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Update annotations to use BQM qualifier for compartment annotations w…
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…ith PBPK ontology compartment terms
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@jwkruisselbrink
jwkruisselbrink committed Aug 9, 2024
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18 changes: 9 additions & 9 deletions model/euromix.annotations.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -5,27 +5,27 @@ volumeUnits,document,model volume unit,L,,,,Model volume unit.,
euromix,model,,,rdf,BQM_IS,http://identifiers.org/mamo/MAMO_0000203,physiologically based pharmacokinetic model,
euromix,model,,,rdf,BQM_IS,http://identifiers.org/mamo/MAMO_0000046,ordinary differential equation model,
euromix,model,,,rdf,BQB_HAS_TAXON,http://identifiers.org/taxonomy/40674,mammalia,
Air,compartment,alveolar air,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00458,Alveolar air compartment.,
Air,compartment,alveolar air,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00458,Alveolar air compartment.,
Air,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/NCIT_C150891,,
Art,compartment,arterial blood,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00462,Arterial blood compartment.,
Art,compartment,arterial blood,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00462,Arterial blood compartment.,
Art,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0013755,,
Urine,compartment,urine,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0001088,Urine compartment.,
Fat,compartment,adipose tissue,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0001013,Adipose tissue (fat) compartment.,
Gut,compartment,gut,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0001555,Gut (digestive tract) compartment.,
Rich,compartment,richly perfused tissue,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00464,Richly perfused tissue compartment.,
Rich,compartment,richly perfused tissue,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00464,Richly perfused tissue compartment.,
Rich,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0013756,,
Liver,compartment,liver,L,,,,Liver compartment.,
Liver,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0002107,,
Poor,compartment,poorly perfused tissue,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00465,Poorly perfused tissue compartment.,
Skin_e,compartment,viable epidermis exposed skin,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00467,Viable epidermis of exposed skin compartment.,
Poor,compartment,poorly perfused tissue,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00465,Poorly perfused tissue compartment.,
Skin_e,compartment,viable epidermis exposed skin,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00467,Viable epidermis of exposed skin compartment.,
Skin_e,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0002097,,
Skin_u,compartment,viable epidermis unexposed skin,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00466,Viable epidermis of unexposed skin compartment.,
Skin_u,compartment,viable epidermis unexposed skin,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00466,Viable epidermis of unexposed skin compartment.,
Skin_u,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0002097,,
Skin_sc_e,compartment,stratum corneum exposed skin,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00469,Stratum corneum of exposed skin compartment.,
Skin_sc_e,compartment,stratum corneum exposed skin,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00469,Stratum corneum of exposed skin compartment.,
Skin_sc_e,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0002027,,
Skin_sc_u,compartment,stratum corneum unexposed skin,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00468,Stratum corneum of unexposed skin compartment.,
Skin_sc_u,compartment,stratum corneum unexposed skin,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00468,Stratum corneum of unexposed skin compartment.,
Skin_sc_u,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0002027,,
Ven,compartment,venous blood,L,rdf,BQB_IS,http://purl.obolibrary.org/obo/PBPKO_00463,Venous blood compartment.,
Ven,compartment,venous blood,L,rdf,BQM_IS,http://purl.obolibrary.org/obo/PBPKO_00463,Venous blood compartment.,
Ven,compartment,,,rdf,BQB_IS,http://purl.obolibrary.org/obo/UBERON_0013756,,
QFat,species,quantity in fat tissues,mmol,rdf,BQB_IS,http://identifiers.org/SBO:0000247,simple chemical,
QRich,species,quantity in richly tissues,mmol,rdf,BQB_IS,http://identifiers.org/SBO:0000247,simple chemical,
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52 changes: 42 additions & 10 deletions model/euromix.sbml
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Expand Up @@ -206,9 +206,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Air">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00458"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/NCIT_C150891"/>
</rdf:Bag>
</bqbiol:is>
Expand Down Expand Up @@ -246,9 +250,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Rich">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00464"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013756"/>
</rdf:Bag>
</bqbiol:is>
Expand All @@ -273,9 +281,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Art">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00462"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013755"/>
</rdf:Bag>
</bqbiol:is>
Expand All @@ -287,9 +299,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Ven">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00463"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013756"/>
</rdf:Bag>
</bqbiol:is>
Expand All @@ -301,9 +317,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Skin_e">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00467"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002097"/>
</rdf:Bag>
</bqbiol:is>
Expand All @@ -315,9 +335,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Skin_u">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00466"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002097"/>
</rdf:Bag>
</bqbiol:is>
Expand All @@ -329,9 +353,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Skin_sc_e">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00469"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002027"/>
</rdf:Bag>
</bqbiol:is>
Expand All @@ -343,9 +371,13 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Skin_sc_u">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00468"/>
</rdf:Bag>
</bqmodel:is>
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002027"/>
</rdf:Bag>
</bqbiol:is>
Expand All @@ -357,11 +389,11 @@
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Poor">
<bqbiol:is>
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="http://purl.obolibrary.org/obo/PBPKO_00465"/>
</rdf:Bag>
</bqbiol:is>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
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