Merge pull request #1023 from hkir-dev/886-fix

Remove and filter operations new "drop_axiom_annotation" option
ontodev · Feb 7, 2024 · c480381 · c480381
2 parents 6e47651 + 1650528
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Updated ELK from 0.4.3 to 0.5.0. [#999]. This is an important change as ELK 0.5.0 is more complete than 0.4.3, which means that it will potentially uncover inferences, in particular unsatisfiable classes, which were not recognised by ELK 0.4.3.
 - Add support for pluggable commands [#1119]
+- Add `--drop-axiom-annotations` option to drop axiom annotations in [`remove`] and [`filter`] [#1023]
 
 ### Changed
 - Migrate to OWL API 4.5.26 to deal with [broken turtle serialiser](https://github.com/ontodev/robot/issues/1129). [#1135]
@@ -382,7 +383,7 @@ First official release of ROBOT!
 [`report`]: http://robot.obolibrary.org/report
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
-
+;
 [#1181]: https://github.com/ontodev/robot/pull/1181
 [#1171]: https://github.com/ontodev/robot/pull/1171
 [#1168]: https://github.com/ontodev/robot/pull/1168
@@ -402,6 +403,7 @@ First official release of ROBOT!
 [#1061]: https://github.com/ontodev/robot/issues/1061
 [#1030]: https://github.com/ontodev/robot/issues/1030
 [#1026]: https://github.com/ontodev/robot/issues/1026
+[#1023]: https://github.com/ontodev/robot/pull/1023
 [#1017]: https://github.com/ontodev/robot/issues/1017
 [#1016]: https://github.com/ontodev/robot/issues/1016
 [#1009]: https://github.com/ontodev/robot/issues/1009

diff --git a/docs/examples/template-drop-axiom-filter.owl b/docs/examples/template-drop-axiom-filter.owl
@@ -0,0 +1,130 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="https://github.com/ontodev/robot/examples/template.owl#"
+     xml:base="https://github.com/ontodev/robot/examples/template.owl"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:example="http://example.com/">
+    <owl:Ontology rdf:about="https://github.com/ontodev/robot/examples/template.owl"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Data properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/propery-1 -->
+
+    <owl:DatatypeProperty rdf:about="http://example.com/propery-1">
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
+    </owl:DatatypeProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/B6C3F1 -->
+
+    <owl:Class rdf:about="http://example.com/B6C3F1">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
+        <owl:disjointWith rdf:resource="http://example.com/F344N"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">B6C3F1</rdfs:label>
+        <rdfs:seeAlso rdf:resource="http://jaxmice.jax.org/strain/100010.html"/>
+    </owl:Class>
+
+
+
+    <!-- http://example.com/F344N -->
+
+    <owl:Class rdf:about="http://example.com/F344N">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">F 344/N</rdfs:label>
+        <rdfs:seeAlso rdf:resource="http://www.informatics.jax.org/external/festing/rat/docs/F344.shtml"/>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_10090 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_10116 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/rat-1234 -->
+
+    <owl:NamedIndividual rdf:about="http://example.com/rat-1234">
+        <rdf:type rdf:resource="http://example.com/F344N"/>
+        <example:propery-1 rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.2</example:propery-1>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rat 1234</rdfs:label>
+    </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+
diff --git a/docs/examples/template-drop-axiom-remove.owl b/docs/examples/template-drop-axiom-remove.owl
@@ -0,0 +1,130 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="https://github.com/ontodev/robot/examples/template.owl#"
+     xml:base="https://github.com/ontodev/robot/examples/template.owl"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:example="http://example.com/">
+    <owl:Ontology rdf:about="https://github.com/ontodev/robot/examples/template.owl"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Data properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/propery-1 -->
+
+    <owl:DatatypeProperty rdf:about="http://example.com/propery-1">
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
+    </owl:DatatypeProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/B6C3F1 -->
+
+    <owl:Class rdf:about="http://example.com/B6C3F1">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
+        <owl:disjointWith rdf:resource="http://example.com/F344N"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">B6C3F1</rdfs:label>
+        <rdfs:seeAlso rdf:resource="http://jaxmice.jax.org/strain/100010.html"/>
+    </owl:Class>
+
+
+
+    <!-- http://example.com/F344N -->
+
+    <owl:Class rdf:about="http://example.com/F344N">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
+        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</obo:IAO_0000115>
+        <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">F 344/N</rdfs:label>
+        <rdfs:seeAlso rdf:resource="http://www.informatics.jax.org/external/festing/rat/docs/F344.shtml"/>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_10090 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_10116 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://example.com/rat-1234 -->
+
+    <owl:NamedIndividual rdf:about="http://example.com/rat-1234">
+        <rdf:type rdf:resource="http://example.com/F344N"/>
+        <example:propery-1 rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.2</example:propery-1>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rat 1234</rdfs:label>
+    </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+
diff --git a/docs/filter.md b/docs/filter.md
@@ -28,6 +28,8 @@ Then `filter --term A --term R --term C --select "self parents" --axioms all --s
     - the objects for `ax2` are `{A, R, C}` (with `R some C` excluded), and all of these are in the target set, so `ax2` is matched and copied
     - the objects for `ax3` are `{D, E}`, and none of these are in the target set, so `ax3` is not matched and is not copied
 
+Finally `--drop-axiom-annotations` option lets you to specify an annotation property to drop all axiom annotations using it. `all` parameter can be used to drop all axiom annotations.
+
 The `remove` and `filter` operations maintains structural integrity by default: lineage is maintained, and gaps will be filled where classes have been removed. If you wish to *not* preserve the hierarchy, include `--preserve-structure false`.
 
 ## Annotations
@@ -94,3 +96,13 @@ Create a "base" subset that only includes internal axioms (alternatively, use `r
       --include-term IAO:0000119 \
       --output results/template-base-filter.owl
 
+Create a "base" subset in which axiom annotations involving IAO:0000117 and IAO:0000119 are removed:
+
+    robot filter --input template.owl \
+      --base-iri http://example.com/ \
+      --select "annotations" \
+      --axioms internal \
+      --drop-axiom-annotations IAO:0000117 \
+      --drop-axiom-annotations IAO:0000119 \
+      --output results/template-drop-axiom-filter.owl
+
diff --git a/docs/remove.md b/docs/remove.md
@@ -49,6 +49,8 @@ Then `remove --term A --term R --term C --select "self parents" --axioms all --s
     - the objects for `ax1` are `{A, B}`, and at least one of these is in the target set, so `ax1` is matched and removed
     - the objects for `ax2` are `{A, R, C}` (with `R some C` excluded), and at least one of these is in the target set, so `ax2` is matched and removed
     - the objects for `ax3` are `{D, E}`, and none of these are in the target set, so `ax3` is not matched and is not removed
+
+Finally `--drop-axiom-annotations` option lets you to specify an annotation property to drop all axiom annotations using it. `all` parameter can be used to drop all axiom annotations.
 
 ## Preserving the Structure
 
@@ -227,3 +229,14 @@ Create a "base" subset by removing external axioms (alternatively, use `filter -
       --select annotation-properties \
       --signature true \
       --output results/filter_annotations.owl
+
+Create a "base" subset in which axiom annotations involving IAO:0000117 and IAO:0000119 are removed:
+
+    robot remove --input template.owl \
+      --base-iri http://example.com/ \
+      --axioms external \
+      --drop-axiom-annotations IAO:0000117 \
+      --drop-axiom-annotations IAO:0000119 \
+      --output results/template-drop-axiom-remove.owl
+
+      
diff --git a/robot-command/src/main/java/org/obolibrary/robot/FilterCommand.java b/robot-command/src/main/java/org/obolibrary/robot/FilterCommand.java
@@ -3,6 +3,7 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
+import java.util.stream.Collectors;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.semanticweb.owlapi.apibinding.OWLManager;
@@ -43,6 +44,11 @@ public FilterCommand() {
     o.addOption("r", "trim", true, "if true, keep axioms containing only selected objects");
     o.addOption(
         "S", "signature", true, "if true, keep axioms with any selected entity in their signature");
+    o.addOption(
+        "d",
+        "drop-axiom-annotations",
+        true,
+        "drop all axiom annotations involving a particular annotation property");
     options = o;
   }
 
@@ -159,10 +165,22 @@ public CommandState execute(CommandState state, String[] args) throws Exception
       }
     }
 
+    List<String> dropParameters =
+        CommandLineHelper.getOptionalValues(line, "drop-axiom-annotations");
+    List<IRI> annotationsToDrop =
+        dropParameters.stream()
+            .filter(s -> !s.equalsIgnoreCase("all"))
+            .map(
+                curie ->
+                    CommandLineHelper.maybeCreateIRI(ioHelper, curie, "drop-axiom-annotations"))
+            .collect(Collectors.toList());
+
     // Use the select statements to get a set of objects to filter
     Set<OWLObject> relatedObjects =
         RemoveCommand.getObjects(line, ioHelper, inputOntology, selectGroups);
     if (relatedObjects.isEmpty()) {
+      // drop specified axiom annotations
+      RelatedObjectsHelper.dropAxiomAnnotations(outputOntology, annotationsToDrop, dropParameters);
       // nothing to filter - save and exit
       CommandLineHelper.maybeSaveOutput(line, outputOntology);
       state.setOntology(outputOntology);
@@ -212,6 +230,9 @@ public CommandState execute(CommandState state, String[] args) throws Exception
           outputOntology, RelatedObjectsHelper.getAnnotationAxioms(inputOntology, relatedObjects));
     }
 
+    // drop specified axiom annotations
+    RelatedObjectsHelper.dropAxiomAnnotations(outputOntology, annotationsToDrop, dropParameters);
+
     // Save the changed ontology and return the state
     CommandLineHelper.maybeSaveOutput(line, outputOntology);
     state.setOntology(outputOntology);