ mirror-iao: | $(TMPDIR)
mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: cro
.PHONY: mirror-cro
.PRECIOUS: $(MIRRORDIR)/cro.owl
mirror-cro: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/cro.owl --create-dirs -o $(MIRRORDIR)/cro.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/cro.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: envo
.PHONY: mirror-envo
.PRECIOUS: $(MIRRORDIR)/envo.owl
Expand Down Expand Up @@ -443,15 +426,6 @@ mirror-obib: | $(TMPDIR)
mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: omrse
.PHONY: mirror-omrse
.PRECIOUS: $(MIRRORDIR)/omrse.owl
mirror-omrse: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/omrse.owl --create-dirs -o $(MIRRORDIR)/omrse.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/omrse.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: oostt
.PHONY: mirror-oostt
.PRECIOUS: $(MIRRORDIR)/oostt.owl
Expand Down
194 changes: 118 additions & 76 deletions src/ontology/aeon-edit.owl
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9 changes: 3 additions & 6 deletions src/ontology/aeon-odk.yaml
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Expand Up @@ -42,11 +42,12 @@ import_group:
- ro
- omo
- iao
- cro
- envo
- txpo
- ico
- obib
- obi
- obib
- oostt
mirror_max_time_download: 200
mirror_retry_download: 4
module_type: slme
Expand All @@ -64,8 +65,6 @@ import_group:
- id: iao
module_type: custom
#slme_individuals: include
- id: cro
module_type: custom
- id: envo
module_type: custom
- id: txpo
Expand All @@ -78,8 +77,6 @@ import_group:
module_type: custom
- id: obib
module_type: custom
- id: omrse
module_type: custom
- id: oostt
module_type: custom
rebuild_if_source_changes: true
Expand Down
31 changes: 1 addition & 30 deletions src/ontology/aeon.Makefile
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Expand Up @@ -49,20 +49,6 @@ $(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms.txt
merge -i [email protected] \
--output [email protected] && mv [email protected] $@; fi


## Module for ontology: cro

$(IMPORTDIR)/cro_import.owl: $(MIRRORDIR)/cro.owl $(IMPORTDIR)/cro_terms.txt
if [ $(IMP) = true ]; then $(ROBOT) filter -i $< -T $(IMPORTDIR)/cro_terms.txt --select "self ancestors" --signature false --trim true \
--output [email protected]; fi
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
query --update ../sparql/preprocess-module_provo.ru \
filter -T $(IMPORTDIR)/cro_terms.txt --select "self annotations ontology" --signature false --trim true \
query --update ../sparql/postprocess-module_2.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
merge -i [email protected] \
--output [email protected] && mv [email protected] $@; fi

## Module for ontology: obib

$(IMPORTDIR)/obib_import.owl: $(MIRRORDIR)/obib.owl $(IMPORTDIR)/obib_terms.txt
Expand All @@ -76,20 +62,7 @@ $(IMPORTDIR)/obib_import.owl: $(MIRRORDIR)/obib.owl $(IMPORTDIR)/obib_terms.txt
merge -i [email protected] \
--output [email protected] && mv [email protected] $@; fi

## Module for ontology: omrse

$(IMPORTDIR)/omrse_import.owl: $(MIRRORDIR)/omrse.owl $(IMPORTDIR)/omrse_terms.txt
if [ $(IMP) = true ]; then $(ROBOT) filter -i $< -T $(IMPORTDIR)/omrse_terms.txt --select "self ancestors domains ranges equivalents" --signature true --trim true \
--output [email protected]; fi
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
query --update ../sparql/preprocess-module_provo.ru \
filter -T $(IMPORTDIR)/omrse_terms.txt --select "self annotations ontology equivalents" --signature true --trim true --axioms "tbox"\
query --update ../sparql/postprocess-module_2.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
merge -i [email protected] \
--output [email protected] && mv [email protected] $@; fi

## Module for ontology: omrse
## Module for ontology: oostt

$(IMPORTDIR)/oostt_import.owl: $(MIRRORDIR)/oostt.owl $(IMPORTDIR)/oostt_terms.txt
if [ $(IMP) = true ]; then $(ROBOT) filter -i $< -T $(IMPORTDIR)/oostt_terms.txt --select "self ancestors domains ranges equivalents" --signature true --trim true \
Expand All @@ -102,8 +75,6 @@ $(IMPORTDIR)/oostt_import.owl: $(MIRRORDIR)/oostt.owl $(IMPORTDIR)/oostt_terms.t
merge -i [email protected] \
--output [email protected] && mv [email protected] $@; fi



## Module for ontology: envo

$(IMPORTDIR)/envo_import.owl: $(MIRRORDIR)/envo.owl $(IMPORTDIR)/envo_terms.txt
Expand Down
4 changes: 0 additions & 4 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -9,8 +9,6 @@
<uri name="http://purl.obolibrary.org/obo/aeon/imports/omo_import.obo" uri="imports/omo_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/iao_import.owl" uri="imports/iao_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/iao_import.obo" uri="imports/iao_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/cro_import.owl" uri="imports/cro_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/cro_import.obo" uri="imports/cro_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/envo_import.owl" uri="imports/envo_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/envo_import.obo" uri="imports/envo_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/txpo_import.owl" uri="imports/txpo_import.owl"/>
Expand All @@ -21,8 +19,6 @@
<uri name="http://purl.obolibrary.org/obo/aeon/imports/obi_import.obo" uri="imports/obi_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/obib_import.owl" uri="imports/obib_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/obib_import.obo" uri="imports/obib_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/omrse_import.owl" uri="imports/omrse_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/omrse_import.obo" uri="imports/omrse_import.obo"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/oostt_import.owl" uri="imports/oostt_import.owl"/>
<uri name="http://purl.obolibrary.org/obo/aeon/imports/oostt_import.obo" uri="imports/oostt_import.obo"/>
</group>
Expand Down
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