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GOOS EOV semantics (#970)
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* updates for #904

* attempting fix for #969

* refresh imports

* add concentrations of compounds for #904 #970

* imports and concentration patterns for EOV seawater chemistry

* build import and module

* setting up Ar-39 import for #904

* added Ar-39 for #904

* adding transient tracer placeholders and axioms for #904

* added transient tracer EOV

* updates to EOV branch

* Delete scratchReleaseNewTerms.Md
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pbuttigieg authored May 14, 2021
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34 changes: 32 additions & 2 deletions src/envo/envo-edit.owl
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ Import(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>)
Annotation(<http://purl.org/dc/elements/1.1/contributor> <https://orcid.org/0000-0002-2996-719X>)
Annotation(<http://purl.org/dc/elements/1.1/creator> <http://orcid.org/0000-0002-4366-3088>)
Annotation(<http://purl.org/dc/elements/1.1/creator> "http://orcid.org/0000-0002-6601-2165")
Annotation(<http://purl.org/dc/elements/1.1/creator> "http://orcid.org/0000-0002-8343-612X")
Expand Down Expand Up @@ -3179,6 +3180,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001873>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001874>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001875>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001876>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001877>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001878>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001879>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001880>))
Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_01001881>))
Expand Down Expand Up @@ -25053,11 +25056,14 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000697> ObjectSomeValuesFrom(<

# Class: <http://purl.obolibrary.org/obo/ENVO_01000698> (debris flow)

AnnotationAssertion(Annotation(<http://purl.obolibrary.org/obo/IAO_0000119> <https://www.usgs.gov/natural-hazards/landslide-hazards/science/landslides-glossary?qt-science_center_objects=0#qt-science_center_objects>) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://orcid.org/0000-0002-2282-7215>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000698> "A debris flow is a mass wasting flow which occurs when masses of poorly sorted sediment are saturated with water and agitated into motion."@en)
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://en.wikipedia.org/wiki/Debris_flow>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01000698> "A mass wasting flow during which water-laden masses of soil and fragmented rock rush down the slopes of elevations, funnel into stream channels, entrain objects in their paths, and form thick, muddy deposits on valley floors.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01000698> "environmental_hazards")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01000698> "debris flow"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000698> <http://purl.obolibrary.org/obo/ENVO_01000696>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000698> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_00002007> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/PATO_0001412>))))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000698> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/ENVO_00000100>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000698> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/ENVO_00001995>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000698> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/ENVO_00001998>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01000698> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/ENVO_01000650>))

# Class: <http://purl.obolibrary.org/obo/ENVO_01000699> (lahar)

Expand Down Expand Up @@ -31508,6 +31514,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <h
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01001375> "http://www.goosocean.org/index.php?option=com_oe&task=viewDocumentRecord&docID=17464")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001375> "envoEOVs")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001375> "envoMarine")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001375> "The EOV specification sheet is simply titled as \"sea ice\", but the description of the EOV is of the variability of sea ice.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001375> "sea ice variability"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001375> <http://purl.obolibrary.org/obo/PATO_0001303>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001375> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/ENVO_00002200>))
Expand Down Expand Up @@ -32775,6 +32782,8 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#created_by> <h
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#creation_date> <http://purl.obolibrary.org/obo/ENVO_01001495> "2018-11-10T15:49:02Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ENVO_01001495> "dissolved oxygen")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ENVO_01001495> "oceanic oxygen")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01001495> <https://www.goosocean.org/components/com_oe/oe.php?task=download&id=35904&version=2.0&lang=1&format=1>)
AnnotationAssertion(Annotation(rdfs:comment "This is the label that GOOS uses in its EOV specification sheet, found here: https://www.goosocean.org/components/com_oe/oe.php?task=download&id=35904&version=2.0&lang=1&format=1") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_01001495> "oxygen")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001495> "envoEOVs")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001495> "envoMarine")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001495> "dioxygen dissolved in marine water"@en)
Expand Down Expand Up @@ -36109,6 +36118,27 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001876> "g
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001876> <http://purl.obolibrary.org/obo/ENVO_01000406>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001876> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> <http://purl.obolibrary.org/obo/ENVO_01001848>))

# Class: <http://purl.obolibrary.org/obo/ENVO_01001877> (transient tracer)

AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_01001877> <http://orcid.org/0000-0002-4366-3088>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_01001877> "2020-08-05T13:41:19Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001877> "transient tracer"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001877> <http://purl.obolibrary.org/obo/CHEBI_35204>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001877> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectUnionOf(<http://purl.obolibrary.org/obo/CHEBI_134024> <http://purl.obolibrary.org/obo/CHEBI_155827> <http://purl.obolibrary.org/obo/CHEBI_29238> <http://purl.obolibrary.org/obo/CHEBI_30218> <http://purl.obolibrary.org/obo/CHEBI_30496> <http://purl.obolibrary.org/obo/CHEBI_36927>)))

# Class: <http://purl.obolibrary.org/obo/ENVO_01001878> (oceanic transient tracer)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001878> "A transient tracer role which inheres in chemical entities in seawater."@en)
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/ENVO_01001878> "The axiomatisation includes the tracers mentioned in the corresponding GOOS EOV specification sheet, viewable here: https://www.goosocean.org/index.php?option=com_oe&task=viewDocumentRecord&docID=17476"@en)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_01001878> <http://orcid.org/0000-0002-4366-3088>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_01001878> "2020-08-05T13:41:33Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ENVO_01001878> "marine transient tracer"@en)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_01001878> <https://www.goosocean.org/index.php?option=com_oe&task=viewDocumentRecord&docID=17476>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_01001878> "envoEOVs")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://www.goosocean.org/index.php?option=com_oe&task=viewDocumentRecord&docID=17476>) rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001878> "Compounds which realise this role can be used in the ocean to quantify ventilation, transit time distribution and transport time-scales. These compounds are all conservative in seawater, or have well-defined decay functions, and a well-established source function over time at the ocean surface."@en)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001878> "oceanic transient tracer"@en)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001878> <http://purl.obolibrary.org/obo/ENVO_01001877>)

# Class: <http://purl.obolibrary.org/obo/ENVO_01001879> (proglacial)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://orcid.org/0000-0003-4808-4736>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001879> "A positional quality which inheres in a bearer by virtue of the bearer in being in physical contact with, or close to, a glacial margin.")
Expand Down
46 changes: 46 additions & 0 deletions src/envo/imports/chebi_import.obo
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,13 @@ id: CHEBI:13392
name: NAD(P)H
is_a: CHEBI:25524 ! NAD(P)

[Term]
id: CHEBI:134024
name: chlorofluorocarbon
is_a: CHEBI:134179 ! volatile organic compound
is_a: CHEBI:36683 ! organochlorine compound
is_a: CHEBI:37143 ! organofluorine compound

[Term]
id: CHEBI:134179
name: volatile organic compound
Expand Down Expand Up @@ -720,6 +727,11 @@ id: CHEBI:24061
name: fluorine atom
is_a: CHEBI:24473 ! halogen

[Term]
id: CHEBI:24062
name: fluorine molecular entity
is_a: CHEBI:24471 ! halogen molecular entity

[Term]
id: CHEBI:24271
name: glucosamines
Expand Down Expand Up @@ -1583,6 +1595,11 @@ id: CHEBI:29237
name: deuterium atom
is_a: CHEBI:49637 ! hydrogen atom

[Term]
id: CHEBI:29238
name: tritium atom
is_a: CHEBI:49637 ! hydrogen atom

[Term]
id: CHEBI:29241
name: silicate(4-)
Expand Down Expand Up @@ -1652,6 +1669,17 @@ name: alpha-particle
is_a: CHEBI:33252 ! atomic nucleus
is_a: CHEBI:33316 ! helium(2+)

[Term]
id: CHEBI:30217
name: helium atom
is_a: CHEBI:33309 ! noble gas atom
is_a: CHEBI:33559 ! s-block element atom

[Term]
id: CHEBI:30218
name: helium-3 atom
is_a: CHEBI:30217 ! helium atom

[Term]
id: CHEBI:30222
name: neutron
Expand Down Expand Up @@ -1989,6 +2017,13 @@ name: carboxylic ester
is_a: CHEBI:35701 ! ester
is_a: CHEBI:36586 ! carbonyl compound

[Term]
id: CHEBI:33309
name: noble gas atom
is_a: CHEBI:138675 ! gas molecular entity
is_a: CHEBI:25585 ! nonmetal atom
is_a: CHEBI:33318 ! main group element atom

[Term]
id: CHEBI:33315
name: monoatomic helium
Expand Down Expand Up @@ -3228,6 +3263,11 @@ id: CHEBI:36916
name: cation
is_a: CHEBI:24870 ! ion

[Term]
id: CHEBI:36928
name: carbon-13 atom
is_a: CHEBI:27594 ! carbon atom

[Term]
id: CHEBI:36934
name: nitrogen-15 atom
Expand Down Expand Up @@ -3311,6 +3351,12 @@ id: CHEBI:37134
name: elemental barium
is_a: CHEBI:37133 ! barium molecular entity

[Term]
id: CHEBI:37143
name: organofluorine compound
is_a: CHEBI:17792 ! organohalogen compound
is_a: CHEBI:24062 ! fluorine molecular entity

[Term]
id: CHEBI:37163
name: glucan
Expand Down
106 changes: 106 additions & 0 deletions src/envo/imports/chebi_import.owl
Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,17 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_134024 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_134024">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_134179"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_36683"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_37143"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">chlorofluorocarbon</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_134179 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_134179">
Expand Down Expand Up @@ -337,6 +348,15 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_155827 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_155827">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_49475"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">argon-39 atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_155903 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_155903">
Expand Down Expand Up @@ -1444,6 +1464,15 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_24062 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_24062">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_24471"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">fluorine molecular entity</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_24271 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_24271">
Expand Down Expand Up @@ -2995,6 +3024,15 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_29238 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_29238">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_49637"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">tritium atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_29241 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_29241">
Expand Down Expand Up @@ -3116,6 +3154,25 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_30217 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_30217">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33309"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33559"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">helium atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_30218 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_30218">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_30217"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">helium-3 atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_30222 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_30222">
Expand Down Expand Up @@ -3723,6 +3780,17 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_33309 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33309">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_138675"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_25585"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33318"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">noble gas atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_33315 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_33315">
Expand Down Expand Up @@ -5942,6 +6010,24 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_36927 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36927">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_27594"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">carbon-14 atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_36928 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36928">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_27594"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">carbon-13 atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_36934 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_36934">
Expand Down Expand Up @@ -6085,6 +6171,16 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_37143 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_37143">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_17792"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_24062"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organofluorine compound</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_37163 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_37163">
Expand Down Expand Up @@ -7068,6 +7164,16 @@



<!-- http://purl.obolibrary.org/obo/CHEBI_49475 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_49475">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33309"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33560"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">argon atom</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/CHEBI_49637 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CHEBI_49637">
Expand Down
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