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update to list like (#201)
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* update to list like

* Build jsonld

Co-authored-by: nf-osi[bot] <[email protected]>
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@allaway @nfosi-service
allaway and nfosi-service authored Oct 7, 2022
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4 changes: 2 additions & 2 deletions NF.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -513,7 +513,7 @@ individualIdSource,Database or repository to which individual ID maps,,,FALSE,,e
tissue,A tissue is a mereologically maximal collection of cells that together perform physiological function.,"nerve tissue,optic nerve,serum,plasma,splenocyte,blood,primary tumor,embryonic tissue,meninges,bone marrow,Buccal Mucosa,Dorsal Root Ganglion,unspecified,whole brain,Buffy Coat,cerebral cortex,sciatic nerve,connective tissue,tumor-adjacent normal, PDX tissue, CDX tissue, metastatic/recurrent tumor, recurrent tumor, metastatic tumor, organoid, spheroid, microtissue, retina",,FALSE,,experimentalData,,,,tissueType,Property,Biosample,annotationProperty,,Tissue,,
isCellLine,Whether or not sample source is a cell line (Yes; No),"Yes, No",,FALSE,,experimentalData,,,,isCellLine,DataProperty,Biosample,annotationProperty,,,,
isPrimaryCell,Whether or not cellType is primary (Yes; No),"Yes, No",,FALSE,,experimentalData,,,,isPrimaryCell,DataProperty,Biosample,annotationProperty,,,,
cellType,A cell type is a distinct morphological or functional form of cell.,"Schwann cell precursor, B-lymphocytes, Embryonic stem cells, iPSC, iPSC-derived telencephalic organoids, GABAergic neurons, monocytes, microglia, macrophages, astrocytes, SH-SY5Y, GLUtamatergic neurons, NeuN+, NeuN-, epithelial, epithelial-like, fibroblast, round, lymphoblast, CD8+ T-Cells, arachnoid, meningioma, schwannoma, oligodendrocyte, schwann, iPSC-derived neuron, iPSC-derived glia, iPSC-derived astrocytes, monocyte-derived microglia, iPSC-derived neuronal progenitor cell, CD138+, CNON, teratoma, cultured Muller glia, DRG/nerve root neurosphere cell",,FALSE,,experimentalData,,,list,cellType,DataProperty,Biosample,annotationProperty,,Cell,,
cellType,A cell type is a distinct morphological or functional form of cell.,"Schwann cell precursor, B-lymphocytes, Embryonic stem cells, iPSC, iPSC-derived telencephalic organoids, GABAergic neurons, monocytes, microglia, macrophages, astrocytes, SH-SY5Y, GLUtamatergic neurons, NeuN+, NeuN-, epithelial, epithelial-like, fibroblast, round, lymphoblast, CD8+ T-Cells, arachnoid, meningioma, schwannoma, oligodendrocyte, schwann, iPSC-derived neuron, iPSC-derived glia, iPSC-derived astrocytes, monocyte-derived microglia, iPSC-derived neuronal progenitor cell, CD138+, CNON, teratoma, cultured Muller glia, DRG/nerve root neurosphere cell",,FALSE,,experimentalData,,,list like,cellType,DataProperty,Biosample,annotationProperty,,Cell,,
isMultiIndividual,Whether or not a file has data for multiple individuals (Yes; No),"Yes, No",,TRUE,,experimentalData,,,,isMultiIndividual,DataProperty,Biosample,annotationProperty,,,,
isMultiSpecimen,Whether or not a file has data for multiple specimens (Yes; No),"Yes, No",,TRUE,,experimentalData,,,,isMultiSpecimen,DataProperty,Biosample,annotationProperty,,,,
sex,"Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","Male, Female, Unknown",,FALSE,http://purl.obolibrary.org/obo/NCIT_C28421,experimentalData,,,,sex,Property,Biosample,annotationProperty,,Sex,,
Expand All @@ -523,7 +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,NRG",,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 like,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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4 changes: 2 additions & 2 deletions NF.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -11955,7 +11955,7 @@
"sms:displayName": "cellType",
"sms:required": "sms:false",
"sms:validationRules": [
"list"
"list like"
]
},
{
Expand Down Expand Up @@ -12510,7 +12510,7 @@
"sms:displayName": "modelSystemName",
"sms:required": "sms:false",
"sms:validationRules": [
"list"
"list like"
]
},
{
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4 changes: 2 additions & 2 deletions modules/Biosample/annotationProperty.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ individualIdSource,Database or repository to which individual ID maps,,,FALSE,,e
tissue,A tissue is a mereologically maximal collection of cells that together perform physiological function.,"nerve tissue,optic nerve,serum,plasma,splenocyte,blood,primary tumor,embryonic tissue,meninges,bone marrow,Buccal Mucosa,Dorsal Root Ganglion,unspecified,whole brain,Buffy Coat,cerebral cortex,sciatic nerve,connective tissue,tumor-adjacent normal, PDX tissue, CDX tissue, metastatic/recurrent tumor, recurrent tumor, metastatic tumor, organoid, spheroid, microtissue, retina",,FALSE,,experimentalData,,,,tissueType,Property,Biosample,annotationProperty,,Tissue,,
isCellLine,Whether or not sample source is a cell line (Yes; No),"Yes, No",,FALSE,,experimentalData,,,,isCellLine,DataProperty,Biosample,annotationProperty,,,,
isPrimaryCell,Whether or not cellType is primary (Yes; No),"Yes, No",,FALSE,,experimentalData,,,,isPrimaryCell,DataProperty,Biosample,annotationProperty,,,,
cellType,A cell type is a distinct morphological or functional form of cell.,"Schwann cell precursor, B-lymphocytes, Embryonic stem cells, iPSC, iPSC-derived telencephalic organoids, GABAergic neurons, monocytes, microglia, macrophages, astrocytes, SH-SY5Y, GLUtamatergic neurons, NeuN+, NeuN-, epithelial, epithelial-like, fibroblast, round, lymphoblast, CD8+ T-Cells, arachnoid, meningioma, schwannoma, oligodendrocyte, schwann, iPSC-derived neuron, iPSC-derived glia, iPSC-derived astrocytes, monocyte-derived microglia, iPSC-derived neuronal progenitor cell, CD138+, CNON, teratoma, cultured Muller glia, DRG/nerve root neurosphere cell",,FALSE,,experimentalData,,,list,cellType,DataProperty,Biosample,annotationProperty,,Cell,,
cellType,A cell type is a distinct morphological or functional form of cell.,"Schwann cell precursor, B-lymphocytes, Embryonic stem cells, iPSC, iPSC-derived telencephalic organoids, GABAergic neurons, monocytes, microglia, macrophages, astrocytes, SH-SY5Y, GLUtamatergic neurons, NeuN+, NeuN-, epithelial, epithelial-like, fibroblast, round, lymphoblast, CD8+ T-Cells, arachnoid, meningioma, schwannoma, oligodendrocyte, schwann, iPSC-derived neuron, iPSC-derived glia, iPSC-derived astrocytes, monocyte-derived microglia, iPSC-derived neuronal progenitor cell, CD138+, CNON, teratoma, cultured Muller glia, DRG/nerve root neurosphere cell",,FALSE,,experimentalData,,,list like,cellType,DataProperty,Biosample,annotationProperty,,Cell,,
isMultiIndividual,Whether or not a file has data for multiple individuals (Yes; No),"Yes, No",,TRUE,,experimentalData,,,,isMultiIndividual,DataProperty,Biosample,annotationProperty,,,,
isMultiSpecimen,Whether or not a file has data for multiple specimens (Yes; No),"Yes, No",,TRUE,,experimentalData,,,,isMultiSpecimen,DataProperty,Biosample,annotationProperty,,,,
sex,"Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","Male, Female, Unknown",,FALSE,http://purl.obolibrary.org/obo/NCIT_C28421,experimentalData,,,,sex,Property,Biosample,annotationProperty,,Sex,,
Expand All @@ -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,NRG",,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 like,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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