Using make-species-subset command to extract plant specific terms from go-plus.owl

I am trying to follow steps mentioned in #165 to make a plant specific obo file using the following command.

 owltools go-plus.owl --reasoner hermit --make-species-subset -t NCBITaxon:33090 -o -f obo plant.obo

This does work and produce a plant.obo file, and I do not encounter memory errors, but there are multiple warnings output by the command. I have given an example of the warnings I see.

2019-05-13 16:44:47,724 WARN  (ChangeIndexingProcessor:66) [reasoner.indexing.axiomIgnored]ELK does not support ObjectAllValuesFrom. Axiom ignored: 
SubClassOf(<http://purl.obolibrary.org/obo/GO_0048838> 
ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> 
<http://purl.obolibrary.org/obo/NCBITaxon_33090>))

I was wondering what this warning means. The GO term itself is plant specific, but does not show up in the plants.obo file that was produced by the command that was run above

id: GO:0048838
name: release of seed from dormancy
namespace: biological_process
def: "The process in which the dormant state is broken in a seed. 
Dormancy is characterized by a suspension of physiological activity 
that can be reactivated upon release." 
[GOC:dph, GOC:jid, GOC:tb, ISBN:9781405139830]
is_a: GO:0010162 ! seed dormancy process
is_a: GO:0097438 ! exit from dormancy

The owl section for GO:0048838 is shown below. It seems that there are two restrictions only_in_taxon and in_taxon, and one of those has the allValuesFrom mentioned in the warning. Is there a workaround that I am missing?

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0048838">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0010162"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0097438"/>
    <rdfs:subClassOf>
        <owl:Restriction>
            <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002160"/>
            <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
        </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
        <owl:Restriction>
            <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
            <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_33090"/>
        </owl:Restriction>
    </rdfs:subClassOf>
    <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The process in which the dormant state is broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated upon release.</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">biological_process</oboInOwl:hasOBONamespace>
    <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0048838</oboInOwl:id>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">release of seed from dormancy</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0048838"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The process in which the dormant state is broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated upon release.</owl:annotatedTarget>
    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:dph</oboInOwl:hasDbXref>
    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:jid</oboInOwl:hasDbXref>
    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:tb</oboInOwl:hasDbXref>
    <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ISBN:9781405139830</oboInOwl:hasDbXref>
</owl:Axiom>

Reproduce the issue with the documented owltools command and inspect the --make-species-subset entry point, using the warning for GO:0048838 as the test case. Trace how the ELK warning and the someValuesFrom/allValuesFrom restrictions affect the generated plant.obo output; done means the behavior is explained and the missing term has a confirmed resolution or documented limitation.