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Updates for assay, platform, template #179

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Jul 15, 2022
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Updates for assay, platform, template #179

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557363f
Revise 'extended' templates per issue #175
anngvu Jul 13, 2022
f41e9aa
Add CUT&RUN per issue #177
anngvu Jul 13, 2022
50b1dd4
Update platforms as much as possible per issue #176
anngvu Jul 13, 2022
aa6814f
Build jsonld
nfosi-service Jul 13, 2022
0dff2ef
Add M3 MPNST cell line
anngvu Jul 15, 2022
0183dc3
Build jsonld
nfosi-service Jul 15, 2022
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74 changes: 38 additions & 36 deletions NF.csv
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204 changes: 122 additions & 82 deletions NF.jsonld
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1 change: 1 addition & 0 deletions modules/Assay/Assay.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -91,3 +91,4 @@ Massively Parallel Reporter Assay,An assay in which multiplexing the constructio
Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,,
Spatial Frequency Domain Imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022.
Optical Coherence Tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,Class,Assay,Assay,Imaging_Assay,,,
CUT&RUN,"Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. (doi:10.7554/eLife.21856)",,,FALSE,,assay,,,,CUT_RUN,Class,Assay,Assay,Epigenetics_Assay,,,
56 changes: 28 additions & 28 deletions modules/Assay/Platform.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -5,44 +5,44 @@ Orbitrap Fusion Lumos Tribrid,Thermo Scientific Orbitrap Fusion Lumos Tribrid Ma
Spectramax M Series,A Spectramax M Series Microplate Reader,,,FALSE,https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers,platform,,,,Spectramax_M_Series,Class,Assay,Platform,Platform,,,
LI-COR Odyssey CLx,A LI-COR Odyssey CLx imaging system,,,FALSE,https://www.licor.com/bio/odyssey-clx/,platform,,,,LI-COR_Odyssey_Clx,Class,Assay,Platform,Platform,,,
Q Exative HF,Thermo scientific Q Exative,,,FALSE,http://purl.obolibrary.org/obo/MS_10025223,platform,,,,Q_Exative_HF,Class,Assay,Platform,Platform,,,
HiSeq3000,Illumina HiSeq 3000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290,platform,,,,HiSeq3000,Class,Assay,Platform,Platform,,,
HiSeq2500,Illumina HiSeq 2500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791,platform,,,,HiSeq2500,Class,Assay,Platform,Platform,,,
HiSeq4000,Illumina HiSeq 4000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301,platform,,,,HiSeq4000,Class,Assay,Platform,Platform,,,
NextSeq500,Illumina NextSeq 500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573,platform,,,,NextSeq500,Class,Assay,Platform,Platform,,,
NextSeq 550,Illumina NextSeq 550,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697,platform,,,,NextSeq 550,Class,Assay,Platform,Platform,,,
NextSeq 1000,Illumina NextSeq 1000,,,FALSE,,platform,,,,NextSeq 1000,Class,Assay,Platform,Platform,,,
NextSeq 2000,Illumina NextSeq 2000,,,FALSE,,platform,,,,NextSeq 2000,Class,Assay,Platform,Platform,,,
HiSeq2000,Illumina HiSeq 2000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154,platform,,,,HiSeq2000,Class,Assay,Platform,Platform,,,
MiSeq,Illumina MiSeq,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520,platform,,,,MiSeq,Class,Assay,Platform,Platform,,,
Illumina HiSeq 3000,Illumina HiSeq 3000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21290,platform,,,,HiSeq3000,Class,Assay,Platform,Platform,,,
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This is great! Do we need to remap values in the portal as well?

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@anngvu anngvu Jul 15, 2022 •
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Yep, can track that in the internal JIRA issue.

Illumina HiSeq 2500,Illumina HiSeq 2500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16791,platform,,,,HiSeq2500,Class,Assay,Platform,Platform,,,
Illumina HiSeq 4000,Illumina HiSeq 4000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20301,platform,,,,HiSeq4000,Class,Assay,Platform,Platform,,,
Illumina NextSeq 500,Illumina NextSeq 500,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18573,platform,,,,NextSeq500,Class,Assay,Platform,Platform,,,
Illumina NextSeq 550,Illumina NextSeq 550,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21697,platform,,,,NextSeq 550,Class,Assay,Platform,Platform,,,
Illumina NextSeq 1000,Illumina NextSeq 1000,,,FALSE,,platform,,,,NextSeq 1000,Class,Assay,Platform,Platform,,,
Illumina NextSeq 2000,Illumina NextSeq 2000,,,FALSE,,platform,,,,NextSeq 2000,Class,Assay,Platform,Platform,,,
Illumina HiSeq 2000,Illumina HiSeq 2000,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11154,platform,,,,HiSeq2000,Class,Assay,Platform,Platform,,,
Illumina MiSeq,Illumina MiSeq,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15520,platform,,,,MiSeq,Class,Assay,Platform,Platform,,,
Zeiss LSM 980,A Zeiss Confocal Microscope,,,FALSE,https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwirj4XuwtXsAhVBrp4KHVZyARIQFjABegQIAhAC&url=https%3A%2F%2Fzeiss.ly%2Flsm980-info&usg=AOvVaw0rD50U0aMwfvt4bdfW0Yjd,platform,,,,Zeiss LSM 980,Class,Assay,Platform,Platform,,,
Affy5.0,Affymetrix Genome-Wide Human SNP 5.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,platform,,,,Affy5.0,Class,Assay,Platform,Platform,,,
Affy6.0,Affymetrix Genome-Wide Human SNP 6.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,platform,,,,Affy6.0,Class,Assay,Platform,Platform,,,
PacBioRSII,PacBio RS II,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311,platform,,,,PacBioRSII,Class,Assay,Platform,Platform,,,
GAIIx,Illumina Genome Analyzer IIx,,,FALSE,https://support.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet_genome_analyzeriix.pdf,platform,,,,GAIIx,Class,Assay,Platform,Platform,,,
Illumina_HumanOmni1-Quadv1.0,,,,FALSE,https://www.illumina.com/documents/products/datasheets/datasheet_humanomni1_quad.pdf,platform,,,,Illumina_HumanOmni1-Quadv1.0,Class,Assay,Platform,Platform,,,
Illumina_1M,,,,FALSE,,platform,,,,Illumina_1M,Class,Assay,Platform,Platform,,,
Illumina_h650,,,,FALSE,,platform,,,,Illumina_h650,Class,Assay,Platform,Platform,,,
Illumina_Omni2pt5M,,,,FALSE,,platform,,,,Illumina_Omni2pt5M,Class,Assay,Platform,Platform,,,
Illumina_Omni5M,,,,FALSE,,platform,,,,Illumina_Omni5M,Class,Assay,Platform,Platform,,,
Affymetrix Genome-Wide Human SNP 5.0 Array,Affymetrix Genome-Wide Human SNP 5.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,platform,,,,Affy5.0,Class,Assay,Platform,Platform,,,
Affymetrix Genome-Wide Human SNP 6.0 Array,Affymetrix Genome-Wide Human SNP 6.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,platform,,,,Affy6.0,Class,Assay,Platform,Platform,,,
PacBio RS II,PacBio RS II,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21311,platform,,,,PacBioRSII,Class,Assay,Platform,Platform,,,
Illumina Genome Analyzer IIx,Illumina Genome Analyzer IIx,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16061,platform,,,,GAIIx,Class,Assay,Platform,Platform,,,
Illumina HumanOmni1-Quadv1.0,,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL24663,platform,,,,Illumina_HumanOmni1-Quadv1.0,Class,Assay,Platform,Platform,,,
Illumina 1M,,,,FALSE,,platform,,,,Illumina_1M,Class,Assay,Platform,Platform,,,
Illumina h650,,,,FALSE,,platform,,,,Illumina_h650,Class,Assay,Platform,Platform,,,
Illumina Omni2pt5M,,,,FALSE,,platform,,,,Illumina_Omni2pt5M,Class,Assay,Platform,Platform,,,
Illumina Omni5M,,,,FALSE,,platform,,,,Illumina_Omni5M,Class,Assay,Platform,Platform,,,
Illumina MouseWG-6 v2.0 expression beadchip,Whole-genome expression profiling in the mouse,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6887,platform,,,,Illumina MouseWG-6_v2.0_expression_beadchip,Class,Assay,Platform,Platform,,,
Perlegen300Karray,,,,FALSE,,platform,,,,Perlegen300Karray,Class,Assay,Platform,Platform,,,
Agilent44Karray,,,,FALSE,,platform,,,,Agilent44Karray,Class,Assay,Platform,Platform,,,
IlluminaWholeGenomeDASL,Illumina Human Whole-Genome DASL HT,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369,platform,,,,IlluminaWholeGenomeDASL,Class,Assay,Platform,Platform,,,
IlluminaHumanHap300,,,,FALSE,,platform,,,,IlluminaHumanHap300,Class,Assay,Platform,Platform,,,
NanostringnCounter,,,,FALSE,,platform,,,,NanostringnCounter,Class,Assay,Platform,Platform,,,
Perlegen 300Karray,,,,FALSE,,platform,,,,Perlegen300Karray,Class,Assay,Platform,Platform,,,
Agilent 44Karray,,,,FALSE,,platform,,,,Agilent44Karray,Class,Assay,Platform,Platform,,,
Illumina WholeGenome DASL,Illumina Human Whole-Genome DASL HT,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13369,platform,,,,IlluminaWholeGenomeDASL,Class,Assay,Platform,Platform,,,
Illumina HumanHap300,,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6083,platform,,,,IlluminaHumanHap300,Class,Assay,Platform,Platform,,,
Nanostring Counter,,,,FALSE,,platform,,,,NanostringCounter,Class,Assay,Platform,Platform,,,
LTQ Orbitrap XL,LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer,,,FALSE,https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMAOK,platform,,,,LTQ_Orbitrap_XL,Class,Assay,Platform,Platform,,,
IlluminaHumanMethylation450,Illumina HumanMethylation450 BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534,platform,,,,IlluminaHumanMethylation450,Class,Assay,Platform,Platform,,,
Illumina HumanMethylation450,Illumina HumanMethylation450 BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534,platform,,,,IlluminaHumanMethylation450,Class,Assay,Platform,Platform,,,
Illumina Infinium MethylationEPIC BeadChip,"An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002131,platform,,,,Illumina Infinium MethylationEPIC_BeadChip,Class,Assay,Platform,Platform,,,
AffymetrixU133AB,,,,FALSE,,platform,,,,AffymetrixU133AB,Class,Assay,Platform,Platform,,,
Affymetrix U133AB,,,,FALSE,,platform,,,,AffymetrixU133AB,Class,Assay,Platform,Platform,,,
Affymetrix Human Gene 1.0 ST Array,Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] in situ oligonucleotide,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6244,platform,,,,Affymetrix_Human_Gene_1.0_ST_Array,Class,Assay,Platform,Platform,,,
AffymetrixU133Plus2,Affymetrix Human Genome U133 Plus 2.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570,platform,,,,AffymetrixU133Plus2,Class,Assay,Platform,Platform,,,
HiSeqX,Illumina HiSeq X Platform for whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html,platform,,,,HiSeqX,Class,Assay,Platform,Platform,,,
Affymetrix Human Genome U133 Plus 2.0 Array,Affymetrix Human Genome U133 Plus 2.0 Array,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570,platform,,,,AffymetrixU133Plus2,Class,Assay,Platform,Platform,,,
Illumina HiSeq X,Illumina HiSeq X Platform for whole-genome sequencing,,,FALSE,https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html,platform,,,,HiSeqX,Class,Assay,Platform,Platform,,,
Bionano Irys,Performs whole genome mapping in a nanoscale fluidic environment enabling the structure of the genome to be imaged and then analyzed at the single molecule level,,,FALSE,https://bionanogenomics.com/products/irys/,platform,,,,Bionano_Irys,Class,Assay,Platform,Platform,,,
Infinium HumanOmniExpressExome,Infinium HumanOmniExpressExome BeadChip,,,FALSE,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18224,platform,,,,Infinium_HumanOmniExpressExome,Class,Assay,Platform,Platform,,,
Illumina NovaSeq 6000,"A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002630,platform,,,,Illumina_NovaSeq_6000,Class,Assay,Platform,Platform,,,
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,,,
Nanostring GeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,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,,,
10x Visium Spatial Gene Expression,"10x Genomics product that includes special slides, reagents and technology to allow whole transcriptome profiling with morphological (spatial) context in FFPE or fresh-frozen tissues. Vendor ref: https://www.10xgenomics.com/products/spatial-gene-expression",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0010961,platform,,,,10x_Visium_Spatial_Gene_Expression,Class,Assay,Platform,Platform,,,
EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platform,,,,EnVision_2103,Class,Assay,Platform,Platform,,,
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