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Merge pull request #725 from vaccineontology/update-terms
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Updated high-level VO terms

Relabel two terms:
VO:0001243 ‘immunizes host’ -> ‘immunizes recipient’
VO:0001274 ‘vaccine host role’ -> ‘vaccine recipient role’

Update definition of following terms:
VO:0000002 vaccination
VO:0000494 vaccine immunization
VO:0000490 immunization
VO:0000492 passive immunization
VO:0000491 active immunization
VO:0001274 vaccine recipient role
VO:0000278 vaccine function
VO:0001243 immunizes recipient
VO:0000001 vaccine
VO:0000177	cancer vaccine
VO:0007655 tumor antigen
VO:0005506 canvaxgen

Added two new terms
VO:0010332 tumor-specific antigen
VO:0010333 tumor-associated antigen

Modified definition of “preventive vaccine function” and “therapeutic vaccine function”, issue: #714
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@zhengj2007
zhengj2007 authored Jul 13, 2024
2 parents 813c0d2 + 412fa8b commit 3dc535f
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365 changes: 183 additions & 182 deletions src/VO_merged.owl
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11 changes: 8 additions & 3 deletions src/modules/cancer_vaccine.owl
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Expand Up @@ -484,7 +484,10 @@
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/DOID_162"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A vaccine that prevents or treats cancer. It is produced using the patient&apos;s own whole tumor cells as the source of antigens, or using tumor-specific antigens, often recombinantly produced.</obo:IAO_0000115>
<obo:IAO_0000115>Vaccine that prevents or treats cancer.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<obo:IAO_0000118>neoplasm vaccine</obo:IAO_0000118>
<obo:IAO_0000118>tumor vaccine</obo:IAO_0000118>
Expand Down Expand Up @@ -31613,8 +31616,9 @@ Immunization Route: Intramuscular injection (i.m.)</obo:IAO_0000115>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000177"/>
<obo:IAO_0000115>A cancer vaccine that prevents cancer development associated with viral infections.</obo:IAO_0000115>
<obo:IAO_0000115>Cancer vaccine that prevents cancer formation and development.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<obo:IAO_0000233>https://github.com/vaccineontology/VO/issues/677</obo:IAO_0000233>
Expand All @@ -31638,8 +31642,9 @@ Immunization Route: Intramuscular injection (i.m.)</obo:IAO_0000115>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000177"/>
<obo:IAO_0000115>A cancer vaccine that aims to eliminate or control tumor cells by recognizing the tumor cells and stimulating the immune system via tumor antigens.</obo:IAO_0000115>
<obo:IAO_0000115>Cancer vaccine that aims to eliminate or control tumor cells.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<obo:IAO_0000233>https://github.com/vaccineontology/VO/issues/677</obo:IAO_0000233>
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5 changes: 2 additions & 3 deletions src/modules/gene.owl
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Expand Up @@ -6471,9 +6471,8 @@ MUTATION: An isogenic sodC mutant constructed from B abortus 2308 by gene replac

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0005506">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGG_0000000002"/>
<obo:IAO_0000115>A gene expressing a protein, either partially or entirely, serving as the antigen within a specific cancer vaccine.</obo:IAO_0000115>
<obo:IAO_0000117> Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Yongqun He</obo:IAO_0000117>
<obo:IAO_0000115>Gene expressing a protein which serves, either in whole or in part, as an antigen within a cancer vaccine.</obo:IAO_0000115>
<obo:IAO_0000117>Yongqun He|Anna Maria Masci|Barry Smith|Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000233>https://github.com/vaccineontology/VO/issues/677</obo:IAO_0000233>
<oboInOwl:inSubset>gene</oboInOwl:inSubset>
<rdfs:label>canvaxgen</rdfs:label>
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263 changes: 121 additions & 142 deletions src/modules/other.owl
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29 changes: 23 additions & 6 deletions src/modules/process.owl
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Expand Up @@ -414,7 +414,10 @@
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response.</obo:IAO_0000115>
<obo:IAO_0000115>A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>YH, BP</obo:IAO_0000117>
<obo:IAO_0000118>vaccine administration</obo:IAO_0000118>
<oboInOwl:inSubset>process</oboInOwl:inSubset>
Expand Down Expand Up @@ -1311,7 +1314,10 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000490">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>immunization is a processual entity that primes or modifies an adaptivie immune response to some antigens.</obo:IAO_0000115>
<obo:IAO_0000115>A process that results in an adaptive immune response to one or more antigens.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>YH, XZ, BP</obo:IAO_0000117>
<obo:IAO_0000119>WEB: http://en.wikipedia.org/wiki/Immunization</obo:IAO_0000119>
<oboInOwl:inSubset>process</oboInOwl:inSubset>
Expand All @@ -1324,8 +1330,12 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000491">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VO_0000490"/>
<obo:IAO_0000115>Active immunization is an immunization process that entails the introduction of a foreign molecule into the body, which causes the body itself to generate adaptive immunity against the target.</obo:IAO_0000115>
<obo:IAO_0000117>YH, XZ</obo:IAO_0000117>
<obo:IAO_0000115>An immunization that involves the introduction of foreign molecules into a recipient body, in a way which causes the recipient to actively induce adaptive immunity against the immunization target.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<obo:IAO_0000117>XZ</obo:IAO_0000117>
<obo:IAO_0000119>WEB: http://en.wikipedia.org/wiki/Immunization</obo:IAO_0000119>
<oboInOwl:inSubset>process</oboInOwl:inSubset>
<rdfs:label>active immunization</rdfs:label>
Expand All @@ -1343,9 +1353,13 @@
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000585"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Passive immunization is an immunization process where pre-synthesized elements of the immune system are transferred to an organism so that the body does not need to produce these elements itself.</obo:IAO_0000115>
<obo:IAO_0000115>An immunization where pre-synthesized elements of the immune system are transferred to an organism so that the body does not need to produce these elements itself.</obo:IAO_0000115>
<obo:IAO_0000116>Currently, antibodies can be used for passive immunization. This method of immunization works very quickly. However, it is short lasting. The antibodies are naturally broken down. If there are no B cells to produce more antibodies, they will disappear.</obo:IAO_0000116>
<obo:IAO_0000116>YH, XZ</obo:IAO_0000116>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<obo:IAO_0000119>WEB: http://en.wikipedia.org/wiki/Immunization</obo:IAO_0000119>
<oboInOwl:inSubset>process</oboInOwl:inSubset>
<rdfs:label>passive immunization</rdfs:label>
Expand Down Expand Up @@ -1398,7 +1412,10 @@
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000585"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine.</obo:IAO_0000115>
<obo:IAO_0000115>An immunization that is induced by a vaccine via vaccination process.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>YH, XZ</obo:IAO_0000117>
<obo:IAO_0000118>artificial active immunization</obo:IAO_0000118>
<obo:IAO_0000119>WEB: http://en.wikipedia.org/wiki/Immunization</obo:IAO_0000119>
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43 changes: 23 additions & 20 deletions src/modules/vaccine.owl
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Expand Up @@ -2561,13 +2561,19 @@
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000047"/>
<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:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000278"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000047"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000295"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0000590"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000085"/>
Expand All @@ -2584,15 +2590,12 @@
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<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:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.</obo:IAO_0000115>
<obo:IAO_0000115>Material entity that is manufactured to realize the vaccine function.</obo:IAO_0000115>
<obo:IAO_0000116>Many vaccines are developed to protect against infectious pathogens that causes infectious diseases. Many vaccines are also being developed against other diseases such as cancer, allergy, and autoimmune diseases.</obo:IAO_0000116>
<obo:IAO_0000117>YH, BP, BS, MC, LC, XZ, RS</obo:IAO_0000117>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>YH, BP, MC, LC, XZ, RS</obo:IAO_0000117>
<oboInOwl:inSubset>vaccine</oboInOwl:inSubset>
<rdfs:label>vaccine</rdfs:label>
<rdfs:seeAlso>MeSH: D014612</rdfs:seeAlso>
Expand Down Expand Up @@ -3652,7 +3655,7 @@ Reference: http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=157&
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/VO_0019074"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A vaccine for active immunization to prevent invasive disease caused by Neisseria meningitidis serogroups C and Y and Haemophilus influenzae type b. MENHIBRIX is approved for use in children 6 weeks of age through 18 months of age. </obo:IAO_0000115>
<obo:IAO_0000115>A vaccine for active immunization to prevent invasive disease caused by Neisseria meningitidis serogroups C and Y and Haemophilus influenzae type b. MENHIBRIX is approved for use in children 6 weeks of age through 18 months of age.</obo:IAO_0000115>
<obo:IAO_0000117>Kallan Roan, Oliver He</obo:IAO_0000117>
<obo:IAO_0000119>http://purl.bioontology.org/ontology/RXNORM/1437912</obo:IAO_0000119>
<obo:IAO_0000119>https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm308566.htm</obo:IAO_0000119>
Expand Down Expand Up @@ -6280,8 +6283,8 @@ https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112854.h
<obo:VO_0003162>BL 125296/0</obo:VO_0003162>
<oboInOwl:inSubset>vaccine</oboInOwl:inSubset>
<rdfs:label>Adenovirus Type 4 and Type 7 Vaccine, Live, Oral</rdfs:label>
<rdfs:seeAlso> UMLS_CUI: C0695130</rdfs:seeAlso>
<rdfs:seeAlso>SNOMEDCT: 442561000</rdfs:seeAlso>
<rdfs:seeAlso>UMLS_CUI: C0695130</rdfs:seeAlso>
</owl:Class>


Expand Down Expand Up @@ -10734,6 +10737,12 @@ https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112854.h



<!-- http://purl.obolibrary.org/obo/VO_0000590 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000590"/>



<!-- http://purl.obolibrary.org/obo/VO_0000592 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000592">
Expand Down Expand Up @@ -10933,12 +10942,6 @@ https://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm112854.h



<!-- http://purl.obolibrary.org/obo/VO_0000615 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000615"/>



<!-- http://purl.obolibrary.org/obo/VO_0000619 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000619">
Expand Down Expand Up @@ -11741,7 +11744,7 @@ However, even this may not be comprehensive. </rdfs:comment>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A live attenuated Shigella flexneri 2a vaccine that carries deletions of the plasmid-borne virulence gene icsA (mediating intra- and intercellular spread) and the chromosomal locus iuc (encoding aerobactin). </obo:IAO_0000115>
<obo:IAO_0000115>A live attenuated Shigella flexneri 2a vaccine that carries deletions of the plasmid-borne virulence gene icsA (mediating intra- and intercellular spread) and the chromosomal locus iuc (encoding aerobactin).</obo:IAO_0000115>
<obo:IAO_0000117>YH</obo:IAO_0000117>
<obo:IAO_0000119>PMID:10377124</obo:IAO_0000119>
<oboInOwl:inSubset>vaccine</oboInOwl:inSubset>
Expand Down Expand Up @@ -19237,7 +19240,7 @@ However, running the reasoner takes time. As a way to reducing the time, I have
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/VO_0015481"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>SYNFLORIX is indicated for active immunization of infants and children from 6 weeks up to 5 years of age against Streptococcus pneumoniae serotypes 1, 4, 5, 6B, 7F, 9V, 14, 18C, 19F and 23F and invasive disease caused by these serotypes (including sepsis, meningitis, bacteraemic pneumonia, pleural empyema and bacteraemia). </obo:IAO_0000115>
<obo:IAO_0000115>SYNFLORIX is indicated for active immunization of infants and children from 6 weeks up to 5 years of age against Streptococcus pneumoniae serotypes 1, 4, 5, 6B, 7F, 9V, 14, 18C, 19F and 23F and invasive disease caused by these serotypes (including sepsis, meningitis, bacteraemic pneumonia, pleural empyema and bacteraemia).</obo:IAO_0000115>
<obo:IAO_0000117>ZX</obo:IAO_0000117>
<obo:IAO_0000119>WEB: http://www.gsk.ca/english/docs-pdf/product-monographs/Synflorix.pdf</obo:IAO_0000119>
<oboInOwl:inSubset>vaccine</oboInOwl:inSubset>
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34 changes: 28 additions & 6 deletions src/modules/vo_objectProp.owl
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Expand Up @@ -364,7 +364,7 @@ is_specified_output_of some
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/VO_0001011">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/VO_0000001"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/DOID_4"/>
<obo:IAO_0000115>A shortcut relation that equals to:
<obo:IAO_0000115>A shortcut relation that is equivalent to:
&apos;processed material&apos; and (is_specified_output_of some &apos;vaccine preparation&apos;) and (&apos;has function&apos; some (&apos;vaccine function&apos; and (&apos;is realized by&apos; only (&apos;vaccine immunization&apos; and (realizes some (&apos;vaccine host role&apos; and (role_of some &apos;organism&apos; and has_disposition some disease)))))))).
The domain of this relation is a vaccine.
The range of this relation is a disease.</obo:IAO_0000115>
Expand All @@ -391,16 +391,32 @@ The range of this relation is a disease.</obo:IAO_0000115>

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/VO_0001243">
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/VO_0000001"/>
<rdfs:range rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
<obo:IAO_0000115>A shortcut relation that equals to:
&apos;processed material&apos; and (is_specified_output_of some &apos;vaccine preparation&apos;) and (&apos;has function&apos; some (&apos;vaccine function&apos; and (&apos;is realized by&apos; only (&apos;vaccine immunization&apos; and (realizes some (&apos;vaccine host role&apos; and (role_of some &apos;organism&apos;)))))))).
<rdfs:range>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<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_0001274"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000115>A shortcut relation that is equivalent to:
&apos;processed material&apos; and (is_specified_output_of some &apos;vaccine preparation&apos;) and (&apos;has function&apos; some (&apos;vaccine function&apos; and (&apos;is realized by&apos; only (&apos;vaccine immunization&apos; and (realizes some (&apos;vaccine recipient role&apos; and (role_of some &apos;organism&apos;)))))))).
The domain of this relation is a vaccine.
The range of this relation is a organism.</obo:IAO_0000115>
<obo:IAO_0000117>Anna Maria Masci</obo:IAO_0000117>
<obo:IAO_0000117>Asiyah Yu Lin</obo:IAO_0000117>
<obo:IAO_0000117>Barry Smith</obo:IAO_0000117>
<obo:IAO_0000117>Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000117>Oliver He</obo:IAO_0000117>
<obo:IAO_0000118>immunization for host</obo:IAO_0000118>
<obo:IAO_0000118>immunization for recipient</obo:IAO_0000118>
<obo:IAO_0000118>immunizes host</obo:IAO_0000118>
<obo:IAO_0000118>vaccine immunization for host</obo:IAO_0000118>
<rdfs:label>immunizes host</rdfs:label>
<obo:IAO_0000118>vaccine immunization for recipient</obo:IAO_0000118>
<rdfs:label>immunizes recipient</rdfs:label>
</owl:ObjectProperty>


Expand Down Expand Up @@ -442,7 +458,7 @@ The range of this relation is a organism.</obo:IAO_0000115>
</owl:intersectionOf>
</owl:Class>
</rdfs:range>
<obo:IAO_0000115>A shortcut relation that equals to:
<obo:IAO_0000115>A shortcut relation that is equivalent to:
processed material and (is_specified_output_of some vaccine preparation) and (has function some (vaccine function and (is realized by only (vaccine immunization and (realizes some (&apos;immunization target role&apos; and (role_of some &apos;pathogen&apos;))))))))

The domain of this relation is a vaccine.
Expand Down Expand Up @@ -635,6 +651,12 @@ Ranges: organism and &apos;has role&apos; some &apos;pathogen role&apos;</obo:IA
<!-- http://purl.obolibrary.org/obo/VO_0000599 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0000599"/>



<!-- http://purl.obolibrary.org/obo/VO_0001274 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0001274"/>
</rdf:RDF>


Expand Down
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