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add cNF cell line terms (#128)
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* add cNF cell line terms

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Co-authored-by: nf-osi[bot] <[email protected]>
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allaway and nfosi-service authored Apr 5, 2022
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22 changes: 19 additions & 3 deletions NF.csv
Original file line number Diff line number Diff line change
Expand Up @@ -389,7 +389,21 @@ Fb93.1,Cell line generated by Ray Mattingly's lab.,,,FALSE,,modelSystemName,,,,F
JH-2-002-CL,Cell line derived from JHU biobank individual,,,FALSE,,modelSystemName,,,,JH-2-002-CL,Class,Model_System,Cell_Line_Model,,,
JH-2-079-CL,Cell line derived from JHU biobank individual,,,FALSE,,modelSystemName,,,,JH-2-079-CL,Class,Model_System,Cell_Line_Model,,,
JH-2-103-CL,Cell line derived from JHU biobank individual,,,FALSE,,modelSystemName,,,,JH-2-103-CL,Class,Model_System,Cell_Line_Model,,,
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",,FALSE,http://purl.obolibrary.org/obo/NCIT_C94171,neuro,,,list,modelSystemName,Property,,,Model_System,,
icNF00.10a,An hTERT-immortalized cutaneous neurofibroma cell line derived from a primary cell culture (cNF00.10a).,,,FALSE,,modelSystemName,,,,icNF00.10a,Class,Model_System,Cell_Line_Model,,,
cNF00.10a,A primary cutaneous neurofibroma cell line; not broadly available. See the immortalized version (icNF00.10a).,,,FALSE,,modelSystemName,,,,cNF00.10a,Class,Model_System,Cell_Line_Model,,,
icNF97.2a,An hTERT-immortalized cutaneous neurofibroma cell line derived from a primary cell culture (cNF97.2a).,,,FALSE,,modelSystemName,,,,icNF97.2a,Class,Model_System,Cell_Line_Model,,,
cNF97.2a,A primary cutaneous neurofibroma cell line; not broadly available. See the immortalized version (icNF97.2a).,,,FALSE,,modelSystemName,,,,cNF97.2a,Class,Model_System,Cell_Line_Model,,,
icNF97.2b,An hTERT-immortalized cutaneous neurofibroma cell line derived from a primary cell culture (cNF97.2b).,,,FALSE,,modelSystemName,,,,icNF97.2b,Class,Model_System,Cell_Line_Model,,,
cNF97.2b,A primary cutaneous neurofibroma cell line; not broadly available. See the immortalized version (icNF97.2b).,,,FALSE,,modelSystemName,,,,cNF97.2b,Class,Model_System,Cell_Line_Model,,,
icNF98.4d,An hTERT-immortalized cutaneous neurofibroma cell line derived from a primary cell culture (cNF98.4d).,,,FALSE,,modelSystemName,,,,icNF98.4d,Class,Model_System,Cell_Line_Model,,,
cNF98.4d,A primary cutaneous neurofibroma cell line; not broadly available. See the immortalized version (icNF98.4d).,,,FALSE,,modelSystemName,,,,cNF98.4d,Class,Model_System,Cell_Line_Model,,,
i28NF,An hTERT-immortalized cutaneous neurofibroma cell line derived from a primary cell culture (28NF).,,,FALSE,,modelSystemName,,,,i28NF,Class,Model_System,Cell_Line_Model,,,
28NF,A primary cutaneous neurofibroma cell line; not broadly available. See the immortalized version (i28NF).,,,FALSE,,modelSystemName,,,,28NF,Class,Model_System,Cell_Line_Model,,,
icNF04.9a,An hTERT-immortalized cutaneous neurofibroma cell line derived from a primary cell culture (cNF04.9a).,,,FALSE,,modelSystemName,,,,icNF04.9a,Class,Model_System,Cell_Line_Model,,,
cNF04.9a,A primary cutaneous neurofibroma cell line; not broadly available. See the immortalized version (icNF04.9a).,,,FALSE,,modelSystemName,,,,cNF04.9a,Class,Model_System,Cell_Line_Model,,,
icNF98.4c,An hTERT-immortalized cutaneous neurofibroma cell line derived from a primary cell culture (cNF98.4c).,,,FALSE,,modelSystemName,,,,icNF98.4c,Class,Model_System,Cell_Line_Model,,,
cNF98.4c,A primary cutaneous neurofibroma cell line; not broadly available. See the immortalized version (icNF98.4c).,,,FALSE,,modelSystemName,,,,cNF98.4c,Class,Model_System,Cell_Line_Model,,,
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,,,Model_System,,
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,Mouse_Model,Model_System,,,
Nf1-OPG,,,,FALSE,,modelSystemName,,,,Nf1-OPG,Class,,,,,
Nf1-OPG-Arg816,,,,FALSE,,modelSystemName,,,,Nf1-OPG-Arg816,Class,,,,,
Expand Down Expand Up @@ -424,7 +438,7 @@ fr-firststrand,,,,FALSE,,,,,,Fr-firststrand,Class,NGS_Parameter,Read_Pair_Orient
readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,FALSE,,ngs,,,,readPairOrientation,Property,ngsParameter,,Read_Pair_Orientation,,
readStrandOrigin,The strand from which the read originates in a strand-specific protocol,"forward, reverse",,FALSE,,ngs,,,,readStrandOrigin,Property,ngsParameter,,Read_Strand_Origin,,
libraryPrep,The general strategy by which the library was prepared,"rRNAdepletion, polyAselection, lncRNAenrichment, miRNAenrichment",,FALSE,,ngs,,,,libraryPrep,Property,ngsParameter,,Library_Prep,,
libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano",,FALSE,,ngs,,,,libraryPreparationMethod,Property,ngsParameter,,Library_Preparation_Method,,
libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free",,FALSE,,ngs,,,,libraryPreparationMethod,Property,ngsParameter,,Library_Preparation_Method,,
TruSeq standard total RNA library kit,,,,FALSE,https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-total-rna.html,,,,,Library_Prep_Tru_Seq,Class,,,,,
10x,10x Genomics library preparation,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,libraryPreparationMethod,,,,Library_Prep_10x,Class,,,,,
CEL-seq,CEL-Seq library preparation,,,FALSE,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,libraryPreparationMethod,,,,CEL-seq,Class,,,,,
Expand All @@ -436,6 +450,7 @@ Omni-ATAC,Omni-ATAC-seq library preparation,,,FALSE,https://protocolexchange.res
NEBNext mRNA Library Prep Reagent Set for Illumina,NEBNext mRNA Library Prep Reagent Set for Illumina,,,FALSE,https://www.neb.com/products/e6100-nebnext-mrna-library-prep-reagent-set-for-illumina,libraryPreparationMethod,,,,NEBNext_mRNA_Library_Prep_Reagent_Set_Illumina,Class,,,,,
IDT xGen Exome Research Panel,,,,FALSE,https://www.idtdna.com/pages/products/next-generation-sequencing/targeted-sequencing/hybridization-capture/predesigned-panels/xgen-exome-research-panel-v2,libraryPreparationMethod,,,,IDT_xGen_Exome_Research_Panel,Class,,,,,
Illumina TruSeq DNA Nano,,,,FALSE,Sage Bionetworks,libraryPreparationMethod,,,,Illumina_TruSeq_DNA_Nano,Class,,,,,
KAPA HyperPrep Kit PCR-free,KAPA HyperPrep Kits offer a streamlined library preparation protocol that combines several enzymatic steps and eliminates bead cleanups to significantly reduce library preparation time and improve consistency.,,,FALSE,https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html,libraryPreparationMethod,,,,KAPA HyperPrep Kit PCR-free,Class,,,,,
nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,,,nucleicAcidSource,Property,ngsParameter,,Nucleic_Acid_Source,,
dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,,,dissociationMethod,Property,ngsParameter,,Dissociation_Method,,
readLength,Number of base pairs (bp) sequenced for a read,,,FALSE,,ngs,,,,readLength,DataProperty,ngsParameter,,,,
Expand Down Expand Up @@ -521,12 +536,13 @@ experimentalData,"Any file derived from or pertaining to a scientific experiment
result,"Any file that reports data results. Examples include figures, presentations, analysis, etc.",,,FALSE,Sage Bionetworks,resourceType,,,,Result,Class,Resource,Resource,,,
tool,"Any file or link that represents a tool, model, or algorithm; the tool annotations could be applied",,,FALSE,Sage Bionetworks,resourceType,,,,Tool,Class,Resource,Resource,,,
report,"a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record).",,,FALSE,http://purl.obolibrary.org/obo/IAO_0000088,resourceType,,,,Report,Class,Resource,Resource,,,
metadata,"",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C52095,resourceType,,,,metadata,Class,Resource,Resource,,,
singleEnd,A library preparation that results in the creation of a library of 5' ends of DNA.,,,FALSE,Sage Bionetworks,runType,,,,Single_End,Class,NGS_Parameter,Run_Type,,,
pairedEnd,A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001852,runType,,,,Paired_End,Class,NGS_Parameter,Run_Type,,,
experimentalCondition,A free-text description of the experimental condition (e.g. 5 mM doxorubicin).,,,FALSE,Sage Bionetworks,sageCommunity,,,,experimentalCondition,Class,,,,,
experimentalTimepoint,The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit,,,FALSE,Sage Bionetworks,sageCommunity,,,,experimentalTimepoint,Class,,,,,
genePerturbed,The HUGO gene symbol for the gene that is perturbed. ,,,FALSE,Sage Bionetworks,sageCommunity,,,,genePerturbed,Class,,,,,
resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report",,TRUE,,sageCommunity,,,,resourceType,Class,,,Resource,,
resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report, metadata",,TRUE,,sageCommunity,,,,resourceType,Class,,,Resource,,
fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data",,TRUE,,sageCommunity,,,,fileFormat,Class,,,File_Format,one,
Homo sapiens,Homo sapiens with taxonomy ID: 9606 and Genbank common name: human,,,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,,,Human,Class,Species,Species,,,
Mus musculus,Mus musculus with taxonomy ID: 10090 and Genbank common name: house mouse,,modelSystemName,FALSE,https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10090&lvl=3&lin=f&keep=1&srchmode=1&unlock,species,,,,Mouse,Class,Species,Species,,,
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