Merge pull request #2112 from obophenotype/annotation-violation

Filter annotations not listed
obophenotype · Nov 8, 2021 · aab34a0 · aab34a0
2 parents a8cc9f1 + 50cf4c2
commit aab34a0
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Showing 5 changed files with 126 additions and 8 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -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. 
@@ -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
+
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -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)

diff --git a/src/ontology/profile.txt b/src/ontology/profile.txt
@@ -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
diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml
@@ -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:

diff --git a/src/sparql/illegal-annotation-property-violation.sparql b/src/sparql/illegal-annotation-property-violation.sparql
@@ -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_"))
+}