Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Import ORCIDIO #3071

Merged
merged 2 commits into from
Sep 18, 2023
Merged

Import ORCIDIO #3071

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
52f41a3
import orcidio
anitacaron Sep 18, 2023
323ef88
add orcidio_terms.txt file
anitacaron Sep 18, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ These are the current imports in UBERON
| bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
| nbo | http://purl.obolibrary.org/obo/nbo.owl | None |
| orcidio | https://w3id.org/orcidio/orcidio.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
14 changes: 11 additions & 3 deletions src/ontology/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for uberon
# Generated using ontology-development-kit
# ODK Version: v1.4.1
# ODK Version: v1.4.2
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead

Expand Down Expand Up @@ -44,7 +44,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE)
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format
SPARQL_EXPORTS = basic-report
ODK_VERSION_MAKEFILE = v1.4.1
ODK_VERSION_MAKEFILE = v1.4.2

TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
Expand Down Expand Up @@ -114,7 +114,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo
IMPORTS = pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio

IMPORT_ROOTS = $(IMPORTDIR)/merged_import
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -496,6 +496,14 @@ mirror-nbo: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/nbo/nbo-base.owl --create-dirs -o $(MIRRORDIR)/nbo.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/nbo.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: orcidio
.PHONY: mirror-orcidio
.PRECIOUS: $(MIRRORDIR)/orcidio.owl
mirror-orcidio: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://w3id.org/orcidio/orcidio.owl -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi

ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
MERGE_MIRRORS = true

Expand Down
Loading
Loading