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Merged
XimeAixa merged 6 commits into from
Sep 23, 2026
Merged

Import PR:000000001 for protein #39

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74fbe3c
import PR:000000001 and parents from PR and COB, update repo and refr…
XimeAixa Sep 18, 2026
82a9be9
replace IDPO protein term with PR, obsolete IDPO protein and compound
XimeAixa Sep 18, 2026
fe94628
protein region definition fix
XimeAixa Sep 18, 2026
3e3a912
ontology root added for idp
XimeAixa Sep 18, 2026
8c732c3
remove LLPS axioms
XimeAixa Sep 18, 2026
a5906cf
refresh imports
XimeAixa Sep 23, 2026
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2 changes: 2 additions & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -21,6 +21,8 @@ These are the current imports in IDPO
| bfo | http://purl.obolibrary.org/obo/bfo.owl | slme |
| go | http://purl.obolibrary.org/obo/go.owl | slme |
| iao | http://purl.obolibrary.org/obo/iao.owl | slme |
| pr | http://purl.obolibrary.org/obo/pr.owl | slme |
| cob | http://purl.obolibrary.org/obo/cob.owl | slme |
## 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:

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27 changes: 25 additions & 2 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= 98b52c17665ae96ff0faa9ab8d0db7ef77748df8fe2cf20122e9cab3604e090b
CONFIG_HASH= 7b81db2dfb9d6b1b60d5081ec9ff3101008a1dd872d7573a3fac3c2821f98c57


# ----------------------------------------
Expand Down Expand Up @@ -188,7 +188,7 @@ all_main: $(MAIN_FILES)
# ----------------------------------------


IMPORTS = ro omo bfo go iao
IMPORTS = ro omo bfo go iao pr cob

IMPORT_ROOTS = $(IMPORTDIR)/merged_import
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
Expand Down Expand Up @@ -408,6 +408,11 @@ ALL_TERMS = $(foreach imp, $(IMPORTS), $(IMPORTDIR)/$(imp)_terms.txt)
$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(ALL_TERMS) \
$(IMPORTSEED) | all_robot_plugins
$(ROBOT) merge --input $< \
remove --select "<http://purl.obolibrary.org/obo/CHEBI_*>" \
remove --select "<http://purl.obolibrary.org/obo/SO_*>" \
remove --select "<http://purl.obolibrary.org/obo/UBERON_*>" \
remove --select "<http://purl.obolibrary.org/obo/CL_*>" \
remove --select "<http://purl.obolibrary.org/obo/NCBITaxon_*>" \
extract $(foreach f, $(ALL_TERMS), --term-file $(f)) $(T_IMPORTSEED) \
--force true --copy-ontology-annotations false \
--individuals exclude \
Expand Down Expand Up @@ -492,6 +497,24 @@ 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 $(TMPDIR)/$@.owl


## ONTOLOGY: pr
.PHONY: mirror-pr
.PRECIOUS: $(MIRRORDIR)/pr.owl
ifeq ($(IMP_LARGE),true)
mirror-pr: | $(TMPDIR)
curl -L $(OBOBASE)/pr.owl.gz --create-dirs -o $(MIRRORDIR)/pr.owl.gz --retry 4 --max-time 200 && \
$(ROBOT) remove -i $(MIRRORDIR)/pr.owl.gz --base-iri http://purl.obolibrary.org/obo/PR --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
endif


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

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

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42 changes: 21 additions & 21 deletions src/ontology/idpo-edit.owl
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Expand Up @@ -13,10 +13,9 @@ Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000029>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000075>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000083>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000091>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000092>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000094>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000095>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000096>)
Annotation(<http://purl.obolibrary.org/obo/IAO_0000700> <http://purl.obolibrary.org/obo/IDPO_0000100>)
Annotation(<http://purl.org/dc/terms/description> "It describes structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state.")
Annotation(<http://purl.org/dc/terms/license> <https://creativecommons.org/licenses/by/4.0/>)
Expand Down Expand Up @@ -181,7 +180,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespac
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000001> "IDPO:0000001")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000001> "protein structural state")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000001> <http://purl.obolibrary.org/obo/BFO_0000019>)
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000080> ObjectUnionOf(<http://purl.obolibrary.org/obo/IDPO_0000094> <http://purl.obolibrary.org/obo/IDPO_0000095>)))
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000080> ObjectUnionOf(<http://purl.obolibrary.org/obo/IDPO_0000095> <http://purl.obolibrary.org/obo/PR_000000001>)))

# Class: <http://purl.obolibrary.org/obo/IDPO_0000002> (disorder state)

Expand Down Expand Up @@ -420,8 +419,6 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespac
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000025> "IDPO:0000025")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000025> "liquid-liquid phase separation")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000025> <http://purl.obolibrary.org/obo/IDPO_0000084>)
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000025> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/IDPO_0000087> <http://purl.obolibrary.org/obo/IDPO_0000076>))
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000025> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/IDPO_0000088> <http://purl.obolibrary.org/obo/IDPO_0000076>))

# Class: <http://purl.obolibrary.org/obo/IDPO_0000026> (condensate ageing)

Expand Down Expand Up @@ -824,7 +821,6 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespac
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000075> "IDPO:0000075")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000075> "condensate material state")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000075> <http://purl.obolibrary.org/obo/BFO_0000019>)
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000075> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000092>))

# Class: <http://purl.obolibrary.org/obo/IDPO_0000076> (liquid-like condensate state)

Expand Down Expand Up @@ -870,6 +866,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000079> <http://purl.obolibrary
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000080> "OBSOLETE. A temporally extended process in which a protein or protein region changes from one state to another, under specific conditions.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000010>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000080> <http://purl.obolibrary.org/obo/IDPO_0000083>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000080> "IDPO:0000080")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IDPO_0000080> "Obsolete due to semantic ambiguity and excessive generality.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000080> "obsolete transition")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/IDPO_0000080> "true"^^xsd:boolean)
Expand Down Expand Up @@ -934,17 +931,19 @@ SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000086> <http://purl.obolibrary
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000089> "OBSOLETE. A quality of a protein or protein region that describes its organization, conformation, or material properties at a given time, under specific conditions, and that can change dynamically.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000089> <http://purl.obolibrary.org/obo/IDPO_0000001>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000089> <http://purl.obolibrary.org/obo/IDPO_0000075>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000089> "IDPO:0000089")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IDPO_0000089> "The term was originally introduced as a high-level grouping class but is now obsolete because it is overly general and semantically ambiguous.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000089> "obsolete state")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/IDPO_0000089> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000091> (compound)
# Class: <http://purl.obolibrary.org/obo/IDPO_0000091> (obsolete compound)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000091> "An object composed of two or more distinct chemical constituents.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000091> "material_entity")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000091> "OBSOLETE. An object composed of two or more distinct chemical constituents.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#consider> <http://purl.obolibrary.org/obo/IDPO_0000091> <http://purl.obolibrary.org/obo/COB_0000013>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000091> "IDPO:0000091")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000091> "compound")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000091> <http://purl.obolibrary.org/obo/BFO_0000030>)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IDPO_0000091> "Obsolete because the term is no longer used in IDPO.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000091> "obsolete compound")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/IDPO_0000091> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000092> (condensate)

Expand All @@ -963,22 +962,23 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000093> "bi
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000093> <http://purl.obolibrary.org/obo/IDPO_0000092>)
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000093> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002353> <http://purl.obolibrary.org/obo/IDPO_0000084>))

# Class: <http://purl.obolibrary.org/obo/IDPO_0000094> (protein)
# Class: <http://purl.obolibrary.org/obo/IDPO_0000094> (obsolete protein)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000094> "An object composed of one or more polypeptide chains.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000094> "material_entity")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000094> "OBSOLETE. An object composed of one or more polypeptide chains.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/IDPO_0000094> <http://purl.obolibrary.org/obo/PR_000000001>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000094> "IDPO:0000094")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000094> "protein")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000094> <http://purl.obolibrary.org/obo/BFO_0000030>)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/IDPO_0000094> "Obsolete because the term duplicates PR:000000001, which is reused directly.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000094> "obsolete protein")
AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/IDPO_0000094> "true"^^xsd:boolean)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000095> (protein region)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000095> "A fiat object part that is a contiguous portion of a protein distinguishable by its structural, functional, or sequence properties.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/IDPO_0000095> "A fiat object part that is a contiguous portion of a protein.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000095> "material_entity")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000095> "IDPO:0000095")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000095> "protein region")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000095> <http://purl.obolibrary.org/obo/BFO_0000024>)
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000095> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/IDPO_0000094>))
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000095> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/PR_000000001>))

# Class: <http://purl.obolibrary.org/obo/IDPO_0000096> (intrinsically disordered protein)

Expand All @@ -987,8 +987,8 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/OMO_0003000> <http://purl.ob
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/IDPO_0000096> "material_entity")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000096> "IDPO:0000096")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000096> "intrinsically disordered protein")
EquivalentClasses(<http://purl.obolibrary.org/obo/IDPO_0000096> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/IDPO_0000094> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/IDPO_0000002>)))
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000096> <http://purl.obolibrary.org/obo/IDPO_0000094>)
EquivalentClasses(<http://purl.obolibrary.org/obo/IDPO_0000096> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PR_000000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/IDPO_0000002>)))
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000096> <http://purl.obolibrary.org/obo/PR_000000001>)

# Class: <http://purl.obolibrary.org/obo/IDPO_0000097> (intrinsically disordered region)

Expand Down Expand Up @@ -1025,7 +1025,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespac
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/IDPO_0000100> "IDPO:0000100")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IDPO_0000100> "disorder role")
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000100> <http://purl.obolibrary.org/obo/BFO_0000023>)
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000100> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000081> ObjectUnionOf(<http://purl.obolibrary.org/obo/IDPO_0000094> <http://purl.obolibrary.org/obo/IDPO_0000095>)))
SubClassOf(<http://purl.obolibrary.org/obo/IDPO_0000100> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000081> ObjectUnionOf(<http://purl.obolibrary.org/obo/IDPO_0000095> <http://purl.obolibrary.org/obo/PR_000000001>)))

# Class: <http://purl.obolibrary.org/obo/IDPO_0000101> (N-glycosylation target role)

Expand Down
12 changes: 12 additions & 0 deletions src/ontology/idpo-odk.yaml
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Expand Up @@ -15,6 +15,12 @@ export_formats:
import_group:
use_base_merging: TRUE
slme_individuals: exclude
exclude_iri_patterns:
- <http://purl.obolibrary.org/obo/CHEBI_*>
- <http://purl.obolibrary.org/obo/SO_*>
- <http://purl.obolibrary.org/obo/UBERON_*>
- <http://purl.obolibrary.org/obo/CL_*>
- <http://purl.obolibrary.org/obo/NCBITaxon_*>
products:
- id: ro
use_base: TRUE
Expand All @@ -23,6 +29,12 @@ import_group:
- id: go
use_base: TRUE
- id: iao
- id: pr
use_gzipped: TRUE
is_large: TRUE
make_base: TRUE
- id: cob
use_base: TRUE
documentation:
documentation_system: mkdocs
robot_java_args: "-Xmx8G"
Expand Down
1 change: 1 addition & 0 deletions src/ontology/imports/cob_terms.txt
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@@ -0,0 +1 @@
COB:0000013
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