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Add terms for JIRA ticket #129 (#146)
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* Update platforms

* Add new cell lines

* Lint csv file

* Lint platform csv

* Add changes

* Remember to add new platform to valid values

Co-authored-by: Robert Allaway <[email protected]>

* Add platform enum to correct file

* Add changes

* Revise cell line refs

* Add changes

* Update annotationProperty.csv

* Clean label with :

* Add changes

Co-authored-by: nf-osi[bot] <[email protected]>
Co-authored-by: Robert Allaway <[email protected]>
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@anngvu @nfosi-service @allaway
3 people authored May 18, 2022
1 parent c22f321 commit 06b6ca0
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13 changes: 9 additions & 4 deletions NF.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -184,11 +184,11 @@ Illumina NovaSeq 6000,"A DNA sequencer which is manufactured by the Illumina cor
PacBio Sequel IIe System,PacBio Sequel IIe System,,,FALSE,,platform,,,,PacBio_Sequel_Iie_System,Class,Assay,Platform,Platform,,,
PacBio Sequel II System,PacBio Sequel II System,,,FALSE,,platform,,,,PacBio_Sequel_II_System,Class,Assay,Platform,Platform,,,
NanostringGeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assay,Platform,Platform,,,
Chromium X,"(From 10x Genomics) A single-cell platform with capability for hundreds to hundreds of thousands of cells in a single run, used for analysis of cell activity in multiple dimensions, including gene expression,
chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, and CRISPR perturbation screens.",,,FALSE,https://www.10xgenomics.com/chromium-x,platform,,,,Chromium_X,Class,Assay,Platform,Platform,,,
Chromium X,"(From 10x Genomics) Single-cell platform that can analyze hundreds to hundreds of thousands of cells in single run for e.g. gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, CRISPR perturbation screens).",,,FALSE,https://www.10xgenomics.com/chromium-x,platform,,,,Chromium_X,Class,Assay,Platform,Platform,,,
EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platform,,,,EnVision_2103,Class,Assay,Platform,Platform,,,
drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,,
assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,,
platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,,
libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,,
assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,,
proteinExtractSource,Source of the extracted protein used in the experiment,"cell lysate, nuclei, mitochondria, cytoplasm",,TRUE,http://purl.obolibrary.org/obo/OBI_0000894,experimentalData,,,,proteinExtractSource,Property,Assay,annotationProperty,,,,
Expand Down Expand Up @@ -377,6 +377,11 @@ cNF98.4c,A primary cutaneous neurofibroma cell line; not broadly available. See
Prss56Cre;R26mT,"Prss56Cre;R26mT is a transgenic non-human animal model for Neurofibromatosis type 1, wherein the Nf1 gene is specifically inactivated in BC cells and derivatives thereof.","","",FALSE,https://patents.google.com/patent/EP3420811A1/en,modelSystemName,,"","",Prss56Cre;R26mT,Class,Biosample,Model_System,Mouse_Model,"","",""
Nf1-OPG,"","","",FALSE,"",modelSystemName,,"","",Nf1-OPG,Class,Biosample,Model_System,Mouse_Model,"","",""
Nf1-OPG-Arg816,"","","",FALSE,"",modelSystemName,,"","",Nf1-OPG-Arg816,Class,Biosample,Model_System,Mouse_Model,"","",""
Nf2-/- Schwann SC (mouse) (PMID26554010),"A Nf2-/- mouse schwann cell line; see PMID:26554010","","",FALSE,"",modelSystemName,,"","",Nf2-/-Schwann_mouse,Class,Biosample,Model_System,Cell_Line_Model,"","",""
SC4 [Mouse schwannoma],"Mouse schwannoma knock-out cell line (RRID:CVCL_JK03)","","",FALSE,"https://web.expasy.org/cellosaurus/CVCL_JK03",modelSystemName,,"","",SC4,Class,Biosample,Model_System,Cell_Line_Model,"","",""
AC007-hTERT,"Human arachnoid cell line","","",FALSE,"",modelSystemName,,"","",AC007-hTERT,Class,Biosample,Model_System,Cell_Line_Model,"","",""
NF2-/- AC007-hTERT,"Knock-out cell line developed by CRISPR targeting NF2 exon 8 in AC007-hTERT","","",FALSE,"",modelSystemName,,"","",hTERT_NF2_arachnoid,Class,Biosample,Model_System,Cell_Line_Model,"","",""
Ben-Men-1,"Human meningioma cell line (RRID:CVCL_1959)","","",FALSE,"https://web.expasy.org/cellosaurus/CVCL_1959",modelSystemName,,"","",Ben-Men-1,Class,Biosample,Model_System,Cell_Line_Model,"","",""
Male,"A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both.","","",FALSE,http://purl.obolibrary.org/obo/NCIT_C20197,sex,,"","",Male,Class,Biosample,Sex,"","","",""
Female,"A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both.","","",FALSE,http://purl.obolibrary.org/obo/NCIT_C16576,sex,,"","",Female,Class,Biosample,Sex,"","","",""
Unknown,"Not known, observed, recorded; or reported as unknown by the data contributor.","","",FALSE,http://purl.obolibrary.org/obo/NCIT_C17998,sex,,"","",Unknown_Sex,Class,Biosample,Sex,"","","",""
Expand Down Expand Up @@ -492,7 +497,7 @@ 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",,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",,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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122 changes: 121 additions & 1 deletion NF.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -5147,7 +5147,7 @@
{
"@id": "bts:ChromiumX",
"@type": "rdfs:Class",
"rdfs:comment": "(From 10x Genomics) A single-cell platform with capability for hundreds to hundreds of thousands of cells in a single run, used for analysis of cell activity in multiple dimensions, including gene expression,\nchromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, and CRISPR perturbation screens.",
"rdfs:comment": "(From 10x Genomics) Single-cell platform that can analyze hundreds to hundreds of thousands of cells in single run for e.g. gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, CRISPR perturbation screens).",
"rdfs:label": "ChromiumX",
"rdfs:subClassOf": [
{
Expand All @@ -5161,6 +5161,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:EnVision2103MultiplateReader",
"@type": "rdfs:Class",
"rdfs:comment": "EnVision 2103 Multiplate Reader",
"rdfs:label": "EnVision2103MultiplateReader",
"rdfs:subClassOf": [
{
"@id": "bts:Platform"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "EnVision 2103 Multiplate Reader",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:DrugScreenType",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -5596,6 +5613,9 @@
},
{
"@id": "bts:ChromiumX"
},
{
"@id": "bts:EnVision2103MultiplateReader"
}
],
"sms:displayName": "platform",
Expand Down Expand Up @@ -9012,6 +9032,91 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Nf2-/-SchwannSC(mouse)(PMID26554010)",
"@type": "rdfs:Class",
"rdfs:comment": "A Nf2-/- mouse schwann cell line; see PMID:26554010",
"rdfs:label": "Nf2-/-SchwannSC(mouse)(PMID26554010)",
"rdfs:subClassOf": [
{
"@id": "bts:ModelSystemName"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Nf2-/- Schwann SC (mouse) (PMID26554010)",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:SC4[Mouseschwannoma]",
"@type": "rdfs:Class",
"rdfs:comment": "Mouse schwannoma knock-out cell line (RRID:CVCL_JK03)",
"rdfs:label": "SC4[Mouseschwannoma]",
"rdfs:subClassOf": [
{
"@id": "bts:ModelSystemName"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "SC4 [Mouse schwannoma]",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:AC007-hTERT",
"@type": "rdfs:Class",
"rdfs:comment": "Human arachnoid cell line",
"rdfs:label": "AC007-hTERT",
"rdfs:subClassOf": [
{
"@id": "bts:ModelSystemName"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "AC007-hTERT",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:NF2-/-AC007-hTERT",
"@type": "rdfs:Class",
"rdfs:comment": "Knock-out cell line developed by CRISPR targeting NF2 exon 8 in AC007-hTERT",
"rdfs:label": "NF2-/-AC007-hTERT",
"rdfs:subClassOf": [
{
"@id": "bts:ModelSystemName"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "NF2-/- AC007-hTERT",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Ben-Men-1",
"@type": "rdfs:Class",
"rdfs:comment": "Human meningioma cell line (RRID:CVCL_1959)",
"rdfs:label": "Ben-Men-1",
"rdfs:subClassOf": [
{
"@id": "bts:ModelSystemName"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Ben-Men-1",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Male",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -11893,6 +11998,21 @@
},
{
"@id": "bts:CNF98.4c"
},
{
"@id": "bts:Nf2-/-SchwannSC(mouse)(PMID26554010)"
},
{
"@id": "bts:SC4[Mouseschwannoma]"
},
{
"@id": "bts:AC007-hTERT"
},
{
"@id": "bts:NF2-/-AC007-hTERT"
},
{
"@id": "bts:Ben-Men-1"
}
],
"sms:displayName": "modelSystemName",
Expand Down
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