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Merge pull request #805 from vaccineontology/cleanup_highlevel
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Cleanup high level VO terms
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@zhengj2007
zhengj2007 authored Feb 26, 2025
2 parents 81481a0 + 5f41009 commit cd77c30
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Showing 15 changed files with 33,312 additions and 39,638 deletions.
226 changes: 221 additions & 5 deletions src/modules/obsolete.owl
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229 changes: 55 additions & 174 deletions src/modules/other.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -249,24 +249,12 @@



<!-- http://purl.obolibrary.org/obo/NCBITaxon_10239 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>



<!-- http://purl.obolibrary.org/obo/NCBITaxon_10508 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10508"/>



<!-- http://purl.obolibrary.org/obo/NCBITaxon_2 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2"/>



<!-- http://purl.obolibrary.org/obo/NCBITaxon_2697049 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_2697049"/>
Expand All @@ -291,6 +279,12 @@



<!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>



<!-- http://purl.obolibrary.org/obo/OAE_0000055 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OAE_0000055"/>
Expand Down Expand Up @@ -504,6 +498,17 @@
<!-- http://purl.obolibrary.org/obo/VO_0000126 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000126">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/VO_0000506"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000173"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000506"/>
<rdfs:subClassOf>
<owl:Restriction>
Expand Down Expand Up @@ -557,8 +562,8 @@
<!-- http://purl.obolibrary.org/obo/VO_0000145 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000145">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000617"/>
<obo:IAO_0000115>a vaccine component role that inheres in a recombinant vaccine vector as a vaccine component. The combination of a recombinant vaccine vector and a heterogenous protective antigen(s) inserted inside the vector for a recombinant vector vaccine. </obo:IAO_0000115>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0003439"/>
<obo:IAO_0000115>A vaccine vector role that inheres in a recombinant vaccine vector as a vaccine component. The combination of a recombinant vaccine vector and a heterogenous protective antigen(s) inserted inside the vector for a recombinant vector vaccine. </obo:IAO_0000115>
<obo:IAO_0000117>Asiyah Yu Lin</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
Expand Down Expand Up @@ -975,6 +980,17 @@ Ref: Hadler TC, et al. Immunization in developing countries. In: Vaccines. Edito
<!-- http://purl.obolibrary.org/obo/VO_0000368 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000368">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/VO_0000506"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0001145"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000506"/>
<rdfs:subClassOf>
<owl:Restriction>
Expand All @@ -993,6 +1009,17 @@ Ref: Hadler TC, et al. Immunization in developing countries. In: Vaccines. Edito
<!-- http://purl.obolibrary.org/obo/VO_0000395 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000395">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/VO_0000506"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000211"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000506"/>
<rdfs:subClassOf>
<owl:Restriction>
Expand Down Expand Up @@ -1192,18 +1219,6 @@ Ref: Hadler TC, et al. Immunization in developing countries. In: Vaccines. Edito



<!-- http://purl.obolibrary.org/obo/VO_0000499 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000499">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000452"/>
<obo:IAO_0000117>Allen Xiang</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>disposition</oboInOwl:inSubset>
<rdfs:label>preventive infectious disease vaccine function</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0000504 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000504">
Expand All @@ -1225,7 +1240,7 @@ Ref: Hadler TC, et al. Immunization in developing countries. In: Vaccines. Edito
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000615"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000617"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
Expand All @@ -1234,7 +1249,7 @@ Ref: Hadler TC, et al. Immunization in developing countries. In: Vaccines. Edito
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000615"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000617"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>an organism that is used as part of a vaccine</obo:IAO_0000115>
Expand Down Expand Up @@ -1655,18 +1670,6 @@ Toxins can be small molecules, peptides, or proteins that are capable of causing



<!-- http://purl.obolibrary.org/obo/VO_0000685 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000685">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000636"/>
<obo:IAO_0000115>a recombinant vector vaccine role that inheres in a bacterium that carries a vaccine antigen for development of a particular vaccine </obo:IAO_0000115>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>recombinant bacterial vector vaccine role</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0000692 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000692">
Expand All @@ -1679,18 +1682,6 @@ Toxins can be small molecules, peptides, or proteins that are capable of causing



<!-- http://purl.obolibrary.org/obo/VO_0000702 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000702">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000636"/>
<obo:IAO_0000115>a recombinant vector vaccine role that inheres in a virus that carries a vaccine antigen for development of a particular vaccine </obo:IAO_0000115>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>recombinant viral vector vaccine role</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0000713 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000713">
Expand Down Expand Up @@ -1997,64 +1988,6 @@ of minimal anatomy terminology and NCBI taxonomy... Eventually, this term chicke



<!-- http://purl.obolibrary.org/obo/VO_0001014 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001014">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/VO_0000173"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000173"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>a live attenuated quality of a bacterial vaccine strain. </obo:IAO_0000115>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>quality</oboInOwl:inSubset>
<rdfs:label>bacterial vaccine organism live attenuated</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0001015 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001015">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/VO_0000173"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000173"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10239"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>a live attenuated quality of a virus vaccine strain. </obo:IAO_0000115>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>quality</oboInOwl:inSubset>
<rdfs:label>viral vaccine organism live attenuated</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0001080 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001080">
Expand Down Expand Up @@ -2431,64 +2364,6 @@ of minimal anatomy terminology and NCBI taxonomy... Eventually, this term chicke



<!-- http://purl.obolibrary.org/obo/VO_0001280 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001280">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0001275"/>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>immunization target role of pathogen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0001281 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001281">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0001280"/>
<obo:IAO_0000117>Allen Xiang</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>immunization target role of bacterial pathogen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0001282 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001282">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0001280"/>
<obo:IAO_0000117>Allen Xiang</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>immunization target role of viral pathogen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0001283 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001283">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0001280"/>
<obo:IAO_0000117>Allen Xiang</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>immunization target role of parasite pathogen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0001284 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001284">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0001280"/>
<obo:IAO_0000117>Allen Xiang</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>immunization target role of fungal pathogen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0001361 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001361">
Expand Down Expand Up @@ -2687,14 +2562,14 @@ of minimal anatomy terminology and NCBI taxonomy... Eventually, this term chicke



<!-- http://purl.obolibrary.org/obo/VO_0003142 -->
<!-- http://purl.obolibrary.org/obo/VO_0003439 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0003142">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000615"/>
<obo:IAO_0000115>A vaccine role that indicates a clinical trial status of a vaccine</obo:IAO_0000115>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0003439">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000617"/>
<obo:IAO_0000115>Vaccine component role inheres in a vaccine vector.</obo:IAO_0000115>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<oboInOwl:inSubset>role</oboInOwl:inSubset>
<rdfs:label>clinical trial vaccine role</rdfs:label>
<rdfs:label>vaccine vector role</rdfs:label>
</owl:Class>


Expand Down Expand Up @@ -2746,6 +2621,12 @@ of minimal anatomy terminology and NCBI taxonomy... Eventually, this term chicke

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0004921">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Anthony Huffman</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
Expand Down
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