robot extract/merge should optionally inject provenance

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Optimize memory usage for update queries using `--temporary-file` switch [#978]
 - Sort [`report`] violations by rule name within level [#955]
 - Allow any case builtin `TYPE` in `template` [#971]
+- [`extract`] and [`merge`] should optionally inject provenance [#977]
 
 ### Fixed
 - Fix subClassOf cycles in related object selection [#979]
@@ -309,6 +310,7 @@ First official release of ROBOT!
 
 [#979]: https://github.com/ontodev/robot/pull/979
 [#978]: https://github.com/ontodev/robot/pull/978
+[#977]: https://github.com/ontodev/robot/pull/977
 [#973]: https://github.com/ontodev/robot/pull/973
 [#971]: https://github.com/ontodev/robot/pull/971
 [#960]: https://github.com/ontodev/robot/pull/960

docs/annotate.md

@@ -2,7 +2,7 @@
 
 It's important to add metadata to an ontology before releasing it, and to update the ontology version IRI.
 
-General annotations can be added one-by-one with `--anotation`, and the IRIs can be set with `--version-iri` and `--ontology-iri`. You can specify as many annotation flags as you'd like in one command:
+General annotations can be added one-by-one with `--annotation`, and the IRIs can be set with `--version-iri` and `--ontology-iri`. You can specify as many annotation flags as you'd like in one command:
 
     robot annotate --input edit.owl \
       --ontology-iri "https://github.com/ontodev/robot/examples/annotated.owl" \
@@ -38,6 +38,23 @@ This command can also remove all ontology annotations from your file with `--rem
       --annotation-file annotations.ttl \
       --output results/annotated_2.owl
 
+
+## Annotating the Source
+
+It’s also possible to annotate the ontology axioms with the ontology IRI or version IRI.
+
+  * `--annotate-derived-from true`: annotates all axioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added.
+
+    robot annotate --input example2.owl \
+      --annotate-derived-from true \
+      --output results/example2_derived_from.owl
+
+  * `--annotate-defined-by true`: annotates all entities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added.
+
+    robot annotate --input example2.owl \
+      --annotate-defined-by true \
+      --output results/example2_defined_by.owl
+
 ---
 
 ## Error Messages

docs/examples/example2.owl

@@ -0,0 +1,173 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="https://github.com/ontodev/robot/examples/edit.owl#"
+     xml:base="https://github.com/ontodev/robot/examples/edit.owl"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+     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:obo="http://purl.obolibrary.org/obo/"
+     xmlns:foaf="http://xmlns.com/foaf/0.1/"
+     xmlns:prov="http://www.w3.org/ns/prov#">
+    <owl:Ontology rdf:about="https://github.com/ontodev/robot/examples/edit.owl">
+        <owl:versionIRI rdf:resource="https://github.com/ontodev/robot/examples/2022-03-11/edit.owl"/>
+        <rdfs:comment>Comment from annotations.ttl file.</rdfs:comment>
+    </owl:Ontology>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotation properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    <!-- http://www.w3.org/ns/prov#wasDerivedFrom -->
+
+    <owl:AnnotationProperty rdf:about="http://www.w3.org/ns/prov#wasDerivedFrom"/>  
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
+    </owl:AnnotationProperty>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"/>
+        <owl:annotatedTarget rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
+        <prov:wasDerivedFrom rdf:resource="https://github.com/ontodev/robot/some_other_ont.owl"/>
+    </owl:Axiom>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">editor note</rdfs:label>
+        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
+        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">curator notes</rdfs:label>
+    </owl:AnnotationProperty>
+
+
+
+    <!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasAlternativeId"/>
+
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</rdfs:label>
+    </owl:ObjectProperty>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000061 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000061">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical structure</rdfs:label>
+        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000062 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000062">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0010000"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000467"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organ</rdfs:label>
+    </owl:Class>
+
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv1">
+        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 1</rdfs:label>
+    </owl:NamedIndividual>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv1"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"/>
+        <owl:annotatedTarget rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+        <prov:wasDerivedFrom rdf:resource="https://github.com/ontodev/robot/examples/2022-03-11/some_other_ontology.owl"/>
+    </owl:Axiom>
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv2">
+        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 2</rdfs:label>
+    </owl:NamedIndividual>
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv3">
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 3</rdfs:label>
+    </owl:NamedIndividual>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv3"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"/>
+        <owl:annotatedTarget rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+        <prov:wasDerivedFrom rdf:resource="https://github.com/ontodev/robot/examples/2022-03-11/some_other_ontology.owl"/>
+    </owl:Axiom>
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv4">
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 4</rdfs:label>
+    </owl:NamedIndividual>
+
+    <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv5">
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 5</rdfs:label>
+    </owl:NamedIndividual>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv5"/>
+        <owl:annotatedProperty rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"/>
+        <owl:annotatedTarget rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    </owl:Axiom>
+
+
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 0.0.1-SNAPSHOT) https://github.com/owlcs/owlapi -->
+