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Add NRG per #205 (#206)
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* Add NRG per #205

* Build jsonld

Co-authored-by: nf-osi[bot] <nf-osi@sagebionetworks.org>
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anngvu and nfosi-service authored Oct 5, 2022
1 parent 4773e5f commit f00b06a
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Showing 4 changed files with 27 additions and 5 deletions.
5 changes: 3 additions & 2 deletions NF.csv
Original file line number Diff line number Diff line change
Expand Up @@ -314,7 +314,8 @@ Unknown,unknown,"","",FALSE,Sage Bionetworks,nf1Genotype,,"","",NF1_Unknown_Geno
+/+,Homozygous wild type,"","",FALSE,Sage Bionetworks,nf2Genotype,,"","",NF2_Wildtype,Class,Biosample,Genotype,NF2_Genotype,"","",""
Unknown,unknown,"","",FALSE,Sage Bionetworks,nf2Genotype,,"","",NF2_Unknown_Genotype,Class,Biosample,Genotype,NF2_Genotype,"","",""
C57BL/6J,C57BL/6 is the most widely used inbred strain. It is commonly used as a general purpose strain and background strain for the generation of congenics carrying both spontaneous and induced mutations.,"","",FALSE,https://www.jax.org/strain/000664,modelSystemName,,"","",C57BL/6J,Class,Biosample,Model_System,Mouse_Model,"","",""
NOD scid gamma,"These mice are most often referred to using their branded name """"NSG™"""" and are extremely immunodeficient.","","",FALSE,https://www.jax.org/strain/005557,modelSystemName,,"","",NOD_scid_gamma,Class,Biosample,Model_System,Mouse_Model,"","",""
NOD scid gamma,"These mice are most often referred to using their branded name NSG™ and are extremely immunodeficient.","","",FALSE,https://www.jax.org/strain/005557,modelSystemName,,"","",NOD_scid_gamma,Class,Biosample,Model_System,Mouse_Model,"","",""
NRG,"Extremely immunodeficient mice with a targeted knockout mutation in recombination activating gene 1 (Rag1) and a complete null allele of the IL2 receptor common gamma chain.","","",FALSE,https://www.jax.org/strain/007799,modelSystemName,,"","",NRG,Class,Biosample,Model_System,Mouse_Model,"","",""
B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,"","","",FALSE,https://www.jax.org/strain/008191,modelSystemName,,"","",B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,Class,Biosample,Model_System,Mouse_Model,"","",""
B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,"","","",FALSE,https://www.jax.org/strain/027678,modelSystemName,,"","",B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,Class,Biosample,Model_System,Mouse_Model,"","",""
B6.129S2-Nf1tm1Tyj/J,"","","",FALSE,https://www.jax.org/strain/008192,modelSystemName,,"","",B6.129S2-Nf1tm1Tyj/J,Class,Biosample,Model_System,Mouse_Model,"","",""
Expand Down Expand Up @@ -522,7 +523,7 @@ parentSpecimenID,"A unique identifier (non-PII) that represents the parent speci
specimenID,"A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the",,,FALSE,,experimentalData,,,,specimenID,Property,Biosample,annotationProperty,,,many,"Typically annotated with a single ID, but many allowed for summary data."
specimenIDSource,"Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.",,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,,This is not officially part of the template and only used as needed.
aliquotID,A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ,,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,,
modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1,M3 MPNST",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,,
modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1,M3 MPNST,NRG",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,,
nf2Genotype,"Genotype of NF2 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf2Genotype,Property,Biosample,annotationProperty,,Genotype,,
nf1Genotype,"Genotype of NF1 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf1Genotype,Property,Biosample,annotationProperty,,Genotype,,
specimenPreparationMethod,"Term that represents preservation of the sample before usage in, e.g. sequencing","Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNAlater, formalin-fixed, ethanol, Viably frozen",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample&anchor=preservation_method,ngs,,,,specimenPreparationMethod,Property,Biosample,annotationProperty,,Specimen_State,,
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22 changes: 21 additions & 1 deletion NF.jsonld
Original file line number Diff line number Diff line change
Expand Up @@ -8010,7 +8010,7 @@
{
"@id": "bts:NODscidgamma",
"@type": "rdfs:Class",
"rdfs:comment": "These mice are most often referred to using their branded name \"\"NSG™\"\" and are extremely immunodeficient.",
"rdfs:comment": "These mice are most often referred to using their branded name NSG™ and are extremely immunodeficient.",
"rdfs:label": "NODscidgamma",
"rdfs:subClassOf": [
{
Expand All @@ -8024,6 +8024,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:NRG",
"@type": "rdfs:Class",
"rdfs:comment": "Extremely immunodeficient mice with a targeted knockout mutation in recombination activating gene 1 (Rag1) and a complete null allele of the IL2 receptor common gamma chain.",
"rdfs:label": "NRG",
"rdfs:subClassOf": [
{
"@id": "bts:ModelSystemName"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "NRG",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:B6;129S2-Trp53tm1TyjNf1tm1Tyj/J",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -12485,6 +12502,9 @@
},
{
"@id": "bts:M3MPNST"
},
{
"@id": "bts:NRG"
}
],
"sms:displayName": "modelSystemName",
Expand Down
3 changes: 2 additions & 1 deletion modules/Biosample/Model_System.csv
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote
C57BL/6J,C57BL/6 is the most widely used inbred strain. It is commonly used as a general purpose strain and background strain for the generation of congenics carrying both spontaneous and induced mutations.,"","",FALSE,https://www.jax.org/strain/000664,modelSystemName,,"","",C57BL/6J,Class,Biosample,Model_System,Mouse_Model,"","",""
NOD scid gamma,"These mice are most often referred to using their branded name """"NSG™"""" and are extremely immunodeficient.","","",FALSE,https://www.jax.org/strain/005557,modelSystemName,,"","",NOD_scid_gamma,Class,Biosample,Model_System,Mouse_Model,"","",""
NOD scid gamma,"These mice are most often referred to using their branded name NSG™ and are extremely immunodeficient.","","",FALSE,https://www.jax.org/strain/005557,modelSystemName,,"","",NOD_scid_gamma,Class,Biosample,Model_System,Mouse_Model,"","",""
NRG,"Extremely immunodeficient mice with a targeted knockout mutation in recombination activating gene 1 (Rag1) and a complete null allele of the IL2 receptor common gamma chain.","","",FALSE,https://www.jax.org/strain/007799,modelSystemName,,"","",NRG,Class,Biosample,Model_System,Mouse_Model,"","",""
B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,"","","",FALSE,https://www.jax.org/strain/008191,modelSystemName,,"","",B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,Class,Biosample,Model_System,Mouse_Model,"","",""
B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,"","","",FALSE,https://www.jax.org/strain/027678,modelSystemName,,"","",B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,Class,Biosample,Model_System,Mouse_Model,"","",""
B6.129S2-Nf1tm1Tyj/J,"","","",FALSE,https://www.jax.org/strain/008192,modelSystemName,,"","",B6.129S2-Nf1tm1Tyj/J,Class,Biosample,Model_System,Mouse_Model,"","",""
Expand Down
2 changes: 1 addition & 1 deletion modules/Biosample/annotationProperty.csv
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ parentSpecimenID,"A unique identifier (non-PII) that represents the parent speci
specimenID,"A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the",,,FALSE,,experimentalData,,,,specimenID,Property,Biosample,annotationProperty,,,many,"Typically annotated with a single ID, but many allowed for summary data."
specimenIDSource,"Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.",,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,,This is not officially part of the template and only used as needed.
aliquotID,A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ,,,FALSE,,,,,,,Property,Biosample,annotationProperty,,,,
modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1,M3 MPNST",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,,
modelSystemName,"A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293T (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)","C57BL/6J,NOD scid gamma,B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J,B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ,B6.129S2-Nf1tm1Tyj/J,B6.129S1-Nf1tm1Cbr/J,B6.129(Cg)-Nf1tm1Par/J,hiPSC-SCP,hiPSC,JHU 2-103-CL,JHU 2-002-CL,JHU 2-079-CL,JHU 2-103-PDX,JHU 2-002-PDX,JHU 2-079-PDX,human foreskin fibroblasts,hTERT NF1 ipNF05.5,hTERT NF1 ipNF05.5 (Mixed clones),hTERT NF1 ipn06.2 A,hTERT NF1 ipNF95.11b C/T,hTERT NF1 ipNF95.6,hTERT SC ipn02.8,hTERT NF1 ipnNF95.11c,hTERT NF1 ipNF95.11b C,hTERT NF1 ipnNF09.4,hTERT NF1 ipNF04.4,hTERT NF1 sipnNF95.12B,hTERT NF1 ipNF00.6,hTERT NF1 ipNF03.3,hTERT NF1 ipn02.3 2λ,hTERT SC ipn02.8,SZ-NF1,SZ-NF2,SZ-NF4,NF1,Lis42_NF1_1N,Lis47_NF1_2N,ST88-14,sNF96.2,sNF02.2,sNF94.3,GM11602,GM11601,KCL024,KCL025,5PNF_TdiPSsv_PM_6,5PNF_TdiPSsv_MM_4,7PNF_SiPSrv_PM_12,6PNF_SiPSrv_PM_2,3PNF_SiPSsv_MM_11,3PNF_FiPSsv_PM_2,NCC-MPNST5-C1,NCC-MPNST3-C1,NCC-MPNST4-C1,NCC-MPNST3-X2-C1,NCC-MPNST2-C1,STS-26T,YST-1,90-8,S520,S462,S462.TY,sc93.1,Fb93.1, JH-2-002-CL, JH-2-079-CL, JH-2-103-CL, icNF00.10a, cNF00.10a, icNF97.2a, cNF97.2a, icNF97.2b, cNF97.2b, icNF98.4d, cNF98.4d, i28NF, 28NF, icNF04.9a, cNF04.9a, icNF98.4c, cNF98.4c, Nf2-/- Schwann SC (mouse) (PMID26554010), SC4 [Mouse schwannoma], AC007-hTERT, NF2-/- AC007-hTERT, Ben-Men-1,M3 MPNST,NRG",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,Biosample,annotationProperty,annotationProperty,Model_System,,
nf2Genotype,"Genotype of NF2 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf2Genotype,Property,Biosample,annotationProperty,,Genotype,,
nf1Genotype,"Genotype of NF1 gene in the biospecimen from which the data were derived, if known","-/-, +/-, +/+, +/?, -/?, Unknown",,FALSE,,neurofibromatosis,,,,nf1Genotype,Property,Biosample,annotationProperty,,Genotype,,
specimenPreparationMethod,"Term that represents preservation of the sample before usage in, e.g. sequencing","Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNAlater, formalin-fixed, ethanol, Viably frozen",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample&anchor=preservation_method,ngs,,,,specimenPreparationMethod,Property,Biosample,annotationProperty,,Specimen_State,,
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