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Filter annotations not listed #2112

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merged 6 commits into from
Nov 8, 2021
Merged

Filter annotations not listed #2112

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238a3d3
Add SPARQL file to filter annotations not listed
Oct 20, 2021
2f1686c
makefile changes
shawntanzk Oct 25, 2021
909aa45
Update sparql file
Oct 26, 2021
8a212f5
Update profile.txt
shawntanzk Oct 26, 2021
598ad70
Merge branch 'master' into annotation-violation
shawntanzk Nov 1, 2021
50cf4c2
Merge branch 'master' into annotation-violation
Nov 8, 2021
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6 changes: 3 additions & 3 deletions .github/workflows/docs.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
# This is a basic workflow to help you get started with Actions

# Basic ODK workflow
name: Docs

# Controls when the action will run.
Expand All @@ -21,4 +20,5 @@ jobs:
# Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
CONFIG_FILE: mkdocs.yaml
CONFIG_FILE: mkdocs.yaml

11 changes: 6 additions & 5 deletions src/ontology/Makefile
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Expand Up @@ -31,12 +31,13 @@ TMPDIR= tmp
SCRIPTSDIR= ../scripts
SPARQLDIR = ../sparql
COMPONENTSDIR = components
REPORT_FAIL_ON = None
REPORT_LABEL = -l true
REPORT_PROFILE_OPTS =
ROBOT_PROFILE = profile.txt
REPORT_FAIL_ON = ERROR
REPORT_LABEL =
REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE)
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference
SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference illegal-annotation-property
SPARQL_EXPORTS = basic-report
ODK_VERSION_MAKEFILE = v1.2.31

TODAY ?= $(shell date +%Y-%m-%d)
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25 changes: 25 additions & 0 deletions src/ontology/profile.txt
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@@ -0,0 +1,25 @@
WARN annotation_whitespace
ERROR deprecated_boolean_datatype
ERROR deprecated_class_reference
ERROR deprecated_property_reference
WARN duplicate_definition
WARN duplicate_exact_synonym
WARN duplicate_label_synonym
ERROR duplicate_label
WARN duplicate_scoped_synonym
WARN equivalent_pair
WARN invalid_xref
ERROR label_formatting
ERROR label_whitespace
INFO lowercase_definition
WARN missing_definition
ERROR missing_label
WARN missing_obsolete_label
ERROR missing_ontology_description
ERROR missing_ontology_license
ERROR missing_ontology_title
INFO missing_superclass
ERROR misused_obsolete_label
ERROR multiple_definitions
WARN multiple_equivalent_classes
ERROR multiple_labels
13 changes: 13 additions & 0 deletions src/ontology/uberon-odk.yaml
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Expand Up @@ -85,6 +85,19 @@ subset_group:
- id: amniote-basic
- id: euarchontoglires-basic
robot_java_args: '-Xmx20G'
robot_report:
release_reports: False
fail_on : ERROR
use_labels : False
custom_profile : True
report_on :
- edit
custom_sparql_checks :
- equivalent-classes
- owldef-self-reference
- illegal-annotation-property
custom_sparql_exports :
- basic-report
owltools_memory: '20G'
create_obo_metadata: FALSE
documentation:
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79 changes: 79 additions & 0 deletions src/sparql/illegal-annotation-property-violation.sparql
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@@ -0,0 +1,79 @@
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?annotation WHERE {
?annotation a owl:AnnotationProperty .
?subj ?annotation ?o .
FILTER (?annotation NOT IN (
<http://geneontology.org/formats/oboInOwl#created_by>,
<http://purl.obolibrary.org/obo/IAO_0000115>,
<http://purl.obolibrary.org/obo/IAO_0000116>,
<http://purl.obolibrary.org/obo/IAO_0000231>,
<http://purl.obolibrary.org/obo/IAO_0000232>,
<http://purl.obolibrary.org/obo/IAO_0000412>,
<http://purl.obolibrary.org/obo/IAO_0000589>,
<http://purl.obolibrary.org/obo/IAO_0100001>,
<http://purl.obolibrary.org/obo/RO_0002161>,
<http://purl.obolibrary.org/obo/RO_0002171>,
<http://purl.obolibrary.org/obo/RO_0002173>,
<http://purl.obolibrary.org/obo/RO_0002174>,
<http://purl.obolibrary.org/obo/RO_0002175>,
<http://purl.obolibrary.org/obo/RO_0002423>,
<http://purl.obolibrary.org/obo/RO_0002475>,
<http://purl.obolibrary.org/obo/RO_0002575>,
<http://purl.obolibrary.org/obo/RO_0002579>,
<http://purl.obolibrary.org/obo/RO_0002604>,
<http://purl.obolibrary.org/obo/RO_0004049>,
<http://purl.obolibrary.org/obo/RO_0004050>,
<http://purl.obolibrary.org/obo/RO_0040042>,
<http://purl.obolibrary.org/obo/UBPROP_0000001>,
<http://purl.obolibrary.org/obo/UBPROP_0000002>,
<http://purl.obolibrary.org/obo/UBPROP_0000003>,
<http://purl.obolibrary.org/obo/UBPROP_0000004>,
<http://purl.obolibrary.org/obo/UBPROP_0000005>,
<http://purl.obolibrary.org/obo/UBPROP_0000006>,
<http://purl.obolibrary.org/obo/UBPROP_0000007>,
<http://purl.obolibrary.org/obo/UBPROP_0000008>,
<http://purl.obolibrary.org/obo/UBPROP_0000009>,
<http://purl.obolibrary.org/obo/UBPROP_0000010>,
<http://purl.obolibrary.org/obo/UBPROP_0000011>,
<http://purl.obolibrary.org/obo/UBPROP_0000012>,
<http://purl.obolibrary.org/obo/UBPROP_0000013>,
<http://purl.obolibrary.org/obo/UBPROP_0000014>,
<http://purl.obolibrary.org/obo/UBPROP_0000015>,
<http://purl.obolibrary.org/obo/UBPROP_0000103>,
<http://purl.obolibrary.org/obo/UBPROP_0000104>,
<http://purl.obolibrary.org/obo/UBPROP_0000105>,
<http://purl.obolibrary.org/obo/UBPROP_0000106>,
<http://purl.obolibrary.org/obo/UBPROP_0000107>,
<http://purl.obolibrary.org/obo/UBPROP_0000108>,
<http://purl.obolibrary.org/obo/UBPROP_0000111>,
<http://purl.obolibrary.org/obo/UBPROP_0000112>,
<http://purl.obolibrary.org/obo/UBPROP_0000201>,
<http://purl.obolibrary.org/obo/UBPROP_0000202>,
<http://purl.obolibrary.org/obo/term_editor>,
<http://purl.org/dc/elements/1.1/contributor>,
<http://purl.org/dc/elements/1.1/creator>,
<http://purl.org/dc/elements/1.1/date>,
<http://purl.org/dc/elements/1.1/description>,
<http://purl.org/dc/terms/source>,
<http://purl.org/spar/cito/citesAsAuthority>,
<http://www.geneontology.org/formats/oboInOwl#consider>,
<http://www.geneontology.org/formats/oboInOwl#created_by>,
<http://www.geneontology.org/formats/oboInOwl#creation_date>,
<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId>,
<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>,
<http://www.geneontology.org/formats/oboInOwl#hasDbXref>,
<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>,
<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym>,
<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace>,
<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>,
<http://www.geneontology.org/formats/oboInOwl#id>,
<http://www.geneontology.org/formats/oboInOwl#inSubset>,
<http://www.w3.org/2000/01/rdf-schema#comment>,
<http://www.w3.org/2000/01/rdf-schema#label>,
<http://www.w3.org/2000/01/rdf-schema#seeAlso>,
<http://www.w3.org/2004/02/skos/core#closeMatch>,
<http://www.w3.org/2002/07/owl#deprecated>,
<http://xmlns.com/foaf/0.1/depicted_by>
))
FILTER (isIRI(?subj) && STRSTARTS(str(?subj), "http://purl.obolibrary.org/obo/UBERON_"))
}