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Add term for mouth rinse specimen #1809

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Aug 26, 2024
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Add term for mouth rinse specimen #1809

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b8f9e8a
Add mouth rinse specimen term
sebastianduesing Aug 7, 2024
b89f5c5
Merge branch 'master' into 1803_mouth_rinse_specimen
jamesaoverton Aug 26, 2024
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150 changes: 127 additions & 23 deletions src/ontology/modules/biobank-specimens.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,18 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
Expand Down Expand Up @@ -52,6 +64,18 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000233 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000233"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000234 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000234"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand Down Expand Up @@ -3916,42 +3940,116 @@
<!-- http://purl.obolibrary.org/obo/OBI_0003595 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003595">
<rdfs:subClassOf>
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600005"/>
</owl:Restriction>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600044"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000659"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001826"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
</owl:equivalentClass>
<obo:IAO_0000115 xml:lang="en">A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<rdfs:label>nasal lavage fluid</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003666 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003666">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000659"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001826"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600044"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
</owl:equivalentClass>
<obo:IAO_0000111>lavage fluid specimen</obo:IAO_0000111>
<obo:IAO_0000112>The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present.</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions.</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<rdfs:label>nasal lavage fluid</rdfs:label>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1803</obo:IAO_0000233>
<rdfs:label>lavage fluid specimen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003667 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003667">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600044"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000659"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000165"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000111>oral lavage fluid</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space.</obo:IAO_0000115>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>mouth rinse specimen</obo:IAO_0000118>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1803</obo:IAO_0000233>
<obo:IAO_0000234>Anna Maria Masci</obo:IAO_0000234>
<rdfs:label>oral lavage fluid</rdfs:label>
</owl:Class>


Expand All @@ -3968,6 +4066,12 @@



<!-- http://purl.obolibrary.org/obo/OBI_0600044 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600044"/>



<!-- http://purl.obolibrary.org/obo/OBI_2000000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_2000000">
Expand Down
4 changes: 3 additions & 1 deletion src/ontology/templates/biobank-specimens.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,9 @@ OBI:0003380 placental blood specimen A specimen that is derived from placenta
OBI:0003415 peripheral blood mononuclear cell specimen PBMC specimen A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell Jie Zheng|Chris Stoeckert subclass collecting specimen from organism peripheral blood mononuclear cell CL_2000001
OBI:0003482 lymph specimen A specimen that is derived from a portion of lymph collected from an organism. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some lymph)) UBERON_0002391
OBI:0003483 digestive tract specimen A specimen that is derived from part of a digestive tract. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 collecting specimen from organism (tissue and ('part of' some 'digestive tract')) UBERON_0001555
OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita subclass collecting specimen from organism nasal cavity mucosa UBERON_0001826
OBI:0003595 nasal lavage fluid A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. Sebastian Duesing|Randi Vita equivalent lavage nasal cavity mucosa UBERON_0001826
OBI:0003666 lavage fluid specimen lavage fluid specimen A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions. The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1803 equivalent lavage
OBI:0003667 oral lavage fluid oral lavage fluid mouth rinse specimen A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space. Sebastian Duesing Anna Maria Masci https://github.com/obi-ontology/obi/issues/1803 equivalent lavage mouth UBERON_0000165
OBI:2000000 uterine cervix specimen A specimen that is derived from some uterine cervix Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some 'uterine cervix')) UBERON_0000002
OBI:2000001 urethra specimen A specimen that is derived from some urethra Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism (tissue and ('part of' some urethra)) UBERON_0000057
OBI:2000002 cervical mucus specimen A specimen that is derived from some cervical mucus Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X Mark A. Miller ORCID:0000-0001-9076-6066|Christian Stoeckert ORCID:0000-0002-5714-991X equivalent collecting specimen from organism cervical mucus UBERON_0000316
Expand Down
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