obophenotype · matentzn · Sep 3, 2024 · Dec 13, 2023 · Dec 13, 2023 · Dec 13, 2023
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4
+    container: obolibrary/odkfull:v1.5.2
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -29,6 +29,5 @@ jobs:
       - name: Run ontology QC checks
         env:
           DEFAULT_BRANCH: master
-        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
-
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 
diff --git a/.gitignore b/.gitignore
@@ -148,13 +148,11 @@ src/curation/s3/
 src/curation/s3/hp/abnormalDegenerationOfAnatomicalEntity.tsv
 src/curation/tmp/
 src/curation/upheno-fillers-no-id/
-src/curation/upheno-fillers/
 src/curation/upheno-profiles/
 src/curation/upheno-release-prepare/
 src/curation/upheno-release/
 src/curation/upheno-stats/
 src/curation/upheno-stats2/
-src/curation/upheno_id_map.txt
 src/curation/upheno_release/all/upheno_old_metazoa.owl
 src/ontology/AWSCLIV2.pkg
 src/ontology/archive/inferred_ontology.owl
@@ -216,3 +214,29 @@ src/scripts/upheno_all_with_relations_mod.owl
 sync.sh
 src/scripts/__pycache__/
 src/scripts/chebi.txt
+src/ontology/log.txt
+src/ontology/imports/merged_import.owl
+upheno-base-with-bridge.json
+upheno-base-with-bridge.obo
+upheno-base-with-bridge.owl
+upheno-base.json
+upheno-base.obo
+upheno-base.owl
+upheno-basic.json
+upheno-basic.obo
+upheno-basic.owl
+upheno-curated.json
+upheno-curated.obo
+upheno-curated.owl
+upheno-equivalence-model.json
+upheno-equivalence-model.obo
+upheno-equivalence-model.owl
+upheno-full.json
+upheno-full.obo
+upheno-full.owl
+upheno-old-model.json
+upheno-old-model.obo
+upheno-old-model.owl
+upheno.json
+upheno.obo
+upheno.owl
diff --git a/mappings/upheno-species-independent.sssom.tsv b/mappings/upheno-species-independent.sssom.tsv
diff --git a/patterns/definitions.owl b/patterns/definitions.owl
diff --git a/patterns/pattern.owl b/patterns/pattern.owl
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -17,6 +17,8 @@ sphinx-rtd-theme = {version = "^1.0.0", extras = ["docs"]}
 sphinx-autodoc-typehints = {version = "^1.19.4", extras = ["docs"]}
 sphinx-click = {version = "^4.3.0", extras = ["docs"]}
 myst-parser = {version = "^0.18.1", extras = ["docs"]}
+pandas = "^2.2.2"
+sssom = "^0.4.9"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.1.2"

diff --git a/reports/upheno-base.owl-obo-report.tsv b/reports/upheno-base.owl-obo-report.tsv
diff --git a/run.sh.conf b/run.sh.conf
@@ -0,0 +1 @@
+ODK_TAG=v1.5.2
diff --git a/src/attic/upheno_id_map_december_2023.txt b/src/attic/upheno_id_map_december_2023.txt
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfAnatomicalEntity.yaml b/src/curation/changed-patterns/abnormalAbsenceOfAnatomicalEntity.yaml
@@ -0,0 +1,39 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+annotations:
+- annotationProperty: exact_synonym
+  text: missing %s
+  vars:
+  - anatomical_entity
+classes:
+  abnormal: PATO:0000460
+  absent: PATO:0000462
+  anatomical entity: UBERON:0001062
+contributors:
+- https://orcid.org/0000-0001-9076-6015
+- https://orcid.org/0000-0002-3528-5267
+- https://orcid.org/0000-0001-5208-3432
+- https://orcid.org/0000-0001-7941-2961
+- https://orcid.org/0000-0003-4148-4606
+def:
+  text: Absence of %s.
+  vars:
+  - anatomical_entity
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absent'' and (''inheres_in'' some %s) and (''has_modifier''
+    some ''abnormal''))'
+  vars:
+  - anatomical_entity
+name:
+  text: absent %s
+  vars:
+  - anatomical_entity
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfAnatomicalEntity.yaml
+pattern_name: abnormalAbsenceOfAnatomicalEntity
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+vars:
+  anatomical_entity: '''anatomical entity'''
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfAnatomicalEntityDueToDegeneration.yaml b/src/curation/changed-patterns/abnormalAbsenceOfAnatomicalEntityDueToDegeneration.yaml
@@ -0,0 +1,36 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+annotations:
+- annotationProperty: exact_synonym
+  text: loss of %s due to degeneration
+  vars:
+  - anatomical_entity
+classes:
+  abnormal: PATO:0000460
+  absence due to degeneration: PATO:0015001
+  anatomical entity: UBERON:0001062
+contributors:
+- https://orcid.org/0000-0002-3528-5267
+- https://orcid.org/0000-0001-5208-3432
+def:
+  text: Complete wasting (loss) of %s tissue that was once present.
+  vars:
+  - anatomical_entity
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absence due to degeneration'' and (''inheres_in'' some
+    %s) and (''has_modifier'' some ''abnormal''))'
+  vars:
+  - anatomical_entity
+name:
+  text: missing %s due to degeneration
+  vars:
+  - anatomical_entity
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfAnatomicalEntityDueToDegeneration.yaml
+pattern_name: abnormalAbsenceOfAnatomicalEntityDueToDegeneration
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+vars:
+  anatomical_entity: '''anatomical entity'''
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfAnatomicalEntityInLocation.yaml b/src/curation/changed-patterns/abnormalAbsenceOfAnatomicalEntityInLocation.yaml
@@ -0,0 +1,42 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+annotations:
+- annotationProperty: exact_synonym
+  text: Missing %s in the %s
+  vars:
+  - anatomical_entity
+  - location
+classes:
+  abnormal: PATO:0000460
+  absent: PATO:0000462
+  anatomical entity: UBERON:0001062
+  independent continuant: BFO:0000004
+contributors:
+- https://orcid.org/0000-0001-5208-3432
+def:
+  text: Absence of the %s in the %s.
+  vars:
+  - anatomical_entity
+  - location
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absent'' and (''inheres_in'' some (%s and (''part_of''
+    some %s))) and (''has_modifier'' some ''abnormal''))'
+  vars:
+  - anatomical_entity
+  - location
+name:
+  text: absent %s in the %s
+  vars:
+  - anatomical_entity
+  - location
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfAnatomicalEntityInLocation.yaml
+pattern_name: abnormalAbsenceOfAnatomicalEntityInLocation
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+  part_of: BFO:0000050
+vars:
+  anatomical_entity: '''anatomical entity'''
+  location: '''independent continuant'''
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfBiologicalProcess.yaml b/src/curation/changed-patterns/abnormalAbsenceOfBiologicalProcess.yaml
@@ -0,0 +1,32 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+classes:
+  abnormal: PATO:0000460
+  absent: PATO:0000462
+  biological process: GO:0008150
+contributors:
+- https://orcid.org/0000-0001-9076-6015
+- https://orcid.org/0000-0001-5208-3432
+- https://orcid.org/0000-0003-4148-4606
+def:
+  text: Lack of %s.
+  vars:
+  - biological_process
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absent'' and (''inheres_in'' some %s) and (''has_modifier''
+    some ''abnormal''))'
+  vars:
+  - biological_process
+name:
+  text: absent %s
+  vars:
+  - biological_process
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfBiologicalProcess.yaml
+pattern_name: abnormalAbsenceOfBiologicalProcess
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+vars:
+  biological_process: '''biological process'''
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfBiologicalProcessInLocation.yaml b/src/curation/changed-patterns/abnormalAbsenceOfBiologicalProcessInLocation.yaml
@@ -0,0 +1,38 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+classes:
+  abnormal: PATO:0000460
+  absent: PATO:0000462
+  biological process: GO:0008150
+  independent continuant: BFO:0000004
+contributors:
+- https://orcid.org/0000-0001-9076-6015
+- https://orcid.org/0000-0001-5208-3432
+- https://orcid.org/0000-0003-4148-4606
+def:
+  text: Absent or undetectable %s in %s.
+  vars:
+  - biological_process
+  - location
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absent'' and (''inheres_in'' some (%s and (''occurs_in''
+    some %s))) and (''has_modifier'' some ''abnormal''))'
+  vars:
+  - biological_process
+  - location
+name:
+  text: absent %s in %s
+  vars:
+  - biological_process
+  - location
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfBiologicalProcessInLocation.yaml
+pattern_name: abnormalAbsenceOfBiologicalProcessInLocation
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+  occurs_in: BFO:0000066
+vars:
+  biological_process: '''biological process'''
+  location: '''independent continuant'''
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfChemicalEntity.yaml b/src/curation/changed-patterns/abnormalAbsenceOfChemicalEntity.yaml
@@ -0,0 +1,35 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+classes:
+  abnormal: PATO:0000460
+  absent: PATO:0000462
+  chemical entity: CHEBI:24431
+contributors:
+- https://orcid.org/0000-0002-9900-7880
+- https://orcid.org/0000-0002-3528-5267
+- https://orcid.org/0000-0001-5208-3432
+- https://orcid.org/0000-0003-4148-4606
+- https://orcid.org/0000-0001-7941-2961
+- https://orcid.org/0000-0001-9076-6015
+def:
+  text: Absent or undetectable level of %s.
+  vars:
+  - chemical_entity
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absent'' and (''inheres_in'' some %s) and (''has_modifier''
+    some ''abnormal''))'
+  vars:
+  - chemical_entity
+name:
+  text: absent %s
+  vars:
+  - chemical_entity
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfChemicalEntity.yaml
+pattern_name: abnormalAbsenceOfChemicalEntity
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+vars:
+  chemical_entity: '''chemical entity'''
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfChemicalEntityInLocation.yaml b/src/curation/changed-patterns/abnormalAbsenceOfChemicalEntityInLocation.yaml
@@ -0,0 +1,41 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+classes:
+  abnormal: PATO:0000460
+  absent: PATO:0000462
+  chemical entity: CHEBI:24431
+  independent continuant: BFO:0000004
+contributors:
+- https://orcid.org/0000-0003-4606-0597
+- https://orcid.org/0000-0002-3528-5267
+- https://orcid.org/0000-0001-5208-3432
+- https://orcid.org/0000-0003-4148-4606
+- https://orcid.org/0000-0001-7941-2961
+- https://orcid.org/0000-0001-9076-6015
+def:
+  text: Absent or undetectable level of %s in %s.
+  vars:
+  - chemical_entity
+  - location
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absent'' and (''inheres_in'' some (%s and (''part_of''
+    some %s))) and (''has_modifier'' some ''abnormal''))'
+  vars:
+  - chemical_entity
+  - location
+name:
+  text: absent %s in %s
+  vars:
+  - chemical_entity
+  - location
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfChemicalEntityInLocation.yaml
+pattern_name: abnormalAbsenceOfChemicalEntityInLocation
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+  part_of: BFO:0000050
+vars:
+  chemical_entity: '''chemical entity'''
+  location: '''independent continuant'''
diff --git a/src/curation/changed-patterns/abnormalAbsenceOfMolecularFunction.yaml b/src/curation/changed-patterns/abnormalAbsenceOfMolecularFunction.yaml
@@ -0,0 +1,30 @@
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+classes:
+  abnormal: PATO:0000460
+  absent: PATO:0000462
+  molecular function: GO:0003674
+contributors:
+- https://orcid.org/0000-0002-3528-5267
+def:
+  text: Absent or undetectable level of %s.
+  vars:
+  - molecular_function
+description: ''
+equivalentTo:
+  text: '''has_part'' some (''absent'' and (''inheres_in'' some %s) and (''has_modifier''
+    some ''abnormal''))'
+  vars:
+  - molecular_function
+name:
+  text: absent %s
+  vars:
+  - molecular_function
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfMolecularFunction.yaml
+pattern_name: abnormalAbsenceOfMolecularFunction
+relations:
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+  inheres_in: RO:0000052
+vars:
+  molecular_function: '''molecular function'''