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update dpbo
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@StellaEggels
StellaEggels committed Aug 27, 2024
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95 changes: 79 additions & 16 deletions DPBO.owl
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Expand Up @@ -1791,11 +1791,11 @@
<!-- http://purl.obolibrary.org/obo/DPBO_0000035 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DPBO_0000035">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DPBO_0000095"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/dpbo#ObsoleteClass"/>
<obo:IAO_0000115>Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>DPBO:0000035</oboInOwl:id>
<rdfs:label>Seurat</rdfs:label>
<rdfs:label>obsolete_Seurat</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>

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<!-- http://purl.obolibrary.org/obo/DPBO_00002008 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DPBO_00002008">
<obo:IAO_0000115>Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. </obo:IAO_0000115>
<oboInOwl:hasDbXref>ENVO:01000813</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>DPBO:00002008</oboInOwl:id>
<rdfs:comment>EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO&quot; []</rdfs:comment>
<rdfs:label>environment (feature)</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/DPBO_0002000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DPBO_0002000">
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<!-- http://purl.obolibrary.org/obo/DPBO_0002008 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DPBO_0002008">
<obo:IAO_0000115>Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. </obo:IAO_0000115>
<oboInOwl:hasDbXref>ENVO:01000813</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>DPBO:0002008</oboInOwl:id>
<rdfs:comment>EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO&quot; []</rdfs:comment>
<rdfs:label>environment (feature)</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/DPBO_0002009 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DPBO_0002009">
Expand Down Expand Up @@ -6380,7 +6380,12 @@

<!-- http://purl.obolibrary.org/obo/EFO_0002694 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/EFO_0002694"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EFO_0002694">
<obo:IAO_0000115>A process performed as part of an experiment or wider study, i.e. intentionally designed.</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>EFO:0002694</oboInOwl:id>
<rdfs:label>experimental process</rdfs:label>
</owl:Class>



Expand Down Expand Up @@ -6935,6 +6940,42 @@



<!-- http://purl.obolibrary.org/obo/ENVO_00000050 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_00000050">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DPBO_00002008"/>
<obo:IAO_0000115>A hot spring that erupts periodically, ejecting a column of hot water and steam into the air.</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>ENVO:00000050</oboInOwl:id>
<rdfs:label>geyser</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ENVO_01000263 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_01000263">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DPBO_00002008"/>
<obo:IAO_0000115>A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor.</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>ENVO:01000263</oboInOwl:id>
<rdfs:label>cold seep</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ENVO_01000403 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_01000403">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DPBO_00002008"/>
<obo:IAO_0000115>This class corresponds to the &apos;Tropical Mixed needleleaf / broadleaf forest&apos; category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the &apos;tropical mixed needleleaf forest&apos; class can be made. The relationship between this &apos;forest&apos; class and the mangrove swamp must be clarified.</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>ENVO:01000403</oboInOwl:id>
<rdfs:label>tropical mangrove</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/ERO_0001788 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0001788">
Expand Down Expand Up @@ -7477,6 +7518,16 @@



<!-- http://purl.obolibrary.org/obo/MIAPPE_0049 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MIAPPE_0049">
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>MIAPPE:0049</oboInOwl:id>
<rdfs:label>Biological material preprocessing</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPPE_0095 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MIAPPE_0095">
Expand Down Expand Up @@ -8003,6 +8054,18 @@



<!-- http://purl.obolibrary.org/obo/PECO_0001001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PECO_0001001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MIAPPE_0049"/>
<obo:IAO_0000115>A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (biotic plant exposurePECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357plant experimental condition) or set of conditions describing the application of an abiotic (abiotic plant exposure) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof.</obo:IAO_0000115>
<oboInOwl:hasOBONamespace>DPBO</oboInOwl:hasOBONamespace>
<oboInOwl:id>PECO:0001001</oboInOwl:id>
<rdfs:label>plant exposure</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000307 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000307">
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21 changes: 18 additions & 3 deletions dpbo.obo
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Expand Up @@ -688,9 +688,9 @@ def: "Health status of the plant at the time of sample collection" []

[Term]
id: DPBO:0000035
name: Seurat
name: obsolete_Seurat
def: "Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data." []
is_a: DPBO:0000095 ! R package
is_a: ObsoleteClass ! Obsolete Class
is_obsolete: true

[Term]
Expand Down Expand Up @@ -3233,6 +3233,11 @@ def: "ChIP-seq is an assay in which chromatin immunoprecipitation with high thro
xref: NCIt:C106049
is_a: GENEPIO:0001973 ! library strategy

[Term]
id: EFO:0002694
name: experimental process
def: "A process performed as part of an experiment or wider study, i.e. intentionally designed." []

[Term]
id: EFO:0003748
name: MRE-seq
Expand Down Expand Up @@ -3511,7 +3516,7 @@ is_a: DPBO:0000012 ! bio entity
[Term]
id: ENVO:01000403
name: tropical mangrove
def: "This class corresponds to the "Tropical Mixed needleleaf / broadleaf forest" category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the "tropical mixed needleleaf forest" class can be made. The relationship between this "forest" class and the mangrove swamp must be clarified."
def: "This class corresponds to the 'Tropical Mixed needleleaf / broadleaf forest' category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the 'tropical mixed needleleaf forest' class can be made. The relationship between this 'forest' class and the mangrove swamp must be clarified."
is_a: DPBO:00002008 ! environment (feature)

[Term]
Expand Down Expand Up @@ -3883,6 +3888,10 @@ id: MI:0507
name: tag
def: "Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule." [PMID:14755292]

[Term]
id: MIAPPE:0049
name: Biological material preprocessing

[Term]
id: MIAPPE:0095
name: Growth facility
Expand Down Expand Up @@ -4150,6 +4159,12 @@ id: PATO:0015031
name: contamination
def: "The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity." [https://en.wikipedia.org/wiki/Contamination, https://github.com/pato-ontology/pato/issues/420]

[Term]
id: PECO:0001001
name: plant exposure
def: "A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (biotic plant exposurePECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357plant experimental condition) or set of conditions describing the application of an abiotic (abiotic plant exposure) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof." []
is_a: MIAPPE:0049 ! Biological material preprocessing

[Term]
id: PRIDE:0000307
name: Quantification method
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