'--annotate-with-source true' does not work with extract --method subset

[allysonlister]

(Apologies if I have named this ticket incorrectly, please update as required).

I'm trying to add --annotate-with-source true to my ODK build procedure and I'm testing the run with this robot command:

java -jar ~/Programs/robot.jar --catalog catalog-v001.xml query -i mirror/po.owl --update ../sparql/preprocess-module.ru extract -T imports/po_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --annotate-with-source true --method subset --output test-po.owl

The above is a modified version of the command that is generated by the ODK's Makefile, and I'll put it in my own makefile if I can get it working. However, this command does not add any rdfs:isDefinedBy annotations at all.
My terms to extract only has one class (http://purl.obolibrary.org/obo/PO_0025131) and it looks great EXCEPT for the lack of an rdfs:isDefinedBy property as outlined in the ROBOT command:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PO_0025131">
        <obo:IAO_0000115>An anatomical entity that is or was part of a plant.</obo:IAO_0000115>
        <oboInOwl:created_by>rwalls</oboInOwl:created_by>
        <oboInOwl:creation_date>2010-11-15T11:41:38Z</oboInOwl:creation_date>
        <oboInOwl:hasDbXref>PO_GIT:224</oboInOwl:hasDbXref>
        <oboInOwl:hasExactSynonym>entidad anat&amp;#243mica vegetal (Spanish, exact)</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym>植物 解剖学（形態）的実体 (Japanese, exact)</oboInOwl:hasExactSynonym>
        <oboInOwl:hasOBONamespace>plant_anatomy</oboInOwl:hasOBONamespace>
        <oboInOwl:id>PO:0025131</oboInOwl:id>
        <rdfs:comment>Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 &apos;anatomical entity&apos; is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex.  Or, a substance produced by a cellular organism with granularity above the level of a protein complex.  Refers to BFO:0000004 &apos;independent continuant&apos;.</rdfs:comment>
        <rdfs:label>plant anatomical entity</rdfs:label>
    </owl:Class>

@jamesaoverton suggests on Slack that it may just be a missing bit of code from subset and would like this ticket created.

Thank you!

(Source)

[jamesaoverton]

@hkir-dev Does the subset method you implemented in #1000 support --annotate-with-source? I skimmed the code and I think it does not, but I could be wrong.

[allysonlister]

BTW, i've just run a similar command using --method MIREOT and I'm also not getting the isDefinedBy...

Command is

extract --lower-terms imports/iao_terms.txt --force true --copy-ontology-annotations true --annotate-with-source true --method MIREOT --intermediates all --output tmp/iao_extracted.owl

and there are no isDefinedBy annotation. Thanks!

[hkir-dev]

Yes, during code review I observed the same. annotate-with-source is only supported by SLME (not supported by MIREOT and subset).

I created a pull request to add support to the subset: #1160

Adding annotate-with-source support to the MIREOT requires further refactoring since it was implemented in a different class.