From 2f6d30d45c21f36ee10696aa1a1a6cf2d4f7ce5a Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Wed, 11 Dec 2024 13:26:39 -0800 Subject: [PATCH] Update schema --- web/templates/wastewater/schema.json | 399 ++++++++++++++++------ web/templates/wastewater/schema.yaml | 178 ++++++++-- web/templates/wastewater/schema_enums.tsv | 140 ++++---- web/templates/wastewater/schema_slots.tsv | 2 +- 4 files changed, 527 insertions(+), 192 deletions(-) diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index d7fd329c..6b138d9f 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -3580,26 +3580,35 @@ "description": "A DNA sequencer manufactured by the Illumina corporation.", "meaning": "GENEPIO:0100105", "exact_mappings": [ - "NCBI_SRA:%23REF%21" + "NCBI_SRA:ILLUMINA" ] }, "Illumina Genome Analyzer [GENEPIO:0100106]": { "text": "Illumina Genome Analyzer [GENEPIO:0100106]", "description": "A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.", "meaning": "GENEPIO:0100106", - "is_a": "Illumina [GENEPIO:0100105]" + "is_a": "Illumina [GENEPIO:0100105]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20Genome%20Analyzer" + ] }, "Illumina Genome Analyzer II [OBI:0000703]": { "text": "Illumina Genome Analyzer II [OBI:0000703]", "description": "A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology.", "meaning": "OBI:0000703", - "is_a": "Illumina [GENEPIO:0100105]" + "is_a": "Illumina [GENEPIO:0100105]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20Genome%20Analyzer%20II" + ] }, "Illumina Genome Analyzer IIx [OBI:0002000]": { "text": "Illumina Genome Analyzer IIx [OBI:0002000]", "description": "An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.", "meaning": "OBI:0002000", - "is_a": "Illumina [GENEPIO:0100105]" + "is_a": "Illumina [GENEPIO:0100105]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20Genome%20Analyzer%20IIx" + ] }, "Illumina HiScanSQ [GENEPIO:0100109]": { "text": "Illumina HiScanSQ [GENEPIO:0100109]", @@ -3617,58 +3626,85 @@ "text": "Illumina HiSeq X [GENEPIO:0100111]", "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000.", "meaning": "GENEPIO:0100111", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20HiSeq%20X" + ] }, - "Illumina HiSeq X Five [GENEPIO:0100112]": { - "text": "Illumina HiSeq X Five [GENEPIO:0100112]", + "Illumina HiSeq X Five [GENEPIO:0100112]": { + "text": "Illumina HiSeq X Five [GENEPIO:0100112]", "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.", "meaning": "GENEPIO:0100112", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:HiSeq%20X%20Five" + ] }, "Illumina HiSeq X Ten [GENEPIO:0100113]": { "text": "Illumina HiSeq X Ten [GENEPIO:0100113]", "description": "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.", "meaning": "GENEPIO:0100113", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:HiSeq%20X%20Ten" + ] }, "Illumina HiSeq 1000 [OBI:0002022]": { "text": "Illumina HiSeq 1000 [OBI:0002022]", "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", "meaning": "OBI:0002022", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20HiSeq%201000" + ] }, "Illumina HiSeq 1500 [GENEPIO:0100115]": { "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day.", "meaning": "GENEPIO:0100115", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20HiSeq%201500" + ] }, - "Illumina HiSeq 2000 [OBI:0002001]": { - "text": "Illumina HiSeq 2000 [OBI:0002001]", + "Illumina HiSeq 2000 [OBI:0002001]": { + "text": "Illumina HiSeq 2000 [OBI:0002001]", "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.", "meaning": "OBI:0002001", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20HiSeq%202000" + ] }, "Illumina HiSeq 2500 [OBI:0002002]": { "text": "Illumina HiSeq 2500 [OBI:0002002]", "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.", "meaning": "OBI:0002002", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20HiSeq%202500" + ] }, "Illumina HiSeq 3000 [OBI:0002048]": { "text": "Illumina HiSeq 3000 [OBI:0002048]", "description": "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.", "meaning": "OBI:0002048", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20HiSeq%203000" + ] }, "Illumina HiSeq 4000 [OBI:0002049]": { "text": "Illumina HiSeq 4000 [OBI:0002049]", "description": "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.", "meaning": "OBI:0002049", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" + "is_a": "Illumina HiSeq [GENEPIO:0100110]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20HiSeq%204000" + ] }, - "Illumina iSeq [GENEPIO:0100120]": { - "text": "Illumina iSeq [GENEPIO:0100120]", + "Illumina iSeq [GENEPIO:0100120]": { + "text": "Illumina iSeq [GENEPIO:0100120]", "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.", "meaning": "GENEPIO:0100120", "is_a": "Illumina [GENEPIO:0100105]" @@ -3677,10 +3713,13 @@ "text": "Illumina iSeq 100 [GENEPIO:0100121]", "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.", "meaning": "GENEPIO:0100121", - "is_a": "Illumina iSeq [GENEPIO:0100120]" + "is_a": "Illumina iSeq [GENEPIO:0100120]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20iSeq%20100" + ] }, - "Illumina NovaSeq [GENEPIO:0100122]": { - "text": "Illumina NovaSeq [GENEPIO:0100122]", + "Illumina NovaSeq [GENEPIO:0100122]": { + "text": "Illumina NovaSeq [GENEPIO:0100122]", "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode.", "meaning": "GENEPIO:0100122", "is_a": "Illumina [GENEPIO:0100105]" @@ -3689,19 +3728,28 @@ "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.", "meaning": "GENEPIO:0100123", - "is_a": "Illumina NovaSeq [GENEPIO:0100122]" + "is_a": "Illumina NovaSeq [GENEPIO:0100122]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20NovaSeq%206000" + ] }, "Illumina MiniSeq [GENEPIO:0100124]": { "text": "Illumina MiniSeq [GENEPIO:0100124]", "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", "meaning": "GENEPIO:0100124", - "is_a": "Illumina [GENEPIO:0100105]" + "is_a": "Illumina [GENEPIO:0100105]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20MiniSeq" + ] }, "Illumina MiSeq [OBI:0002003]": { "text": "Illumina MiSeq [OBI:0002003]", "description": "A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.", "meaning": "OBI:0002003", - "is_a": "Illumina [GENEPIO:0100105]" + "is_a": "Illumina [GENEPIO:0100105]", + "exact_mappings": [ + "NCBI_SRA:Illumina%20MiSeq" + ] }, "Illumina NextSeq [GENEPIO:0100126]": { "text": "Illumina NextSeq [GENEPIO:0100126]", @@ -3713,88 +3761,133 @@ "text": "Illumina NextSeq 500 [OBI:0002021]", "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", "meaning": "OBI:0002021", - "is_a": "Illumina NextSeq [GENEPIO:0100126]" + "is_a": "Illumina NextSeq [GENEPIO:0100126]", + "exact_mappings": [ + "NCBI_SRA:NextSeq%20500" + ] }, "Illumina NextSeq 550 [GENEPIO:0100128]": { "text": "Illumina NextSeq 550 [GENEPIO:0100128]", "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.", "meaning": "GENEPIO:0100128", - "is_a": "Illumina NextSeq [GENEPIO:0100126]" + "is_a": "Illumina NextSeq [GENEPIO:0100126]", + "exact_mappings": [ + "NCBI_SRA:NextSeq%20550" + ] }, "Illumina NextSeq 1000 [GENEPIO:0004432]": { "text": "Illumina NextSeq 1000 [GENEPIO:0004432]", "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.", "meaning": "GENEPIO:0004432", - "is_a": "Illumina NextSeq [GENEPIO:0100126]" + "is_a": "Illumina NextSeq [GENEPIO:0100126]", + "exact_mappings": [ + "NCBI_SRA:NextSeq%201000" + ] }, "Illumina NextSeq 2000 [GENEPIO:0100129]": { "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.", "meaning": "GENEPIO:0100129", - "is_a": "Illumina NextSeq [GENEPIO:0100126]" + "is_a": "Illumina NextSeq [GENEPIO:0100126]", + "exact_mappings": [ + "NCBI_SRA:NextSeq%202000" + ] }, "PacBio [GENEPIO:0100130]": { "text": "PacBio [GENEPIO:0100130]", "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation.", - "meaning": "GENEPIO:0100130" + "meaning": "GENEPIO:0100130", + "exact_mappings": [ + "NCBI_SRA:PACBIO_SMRT" + ] }, - "PacBio RS [GENEPIO:0100131]": { - "text": "PacBio RS [GENEPIO:0100131]", + "PacBio RS [GENEPIO:0100131]": { + "text": "PacBio RS [GENEPIO:0100131]", "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.", "meaning": "GENEPIO:0100131", - "is_a": "PacBio [GENEPIO:0100130]" + "is_a": "PacBio [GENEPIO:0100130]", + "exact_mappings": [ + "NCBI_SRA:PacBio%20RS" + ] }, "PacBio RS II [OBI:0002012]": { "text": "PacBio RS II [OBI:0002012]", "description": "A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.", "meaning": "OBI:0002012", - "is_a": "PacBio [GENEPIO:0100130]" + "is_a": "PacBio [GENEPIO:0100130]", + "exact_mappings": [ + "NCBI_SRA:PacBio%20RS%20II" + ] }, "PacBio Sequel [GENEPIO:0100133]": { "text": "PacBio Sequel [GENEPIO:0100133]", "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation", "meaning": "GENEPIO:0100133", - "is_a": "PacBio [GENEPIO:0100130]" + "is_a": "PacBio [GENEPIO:0100130]", + "exact_mappings": [ + "NCBI_SRA:Sequel" + ] }, "PacBio Sequel II [GENEPIO:0100134]": { "text": "PacBio Sequel II [GENEPIO:0100134]", "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation.", "meaning": "GENEPIO:0100134", - "is_a": "PacBio [GENEPIO:0100130]" + "is_a": "PacBio [GENEPIO:0100130]", + "exact_mappings": [ + "NCBI_SRA:Sequel%20II" + ] }, "Ion Torrent [GENEPIO:0100135]": { "text": "Ion Torrent [GENEPIO:0100135]", "description": "A DNA sequencer manufactured by the Ion Torrent corporation.", - "meaning": "GENEPIO:0100135" + "meaning": "GENEPIO:0100135", + "exact_mappings": [ + "NCBI_SRA:ION_TORRENT" + ] }, "Ion Torrent PGM [GENEPIO:0100136]": { "text": "Ion Torrent PGM [GENEPIO:0100136]", "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.", "meaning": "GENEPIO:0100136", - "is_a": "Ion Torrent [GENEPIO:0100135]" + "is_a": "Ion Torrent [GENEPIO:0100135]", + "exact_mappings": [ + "NCBI_SRA:Ion%20Torrent%20PGM" + ] }, "Ion Torrent Proton [GENEPIO:0100137]": { "text": "Ion Torrent Proton [GENEPIO:0100137]", "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.", "meaning": "GENEPIO:0100137", - "is_a": "Ion Torrent [GENEPIO:0100135]" + "is_a": "Ion Torrent [GENEPIO:0100135]", + "exact_mappings": [ + "NCBI_SRA:Ion%20Torrent%20Proton" + ] }, "Ion Torrent S5 XL [GENEPIO:0100138]": { "text": "Ion Torrent S5 XL [GENEPIO:0100138]", "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.", "meaning": "GENEPIO:0100138", - "is_a": "Ion Torrent [GENEPIO:0100135]" + "is_a": "Ion Torrent [GENEPIO:0100135]", + "exact_mappings": [ + "NCBI_SRA:Ion%20Torrent%20S5%20XL" + ] }, "Ion Torrent S5 [GENEPIO:0100139]": { "text": "Ion Torrent S5 [GENEPIO:0100139]", "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.", "meaning": "GENEPIO:0100139", - "is_a": "Ion Torrent [GENEPIO:0100135]" + "is_a": "Ion Torrent [GENEPIO:0100135]", + "exact_mappings": [ + "NCBI_SRA:Ion%20Torrent%20S5" + ] }, "Oxford Nanopore [GENEPIO:0100140]": { "text": "Oxford Nanopore [GENEPIO:0100140]", "description": "A DNA sequencer manufactured by the Oxford Nanopore corporation.", - "meaning": "GENEPIO:0100140" + "meaning": "GENEPIO:0100140", + "exact_mappings": [ + "NCBI_SRA:OXFORT_NANOPORE" + ] }, "Oxford Nanopore Flongle [GENEPIO:0004433]": { "text": "Oxford Nanopore Flongle [GENEPIO:0004433]", @@ -3806,41 +3899,62 @@ "text": "Oxford Nanopore GridION [GENEPIO:0100141]", "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual", "meaning": "GENEPIO:0100141", - "is_a": "Oxford Nanopore [GENEPIO:0100140]" + "is_a": "Oxford Nanopore [GENEPIO:0100140]", + "exact_mappings": [ + "NCBI_SRA:GridION" + ] }, "Oxford Nanopore MinION [GENEPIO:0100142]": { "text": "Oxford Nanopore MinION [GENEPIO:0100142]", "description": "A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.", "meaning": "GENEPIO:0100142", - "is_a": "Oxford Nanopore [GENEPIO:0100140]" + "is_a": "Oxford Nanopore [GENEPIO:0100140]", + "exact_mappings": [ + "NCBI_SRA:MinION" + ] }, "Oxford Nanopore PromethION [GENEPIO:0100143]": { "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.", "meaning": "GENEPIO:0100143", - "is_a": "Oxford Nanopore [GENEPIO:0100140]" + "is_a": "Oxford Nanopore [GENEPIO:0100140]", + "exact_mappings": [ + "NCBI_SRA:PromethION" + ] }, "BGI Genomics sequencing instrument [GENEPIO:0100144]": { "text": "BGI Genomics sequencing instrument [GENEPIO:0100144]", "description": "A DNA sequencer manufactured by the BGI Genomics corporation.", - "meaning": "GENEPIO:0100144" + "meaning": "GENEPIO:0100144", + "exact_mappings": [ + "NCBI_SRA:BGISEQ" + ] }, "BGISEQ-500 [GENEPIO:0100145]": { "text": "BGISEQ-500 [GENEPIO:0100145]", "description": "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and \"DNA Nanoballs\".", "meaning": "GENEPIO:0100145", - "is_a": "BGI Genomics sequencing instrument [GENEPIO:0100144]" + "is_a": "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "exact_mappings": [ + "NCBI_SRA:BGISEQ-500" + ] }, "MGI sequencing instrument [GENEPIO:0100146]": { "text": "MGI sequencing instrument [GENEPIO:0100146]", "description": "A DNA sequencer manufactured by the MGI corporation.", - "meaning": "GENEPIO:0100146" + "meaning": "GENEPIO:0100146", + "exact_mappings": [ + "NCBI_SRA:BGISEQ" + ] }, "MGISEQ-2000RS [GENEPIO:0100971]": { "text": "MGISEQ-2000RS [GENEPIO:0100971]", "description": "An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing.", "meaning": "GENEPIO:0100971", - "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]", + "exact_mappings": [ + "NCBI_SRA:MGISEQ-2000RS" + ] }, "MGI DNBSEQ-G99 [GENEPIO:0100972]": { "text": "MGI DNBSEQ-G99 [GENEPIO:0100972]", @@ -3852,19 +3966,28 @@ "text": "MGI DNBSEQ-G400 [GENEPIO:0100148]", "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run.", "meaning": "GENEPIO:0100148", - "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]", + "exact_mappings": [ + "NCBI_SRA:DNBSEQ-G400" + ] }, "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]": { "text": "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400.", "meaning": "GENEPIO:0100149", - "is_a": "MGI DNBSEQ-G400 [GENEPIO:0100148]" + "is_a": "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "exact_mappings": [ + "NCBI_SRA:DNBSEQ-G400%20FAST" + ] }, "MGI DNBSEQ-T7 [GENEPIO:0100147]": { "text": "MGI DNBSEQ-T7 [GENEPIO:0100147]", "description": "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day.", "meaning": "GENEPIO:0100147", - "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]", + "exact_mappings": [ + "NCBI_SRA:DNBSEQ-T7" + ] }, "MGI DNBSEQ-E25 [GENEPIO:0100973]": { "text": "MGI DNBSEQ-E25 [GENEPIO:0100973]", @@ -3876,153 +3999,231 @@ "text": "MGI DNBSEQ-G50 [GENEPIO:0100150]", "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.", "meaning": "GENEPIO:0100150", - "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]", + "exact_mappings": [ + "NCBI_SRA:DNBSEQ-G50" + ] }, "454 Genome Sequencer [GENEPIO:0001937]": { "text": "454 Genome Sequencer [GENEPIO:0001937]", "description": "A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing.", - "meaning": "GENEPIO:0001937" + "meaning": "GENEPIO:0001937", + "exact_mappings": [ + "NCBI_SRA:454%20GS" + ] }, "454 Genome Sequencer 20 [OBI:0000689]": { "text": "454 Genome Sequencer 20 [OBI:0000689]", "description": "A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem.", "meaning": "OBI:0000689", - "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]", + "exact_mappings": [ + "NCBI_SRA:454%20GS%2020" + ] }, "454 Genome Sequencer FLX [OBI:0000702]": { "text": "454 Genome Sequencer FLX [OBI:0000702]", "description": "A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.", "meaning": "OBI:0000702", - "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]", + "exact_mappings": [ + "NCBI_SRA:454%20GS%20FLX" + ] }, "454 Genome Sequencer FLX+ [GENEPIO:0100982]": { "text": "454 Genome Sequencer FLX+ [GENEPIO:0100982]", "description": "A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+.", "meaning": "GENEPIO:0100982", - "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]", + "exact_mappings": [ + "NCBI_SRA:454%20GS%20FLX%2B" + ] }, "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]": { "text": "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", "description": "A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads.", "meaning": "GENEPIO:0001936", - "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]", + "exact_mappings": [ + "NCBI_SRA:454%20GS%20FLX%20Titanium" + ] }, "454 Genome Sequencer Junior [GENEPIO:0001938]": { "text": "454 Genome Sequencer Junior [GENEPIO:0001938]", "description": "A 454 Genome Sequencer that performs pyrosequencing and is more compact.", "meaning": "GENEPIO:0001938", - "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]", + "exact_mappings": [ + "NCBI_SRA:454%20GS%20Junior" + ] }, "SOLiD System [OBI:0000696]": { "text": "SOLiD System [OBI:0000696]", "description": "A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation.", - "meaning": "OBI:0000696" + "meaning": "OBI:0000696", + "exact_mappings": [ + "NCBI_SRA:AB%20SOLiD%20System" + ] }, "SOLiD 5500 [GENEPIO:0001929]": { "text": "SOLiD 5500 [GENEPIO:0001929]", "description": "A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series.", "meaning": "GENEPIO:0001929", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%205500%20Genetic%20Analyzer" + ] }, "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]": { "text": "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]", "description": "A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model.", "meaning": "GENEPIO:0001930", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%205500xl%20Genetic%20Analyzer" + ] }, "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]": { "text": "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]", "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer.", "meaning": "GENEPIO:0100984", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%205500x-Wl%20Genetic%20Analyzer" + ] }, "SOLiD 3 Plus System [OBI:0002007]": { "text": "SOLiD 3 Plus System [OBI:0002007]", "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.", "meaning": "OBI:0002007", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%20SOLiD%203%20Plus%20System" + ] }, "SOLiD 4 System [OBI:0002024]": { "text": "SOLiD 4 System [OBI:0002024]", "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput.", "meaning": "OBI:0002024", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%20SOLiD%204%20System" + ] }, "SOLiD 4hq System [GENEPIO:0001928]": { "text": "SOLiD 4hq System [GENEPIO:0001928]", "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput.", "meaning": "GENEPIO:0001928", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%20SOLiD%204hq%20System" + ] }, "SOLiD PI System [GENEPIO:0001931]": { "text": "SOLiD PI System [GENEPIO:0001931]", "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput.", "meaning": "GENEPIO:0001931", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%20SOLiD%20PI%20System" + ] }, "SOLiD System 2.0 [GENEPIO:0001932]": { "text": "SOLiD System 2.0 [GENEPIO:0001932]", "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", "meaning": "GENEPIO:0001932", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%20SOLiD%20System%202.0" + ] }, "SOLiD System 3.0 [GENEPIO:0001933]": { "text": "SOLiD System 3.0 [GENEPIO:0001933]", "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", "meaning": "GENEPIO:0001933", - "is_a": "SOLiD System [OBI:0000696]" + "is_a": "SOLiD System [OBI:0000696]", + "exact_mappings": [ + "NCBI_SRA:AB%20SOLiD%20System%203.0" + ] }, "HeliScope Single Molecule Sequencer [OBI:0000717]": { "text": "HeliScope Single Molecule Sequencer [OBI:0000717]", "description": "A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry.", - "meaning": "OBI:0000717" + "meaning": "OBI:0000717", + "exact_mappings": [ + "NCBI_SRA:Helicos%20HeliScope" + ] }, "Applied Biosystems sequencing instrument model [GENEPIO:0100974]": { "text": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", "description": "A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis.", - "meaning": "GENEPIO:0100974" + "meaning": "GENEPIO:0100974", + "exact_mappings": [ + "NCBI_SRA:CAPILLARY" + ] }, "AB 310 Genetic Analyzer [GENEPIO:0100975]": { "text": "AB 310 Genetic Analyzer [GENEPIO:0100975]", "description": "An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated.", "meaning": "GENEPIO:0100975", - "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "exact_mappings": [ + "NCBI_SRA:AB%20310%20Genetic%20Analyzer" + ] }, "AB 3130 Genetic Analyzer [GENEPIO:0100976]": { "text": "AB 3130 Genetic Analyzer [GENEPIO:0100976]", "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries.", "meaning": "GENEPIO:0100976", - "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "exact_mappings": [ + "NCBI_SRA:AB%203130%20Genetic%20Analyzer" + ] }, "AB 3130xL Genetic Analyzer [GENEPIO:0100977]": { "text": "AB 3130xL Genetic Analyzer [GENEPIO:0100977]", "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries.", "meaning": "GENEPIO:0100977", - "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "exact_mappings": [ + "NCBI_SRA:AB%203130xL%20Genetic%20Analyzer" + ] }, "AB 3500 Genetic Analyzer [GENEPIO:0100978]": { "text": "AB 3500 Genetic Analyzer [GENEPIO:0100978]", "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates.", "meaning": "GENEPIO:0100978", - "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "exact_mappings": [ + "NCBI_SRA:AB%203500%20Genetic%20Analyzer" + ] }, "AB 3500xL Genetic Analyzer [GENEPIO:0100979]": { "text": "AB 3500xL Genetic Analyzer [GENEPIO:0100979]", "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates.", "meaning": "GENEPIO:0100979", - "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "exact_mappings": [ + "NCBI_SRA:AB%203500xL%20Genetic%20Analyzer" + ] }, "AB 3730 Genetic Analyzer [GENEPIO:0100980]": { "text": "AB 3730 Genetic Analyzer [GENEPIO:0100980]", "description": "An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing.", "meaning": "GENEPIO:0100980", - "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "exact_mappings": [ + "NCBI_SRA:AB%203730%20Genetic%20Analyzer" + ] }, "AB 3730xL Genetic Analyzer [GENEPIO:0100981]": { "text": "AB 3730xL Genetic Analyzer [GENEPIO:0100981]", "description": "An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing.", "meaning": "GENEPIO:0100981", - "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "exact_mappings": [ + "NCBI_SRA:AB%203730xL%20Genetic%20Analyzer" + ] } } }, @@ -10079,10 +10280,10 @@ } ] }, - "assay_target_details": { - "name": "assay_target_details", + "assay_target_details_1": { + "name": "assay_target_details_1", "description": "Describe any details of the assay target.", - "title": "assay target details", + "title": "assay target details 1", "comments": [ "Provide details that are applicable to the assay used for the diagnostic test." ], @@ -11507,8 +11708,8 @@ "rank": 189, "slot_group": "Pathogen diagnostic testing" }, - "assay_target_details": { - "name": "assay_target_details", + "assay_target_details_1": { + "name": "assay_target_details_1", "rank": 190, "slot_group": "Pathogen diagnostic testing" }, @@ -17153,17 +17354,17 @@ } ] }, - "assay_target_details": { - "name": "assay_target_details", + "assay_target_details_1": { + "name": "assay_target_details_1", "description": "Describe any details of the assay target.", - "title": "assay target details", + "title": "assay target details 1", "comments": [ "Provide details that are applicable to the assay used for the diagnostic test." ], "from_schema": "https://example.com/GRDI", "rank": 190, "slot_uri": "GENEPIO:0102040", - "alias": "assay_target_details", + "alias": "assay_target_details_1", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18716,8 +18917,8 @@ "rank": 191, "slot_group": "Pathogen diagnostic testing" }, - "assay_target_details": { - "name": "assay_target_details", + "assay_target_details_1": { + "name": "assay_target_details_1", "rank": 192, "slot_group": "Pathogen diagnostic testing" }, @@ -24419,17 +24620,17 @@ } ] }, - "assay_target_details": { - "name": "assay_target_details", + "assay_target_details_1": { + "name": "assay_target_details_1", "description": "Describe any details of the assay target.", - "title": "assay target details", + "title": "assay target details 1", "comments": [ "Provide details that are applicable to the assay used for the diagnostic test." ], "from_schema": "https://example.com/GRDI", "rank": 192, "slot_uri": "GENEPIO:0102040", - "alias": "assay_target_details", + "alias": "assay_target_details_1", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -26077,8 +26278,8 @@ "rank": 210, "slot_group": "Pathogen diagnostic testing" }, - "assay_target_details": { - "name": "assay_target_details", + "assay_target_details_1": { + "name": "assay_target_details_1", "rank": 211, "slot_group": "Pathogen diagnostic testing" }, @@ -32260,17 +32461,17 @@ } ] }, - "assay_target_details": { - "name": "assay_target_details", + "assay_target_details_1": { + "name": "assay_target_details_1", "description": "Describe any details of the assay target.", - "title": "assay target details", + "title": "assay target details 1", "comments": [ "Provide details that are applicable to the assay used for the diagnostic test." ], "from_schema": "https://example.com/GRDI", "rank": 211, "slot_uri": "GENEPIO:0102040", - "alias": "assay_target_details", + "alias": "assay_target_details_1", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index 30ac3e1a..75b53efb 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -208,7 +208,7 @@ classes: - lineage_clade_analysis_software_version - lineage_clade_analysis_report_filename - assay_target_name_1 - - assay_target_details + - assay_target_details_1 - gene_symbol_1 - diagnostic_target_presence_1 - diagnostic_measurement_value_1 @@ -805,7 +805,7 @@ classes: assay_target_name_1: rank: 189 slot_group: Pathogen diagnostic testing - assay_target_details: + assay_target_details_1: rank: 190 slot_group: Pathogen diagnostic testing gene_symbol_1: @@ -1081,7 +1081,7 @@ classes: - amr_analysis_report_filename - target_taxonomic_name_1 - assay_target_name_1 - - assay_target_details + - assay_target_details_1 - gene_symbol_1 - diagnostic_target_presence_1 - diagnostic_measurement_value_1 @@ -1687,7 +1687,7 @@ classes: assay_target_name_1: rank: 191 slot_group: Pathogen diagnostic testing - assay_target_details: + assay_target_details_1: rank: 192 slot_group: Pathogen diagnostic testing gene_symbol_1: @@ -1988,7 +1988,7 @@ classes: - read_mapping_criteria - target_taxonomic_name_1 - assay_target_name_1 - - assay_target_details + - assay_target_details_1 - gene_symbol_1 - diagnostic_target_presence_1 - diagnostic_measurement_value_1 @@ -2650,7 +2650,7 @@ classes: assay_target_name_1: rank: 210 slot_group: Pathogen diagnostic testing - assay_target_details: + assay_target_details_1: rank: 211 slot_group: Pathogen diagnostic testing gene_symbol_1: @@ -5440,9 +5440,9 @@ slots: any_of: - range: WhitespaceMinimizedString - range: NullValueMenu - assay_target_details: - name: assay_target_details - title: assay target details + assay_target_details_1: + name: assay_target_details_1 + title: assay target details 1 description: Describe any details of the assay target. comments: Provide details that are applicable to the assay used for the diagnostic test. @@ -9817,13 +9817,15 @@ enums: description: A DNA sequencer manufactured by the Illumina corporation. meaning: GENEPIO:0100105 exact_mappings: - - NCBI_SRA:%23REF%21 + - NCBI_SRA:ILLUMINA Illumina Genome Analyzer [GENEPIO:0100106]: text: Illumina Genome Analyzer [GENEPIO:0100106] description: A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. meaning: GENEPIO:0100106 + exact_mappings: + - NCBI_SRA:Illumina%20Genome%20Analyzer is_a: Illumina [GENEPIO:0100105] Illumina Genome Analyzer II [OBI:0000703]: text: Illumina Genome Analyzer II [OBI:0000703] @@ -9831,6 +9833,8 @@ enums: which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. meaning: OBI:0000703 + exact_mappings: + - NCBI_SRA:Illumina%20Genome%20Analyzer%20II is_a: Illumina [GENEPIO:0100105] Illumina Genome Analyzer IIx [OBI:0002000]: text: Illumina Genome Analyzer IIx [OBI:0002000] @@ -9840,6 +9844,8 @@ enums: Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. meaning: OBI:0002000 + exact_mappings: + - NCBI_SRA:Illumina%20Genome%20Analyzer%20IIx is_a: Illumina [GENEPIO:0100105] Illumina HiScanSQ [GENEPIO:0100109]: text: Illumina HiScanSQ [GENEPIO:0100109] @@ -9860,19 +9866,25 @@ enums: sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. meaning: GENEPIO:0100111 + exact_mappings: + - NCBI_SRA:Illumina%20HiSeq%20X is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq X Five [GENEPIO:0100112]: - text: Illumina HiSeq X Five [GENEPIO:0100112] + Illumina HiSeq X Five [GENEPIO:0100112]: + text: Illumina HiSeq X Five [GENEPIO:0100112] description: A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. meaning: GENEPIO:0100112 + exact_mappings: + - NCBI_SRA:HiSeq%20X%20Five is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq X Ten [GENEPIO:0100113]: text: Illumina HiSeq X Ten [GENEPIO:0100113] description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. meaning: GENEPIO:0100113 + exact_mappings: + - NCBI_SRA:HiSeq%20X%20Ten is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 1000 [OBI:0002022]: text: Illumina HiSeq 1000 [OBI:0002022] @@ -9881,20 +9893,26 @@ enums: sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. meaning: OBI:0002022 + exact_mappings: + - NCBI_SRA:Illumina%20HiSeq%201000 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 1500 [GENEPIO:0100115]: text: Illumina HiSeq 1500 [GENEPIO:0100115] description: A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. meaning: GENEPIO:0100115 + exact_mappings: + - NCBI_SRA:Illumina%20HiSeq%201500 is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 2000 [OBI:0002001]: - text: Illumina HiSeq 2000 [OBI:0002001] + Illumina HiSeq 2000 [OBI:0002001]: + text: Illumina HiSeq 2000 [OBI:0002001] description: A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. meaning: OBI:0002001 + exact_mappings: + - NCBI_SRA:Illumina%20HiSeq%202000 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 2500 [OBI:0002002]: text: Illumina HiSeq 2500 [OBI:0002002] @@ -9903,21 +9921,27 @@ enums: sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. meaning: OBI:0002002 + exact_mappings: + - NCBI_SRA:Illumina%20HiSeq%202500 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 3000 [OBI:0002048]: text: Illumina HiSeq 3000 [OBI:0002048] description: A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. meaning: OBI:0002048 + exact_mappings: + - NCBI_SRA:Illumina%20HiSeq%203000 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 4000 [OBI:0002049]: text: Illumina HiSeq 4000 [OBI:0002049] description: A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. meaning: OBI:0002049 + exact_mappings: + - NCBI_SRA:Illumina%20HiSeq%204000 is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina iSeq [GENEPIO:0100120]: - text: Illumina iSeq [GENEPIO:0100120] + Illumina iSeq [GENEPIO:0100120]: + text: Illumina iSeq [GENEPIO:0100120] description: A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. meaning: GENEPIO:0100120 @@ -9928,9 +9952,11 @@ enums: sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. meaning: GENEPIO:0100121 - is_a: Illumina iSeq [GENEPIO:0100120] - Illumina NovaSeq [GENEPIO:0100122]: - text: Illumina NovaSeq [GENEPIO:0100122] + exact_mappings: + - NCBI_SRA:Illumina%20iSeq%20100 + is_a: Illumina iSeq [GENEPIO:0100120] + Illumina NovaSeq [GENEPIO:0100122]: + text: Illumina NovaSeq [GENEPIO:0100122] description: A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. @@ -9943,13 +9969,17 @@ enums: The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. meaning: GENEPIO:0100123 - is_a: Illumina NovaSeq [GENEPIO:0100122] + exact_mappings: + - NCBI_SRA:Illumina%20NovaSeq%206000 + is_a: Illumina NovaSeq [GENEPIO:0100122] Illumina MiniSeq [GENEPIO:0100124]: text: Illumina MiniSeq [GENEPIO:0100124] description: A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. meaning: GENEPIO:0100124 + exact_mappings: + - NCBI_SRA:Illumina%20MiniSeq is_a: Illumina [GENEPIO:0100105] Illumina MiSeq [OBI:0002003]: text: Illumina MiSeq [OBI:0002003] @@ -9958,6 +9988,8 @@ enums: solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. meaning: OBI:0002003 + exact_mappings: + - NCBI_SRA:Illumina%20MiSeq is_a: Illumina [GENEPIO:0100105] Illumina NextSeq [GENEPIO:0100126]: text: Illumina NextSeq [GENEPIO:0100126] @@ -9973,6 +10005,8 @@ enums: of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. meaning: OBI:0002021 + exact_mappings: + - NCBI_SRA:NextSeq%20500 is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 550 [GENEPIO:0100128]: text: Illumina NextSeq 550 [GENEPIO:0100128] @@ -9981,6 +10015,8 @@ enums: of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. meaning: GENEPIO:0100128 + exact_mappings: + - NCBI_SRA:NextSeq%20550 is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 1000 [GENEPIO:0004432]: text: Illumina NextSeq 1000 [GENEPIO:0004432] @@ -9988,6 +10024,8 @@ enums: using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. meaning: GENEPIO:0004432 + exact_mappings: + - NCBI_SRA:NextSeq%201000 is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 2000 [GENEPIO:0100129]: text: Illumina NextSeq 2000 [GENEPIO:0100129] @@ -9995,17 +10033,23 @@ enums: using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. meaning: GENEPIO:0100129 + exact_mappings: + - NCBI_SRA:NextSeq%202000 is_a: Illumina NextSeq [GENEPIO:0100126] PacBio [GENEPIO:0100130]: text: PacBio [GENEPIO:0100130] description: A DNA sequencer manufactured by the Pacific Biosciences corporation. meaning: GENEPIO:0100130 - PacBio RS [GENEPIO:0100131]: - text: PacBio RS [GENEPIO:0100131] + exact_mappings: + - NCBI_SRA:PACBIO_SMRT + PacBio RS [GENEPIO:0100131]: + text: PacBio RS [GENEPIO:0100131] description: "A DNA sequencer manufactured by the Pacific Biosciences corporation\ \ which utilizes \u201CSMRT Cells\u201D for single-molecule real-time sequencing.\ \ The RS was the first model made by the company." meaning: GENEPIO:0100131 + exact_mappings: + - NCBI_SRA:PacBio%20RS is_a: PacBio [GENEPIO:0100130] PacBio RS II [OBI:0002012]: text: PacBio RS II [OBI:0002012] @@ -10014,6 +10058,8 @@ enums: the machine is optimized for generation with long reads and high consensus accuracy. meaning: OBI:0002012 + exact_mappings: + - NCBI_SRA:PacBio%20RS%20II is_a: PacBio [GENEPIO:0100130] PacBio Sequel [GENEPIO:0100133]: text: PacBio Sequel [GENEPIO:0100133] @@ -10021,6 +10067,8 @@ enums: technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation meaning: GENEPIO:0100133 + exact_mappings: + - NCBI_SRA:Sequel is_a: PacBio [GENEPIO:0100130] PacBio Sequel II [GENEPIO:0100134]: text: PacBio Sequel II [GENEPIO:0100134] @@ -10028,17 +10076,23 @@ enums: technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. meaning: GENEPIO:0100134 + exact_mappings: + - NCBI_SRA:Sequel%20II is_a: PacBio [GENEPIO:0100130] Ion Torrent [GENEPIO:0100135]: text: Ion Torrent [GENEPIO:0100135] description: A DNA sequencer manufactured by the Ion Torrent corporation. meaning: GENEPIO:0100135 + exact_mappings: + - NCBI_SRA:ION_TORRENT Ion Torrent PGM [GENEPIO:0100136]: text: Ion Torrent PGM [GENEPIO:0100136] description: A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. meaning: GENEPIO:0100136 + exact_mappings: + - NCBI_SRA:Ion%20Torrent%20PGM is_a: Ion Torrent [GENEPIO:0100135] Ion Torrent Proton [GENEPIO:0100137]: text: Ion Torrent Proton [GENEPIO:0100137] @@ -10046,6 +10100,8 @@ enums: utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. meaning: GENEPIO:0100137 + exact_mappings: + - NCBI_SRA:Ion%20Torrent%20Proton is_a: Ion Torrent [GENEPIO:0100135] Ion Torrent S5 XL [GENEPIO:0100138]: text: Ion Torrent S5 XL [GENEPIO:0100138] @@ -10053,6 +10109,8 @@ enums: utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. meaning: GENEPIO:0100138 + exact_mappings: + - NCBI_SRA:Ion%20Torrent%20S5%20XL is_a: Ion Torrent [GENEPIO:0100135] Ion Torrent S5 [GENEPIO:0100139]: text: Ion Torrent S5 [GENEPIO:0100139] @@ -10060,11 +10118,15 @@ enums: utilizes Ion semiconductor sequencing and requires only a small amount of input material. meaning: GENEPIO:0100139 + exact_mappings: + - NCBI_SRA:Ion%20Torrent%20S5 is_a: Ion Torrent [GENEPIO:0100135] Oxford Nanopore [GENEPIO:0100140]: text: Oxford Nanopore [GENEPIO:0100140] description: A DNA sequencer manufactured by the Oxford Nanopore corporation. meaning: GENEPIO:0100140 + exact_mappings: + - NCBI_SRA:OXFORT_NANOPORE Oxford Nanopore Flongle [GENEPIO:0004433]: text: Oxford Nanopore Flongle [GENEPIO:0004433] description: An adapter for MinION or GridION DNA sequencers manufactured @@ -10080,6 +10142,8 @@ enums: utilizes nanopore technology with the option of running the flow cells concurrently or individual meaning: GENEPIO:0100141 + exact_mappings: + - NCBI_SRA:GridION is_a: Oxford Nanopore [GENEPIO:0100140] Oxford Nanopore MinION [GENEPIO:0100142]: text: Oxford Nanopore MinION [GENEPIO:0100142] @@ -10089,6 +10153,8 @@ enums: results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. meaning: GENEPIO:0100142 + exact_mappings: + - NCBI_SRA:MinION is_a: Oxford Nanopore [GENEPIO:0100140] Oxford Nanopore PromethION [GENEPIO:0100143]: text: Oxford Nanopore PromethION [GENEPIO:0100143] @@ -10098,27 +10164,37 @@ enums: Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. meaning: GENEPIO:0100143 + exact_mappings: + - NCBI_SRA:PromethION is_a: Oxford Nanopore [GENEPIO:0100140] BGI Genomics sequencing instrument [GENEPIO:0100144]: text: BGI Genomics sequencing instrument [GENEPIO:0100144] description: A DNA sequencer manufactured by the BGI Genomics corporation. meaning: GENEPIO:0100144 + exact_mappings: + - NCBI_SRA:BGISEQ BGISEQ-500 [GENEPIO:0100145]: text: BGISEQ-500 [GENEPIO:0100145] description: A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". meaning: GENEPIO:0100145 + exact_mappings: + - NCBI_SRA:BGISEQ-500 is_a: BGI Genomics sequencing instrument [GENEPIO:0100144] MGI sequencing instrument [GENEPIO:0100146]: text: MGI sequencing instrument [GENEPIO:0100146] description: A DNA sequencer manufactured by the MGI corporation. meaning: GENEPIO:0100146 + exact_mappings: + - NCBI_SRA:BGISEQ MGISEQ-2000RS [GENEPIO:0100971]: text: MGISEQ-2000RS [GENEPIO:0100971] description: An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. meaning: GENEPIO:0100971 + exact_mappings: + - NCBI_SRA:MGISEQ-2000RS is_a: MGI sequencing instrument [GENEPIO:0100146] MGI DNBSEQ-G99 [GENEPIO:0100972]: text: MGI DNBSEQ-G99 [GENEPIO:0100972] @@ -10133,6 +10209,8 @@ enums: description: A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. meaning: GENEPIO:0100148 + exact_mappings: + - NCBI_SRA:DNBSEQ-G400 is_a: MGI sequencing instrument [GENEPIO:0100146] MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]: text: MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] @@ -10140,12 +10218,16 @@ enums: capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. meaning: GENEPIO:0100149 + exact_mappings: + - NCBI_SRA:DNBSEQ-G400%20FAST is_a: MGI DNBSEQ-G400 [GENEPIO:0100148] MGI DNBSEQ-T7 [GENEPIO:0100147]: text: MGI DNBSEQ-T7 [GENEPIO:0100147] description: A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. meaning: GENEPIO:0100147 + exact_mappings: + - NCBI_SRA:DNBSEQ-T7 is_a: MGI sequencing instrument [GENEPIO:0100146] MGI DNBSEQ-E25 [GENEPIO:0100973]: text: MGI DNBSEQ-E25 [GENEPIO:0100973] @@ -10158,18 +10240,24 @@ enums: description: "A DNA sequencer manufactured by the MGI corporation with an\ \ output capacity of 10\uFF5E150 GB per run and enables different read lengths." meaning: GENEPIO:0100150 + exact_mappings: + - NCBI_SRA:DNBSEQ-G50 is_a: MGI sequencing instrument [GENEPIO:0100146] 454 Genome Sequencer [GENEPIO:0001937]: text: 454 Genome Sequencer [GENEPIO:0001937] description: A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. meaning: GENEPIO:0001937 + exact_mappings: + - NCBI_SRA:454%20GS 454 Genome Sequencer 20 [OBI:0000689]: text: 454 Genome Sequencer 20 [OBI:0000689] description: A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. meaning: OBI:0000689 + exact_mappings: + - NCBI_SRA:454%20GS%2020 is_a: 454 Genome Sequencer [GENEPIO:0001937] 454 Genome Sequencer FLX [OBI:0000702]: text: 454 Genome Sequencer FLX [OBI:0000702] @@ -10179,6 +10267,8 @@ enums: subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. meaning: OBI:0000702 + exact_mappings: + - NCBI_SRA:454%20GS%20FLX is_a: 454 Genome Sequencer [GENEPIO:0001937] 454 Genome Sequencer FLX+ [GENEPIO:0100982]: text: 454 Genome Sequencer FLX+ [GENEPIO:0100982] @@ -10186,30 +10276,40 @@ enums: both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. meaning: GENEPIO:0100982 + exact_mappings: + - NCBI_SRA:454%20GS%20FLX%2B is_a: 454 Genome Sequencer [GENEPIO:0001937] 454 Genome Sequencer FLX Titanium [GENEPIO:0001936]: text: 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] description: A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. meaning: GENEPIO:0001936 + exact_mappings: + - NCBI_SRA:454%20GS%20FLX%20Titanium is_a: 454 Genome Sequencer [GENEPIO:0001937] 454 Genome Sequencer Junior [GENEPIO:0001938]: text: 454 Genome Sequencer Junior [GENEPIO:0001938] description: A 454 Genome Sequencer that performs pyrosequencing and is more compact. meaning: GENEPIO:0001938 + exact_mappings: + - NCBI_SRA:454%20GS%20Junior is_a: 454 Genome Sequencer [GENEPIO:0001937] SOLiD System [OBI:0000696]: text: SOLiD System [OBI:0000696] description: A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. meaning: OBI:0000696 + exact_mappings: + - NCBI_SRA:AB%20SOLiD%20System SOLiD 5500 [GENEPIO:0001929]: text: SOLiD 5500 [GENEPIO:0001929] description: A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. meaning: GENEPIO:0001929 + exact_mappings: + - NCBI_SRA:AB%205500%20Genetic%20Analyzer is_a: SOLiD System [OBI:0000696] SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]: text: SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] @@ -10217,6 +10317,8 @@ enums: has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. meaning: GENEPIO:0001930 + exact_mappings: + - NCBI_SRA:AB%205500xl%20Genetic%20Analyzer is_a: SOLiD System [OBI:0000696] SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]: text: SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] @@ -10224,6 +10326,8 @@ enums: corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. meaning: GENEPIO:0100984 + exact_mappings: + - NCBI_SRA:AB%205500x-Wl%20Genetic%20Analyzer is_a: SOLiD System [OBI:0000696] SOLiD 3 Plus System [OBI:0002007]: text: SOLiD 3 Plus System [OBI:0002007] @@ -10231,6 +10335,8 @@ enums: corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. meaning: OBI:0002007 + exact_mappings: + - NCBI_SRA:AB%20SOLiD%203%20Plus%20System is_a: SOLiD System [OBI:0000696] SOLiD 4 System [OBI:0002024]: text: SOLiD 4 System [OBI:0002024] @@ -10238,6 +10344,8 @@ enums: corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. meaning: OBI:0002024 + exact_mappings: + - NCBI_SRA:AB%20SOLiD%204%20System is_a: SOLiD System [OBI:0000696] SOLiD 4hq System [GENEPIO:0001928]: text: SOLiD 4hq System [GENEPIO:0001928] @@ -10245,6 +10353,8 @@ enums: corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. meaning: GENEPIO:0001928 + exact_mappings: + - NCBI_SRA:AB%20SOLiD%204hq%20System is_a: SOLiD System [OBI:0000696] SOLiD PI System [GENEPIO:0001931]: text: SOLiD PI System [GENEPIO:0001931] @@ -10252,48 +10362,64 @@ enums: corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. meaning: GENEPIO:0001931 + exact_mappings: + - NCBI_SRA:AB%20SOLiD%20PI%20System is_a: SOLiD System [OBI:0000696] SOLiD System 2.0 [GENEPIO:0001932]: text: SOLiD System 2.0 [GENEPIO:0001932] description: A DNA sequencer which is manufactured by the Applied Biosystems corporation. meaning: GENEPIO:0001932 + exact_mappings: + - NCBI_SRA:AB%20SOLiD%20System%202.0 is_a: SOLiD System [OBI:0000696] SOLiD System 3.0 [GENEPIO:0001933]: text: SOLiD System 3.0 [GENEPIO:0001933] description: A DNA sequencer which is manufactured by the Applied Biosystems corporation. meaning: GENEPIO:0001933 + exact_mappings: + - NCBI_SRA:AB%20SOLiD%20System%203.0 is_a: SOLiD System [OBI:0000696] HeliScope Single Molecule Sequencer [OBI:0000717]: text: HeliScope Single Molecule Sequencer [OBI:0000717] description: A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. meaning: OBI:0000717 + exact_mappings: + - NCBI_SRA:Helicos%20HeliScope Applied Biosystems sequencing instrument model [GENEPIO:0100974]: text: Applied Biosystems sequencing instrument model [GENEPIO:0100974] description: A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. meaning: GENEPIO:0100974 + exact_mappings: + - NCBI_SRA:CAPILLARY AB 310 Genetic Analyzer [GENEPIO:0100975]: text: AB 310 Genetic Analyzer [GENEPIO:0100975] description: An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. meaning: GENEPIO:0100975 + exact_mappings: + - NCBI_SRA:AB%20310%20Genetic%20Analyzer is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] AB 3130 Genetic Analyzer [GENEPIO:0100976]: text: AB 3130 Genetic Analyzer [GENEPIO:0100976] description: An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. meaning: GENEPIO:0100976 + exact_mappings: + - NCBI_SRA:AB%203130%20Genetic%20Analyzer is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] AB 3130xL Genetic Analyzer [GENEPIO:0100977]: text: AB 3130xL Genetic Analyzer [GENEPIO:0100977] description: An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. meaning: GENEPIO:0100977 + exact_mappings: + - NCBI_SRA:AB%203130xL%20Genetic%20Analyzer is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] AB 3500 Genetic Analyzer [GENEPIO:0100978]: text: AB 3500 Genetic Analyzer [GENEPIO:0100978] @@ -10301,6 +10427,8 @@ enums: capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. meaning: GENEPIO:0100978 + exact_mappings: + - NCBI_SRA:AB%203500%20Genetic%20Analyzer is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] AB 3500xL Genetic Analyzer [GENEPIO:0100979]: text: AB 3500xL Genetic Analyzer [GENEPIO:0100979] @@ -10308,18 +10436,24 @@ enums: capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. meaning: GENEPIO:0100979 + exact_mappings: + - NCBI_SRA:AB%203500xL%20Genetic%20Analyzer is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] AB 3730 Genetic Analyzer [GENEPIO:0100980]: text: AB 3730 Genetic Analyzer [GENEPIO:0100980] description: An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. meaning: GENEPIO:0100980 + exact_mappings: + - NCBI_SRA:AB%203730%20Genetic%20Analyzer is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] AB 3730xL Genetic Analyzer [GENEPIO:0100981]: text: AB 3730xL Genetic Analyzer [GENEPIO:0100981] description: An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. meaning: GENEPIO:0100981 + exact_mappings: + - NCBI_SRA:AB%203730xL%20Genetic%20Analyzer is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] SequencingAssayTypeMenu: name: SequencingAssayTypeMenu diff --git a/web/templates/wastewater/schema_enums.tsv b/web/templates/wastewater/schema_enums.tsv index 2579e777..718c8e17 100644 --- a/web/templates/wastewater/schema_enums.tsv +++ b/web/templates/wastewater/schema_enums.tsv @@ -624,82 +624,82 @@ sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPI GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). HELICOS GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. CAPILLARY -sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. #REF! - GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. - OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. - OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. ILLUMINA + GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. Illumina Genome Analyzer + OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. Illumina Genome Analyzer II + OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. Illumina Genome Analyzer IIx GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. - GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. - GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. - GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. - OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. - OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. - OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. - OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. - GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. - GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. - GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. - GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. - OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. Illumina HiSeq X + GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. HiSeq X Five + GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. HiSeq X Ten + OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Illumina HiSeq 1000 + GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. Illumina HiSeq 1500 + OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. Illumina HiSeq 2000 + OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. Illumina HiSeq 2500 + OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. Illumina HiSeq 3000 + OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. Illumina HiSeq 4000 + GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. Illumina iSeq 100 + GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. + GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. Illumina NovaSeq 6000 + GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. Illumina MiniSeq + OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. Illumina MiSeq GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. - OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. - GENEPIO:0004432 Illumina NextSeq 1000 [GENEPIO:0004432] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. - GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. - GENEPIO:0100130 PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. - GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. - OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. - GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. - GENEPIO:0100135 Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. - GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. - GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. - GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. - GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. - GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. NextSeq 500 + GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. NextSeq 550 + GENEPIO:0004432 Illumina NextSeq 1000 [GENEPIO:0004432] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. NextSeq 1000 + GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. NextSeq 2000 + GENEPIO:0100130 PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. PACBIO_SMRT + GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. PacBio RS + OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. PacBio RS II + GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation Sequel + GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. Sequel II + GENEPIO:0100135 Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. ION_TORRENT + GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. Ion Torrent PGM + GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. Ion Torrent Proton + GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. Ion Torrent S5 XL + GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. Ion Torrent S5 + GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. OXFORT_NANOPORE GENEPIO:0004433 Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. - GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual - GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - GENEPIO:0100144 BGI Genomics sequencing instrument [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. - GENEPIO:0100145 BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". - GENEPIO:0100146 MGI sequencing instrument [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. - GENEPIO:0100971 MGISEQ-2000RS [GENEPIO:0100971] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. + GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual GridION + GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. MinION + GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. PromethION + GENEPIO:0100144 BGI Genomics sequencing instrument [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. BGISEQ + GENEPIO:0100145 BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". BGISEQ-500 + GENEPIO:0100146 MGI sequencing instrument [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. BGISEQ + GENEPIO:0100971 MGISEQ-2000RS [GENEPIO:0100971] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. MGISEQ-2000RS GENEPIO:0100972 MGI DNBSEQ-G99 [GENEPIO:0100972] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds. - GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. - GENEPIO:0100149 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. - GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. + GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. DNBSEQ-G400 + GENEPIO:0100149 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. DNBSEQ-G400 FAST + GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. DNBSEQ-T7 GENEPIO:0100973 MGI DNBSEQ-E25 [GENEPIO:0100973] An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab. - GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. - GENEPIO:0001937 454 Genome Sequencer [GENEPIO:0001937] A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. - OBI:0000689 454 Genome Sequencer 20 [OBI:0000689] A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. - OBI:0000702 454 Genome Sequencer FLX [OBI:0000702] A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. - GENEPIO:0100982 454 Genome Sequencer FLX+ [GENEPIO:0100982] A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. - GENEPIO:0001936 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. - GENEPIO:0001938 454 Genome Sequencer Junior [GENEPIO:0001938] A 454 Genome Sequencer that performs pyrosequencing and is more compact. - OBI:0000696 SOLiD System [OBI:0000696] A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. - GENEPIO:0001929 SOLiD 5500 [GENEPIO:0001929] A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. - GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. - GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. - OBI:0002007 SOLiD 3 Plus System [OBI:0002007] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. - OBI:0002024 SOLiD 4 System [OBI:0002024] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. - GENEPIO:0001928 SOLiD 4hq System [GENEPIO:0001928] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. - GENEPIO:0001931 SOLiD PI System [GENEPIO:0001931] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. - GENEPIO:0001932 SOLiD System 2.0 [GENEPIO:0001932] A DNA sequencer which is manufactured by the Applied Biosystems corporation. - GENEPIO:0001933 SOLiD System 3.0 [GENEPIO:0001933] A DNA sequencer which is manufactured by the Applied Biosystems corporation. - OBI:0000717 HeliScope Single Molecule Sequencer [OBI:0000717] A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. - GENEPIO:0100974 Applied Biosystems sequencing instrument model [GENEPIO:0100974] A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. - GENEPIO:0100975 AB 310 Genetic Analyzer [GENEPIO:0100975] An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. - GENEPIO:0100976 AB 3130 Genetic Analyzer [GENEPIO:0100976] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. - GENEPIO:0100977 AB 3130xL Genetic Analyzer [GENEPIO:0100977] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. - GENEPIO:0100978 AB 3500 Genetic Analyzer [GENEPIO:0100978] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. - GENEPIO:0100979 AB 3500xL Genetic Analyzer [GENEPIO:0100979] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. - GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. - GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. + GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. DNBSEQ-G50 + GENEPIO:0001937 454 Genome Sequencer [GENEPIO:0001937] A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. 454 GS + OBI:0000689 454 Genome Sequencer 20 [OBI:0000689] A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. 454 GS 20 + OBI:0000702 454 Genome Sequencer FLX [OBI:0000702] A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. 454 GS FLX + GENEPIO:0100982 454 Genome Sequencer FLX+ [GENEPIO:0100982] A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. 454 GS FLX+ + GENEPIO:0001936 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. 454 GS FLX Titanium + GENEPIO:0001938 454 Genome Sequencer Junior [GENEPIO:0001938] A 454 Genome Sequencer that performs pyrosequencing and is more compact. 454 GS Junior + OBI:0000696 SOLiD System [OBI:0000696] A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. AB SOLiD System + GENEPIO:0001929 SOLiD 5500 [GENEPIO:0001929] A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. AB 5500 Genetic Analyzer + GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. AB 5500xl Genetic Analyzer + GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. AB 5500x-Wl Genetic Analyzer + OBI:0002007 SOLiD 3 Plus System [OBI:0002007] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. AB SOLiD 3 Plus System + OBI:0002024 SOLiD 4 System [OBI:0002024] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. AB SOLiD 4 System + GENEPIO:0001928 SOLiD 4hq System [GENEPIO:0001928] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. AB SOLiD 4hq System + GENEPIO:0001931 SOLiD PI System [GENEPIO:0001931] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. AB SOLiD PI System + GENEPIO:0001932 SOLiD System 2.0 [GENEPIO:0001932] A DNA sequencer which is manufactured by the Applied Biosystems corporation. AB SOLiD System 2.0 + GENEPIO:0001933 SOLiD System 3.0 [GENEPIO:0001933] A DNA sequencer which is manufactured by the Applied Biosystems corporation. AB SOLiD System 3.0 + OBI:0000717 HeliScope Single Molecule Sequencer [OBI:0000717] A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. Helicos HeliScope + GENEPIO:0100974 Applied Biosystems sequencing instrument model [GENEPIO:0100974] A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. CAPILLARY + GENEPIO:0100975 AB 310 Genetic Analyzer [GENEPIO:0100975] An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. AB 310 Genetic Analyzer + GENEPIO:0100976 AB 3130 Genetic Analyzer [GENEPIO:0100976] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. AB 3130 Genetic Analyzer + GENEPIO:0100977 AB 3130xL Genetic Analyzer [GENEPIO:0100977] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. AB 3130xL Genetic Analyzer + GENEPIO:0100978 AB 3500 Genetic Analyzer [GENEPIO:0100978] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. AB 3500 Genetic Analyzer + GENEPIO:0100979 AB 3500xL Genetic Analyzer [GENEPIO:0100979] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. AB 3500xL Genetic Analyzer + GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. AB 3730 Genetic Analyzer + GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. AB 3730xL Genetic Analyzer sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. AMPLICON OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. AMPLICON diff --git a/web/templates/wastewater/schema_slots.tsv b/web/templates/wastewater/schema_slots.tsv index 0bc066c9..88e510f7 100644 --- a/web/templates/wastewater/schema_slots.tsv +++ b/web/templates/wastewater/schema_slots.tsv @@ -236,7 +236,7 @@ WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade ana WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102049 target taxonomic name 1 target_taxonomic_name_1 WhitespaceMinimizedString The scientific name of the organism or taxon that is the focus of the study, assay, or diagnostic test. The target taxonomic name refers to the specific species, genus, or other taxonomic classification that the assay or diagnostic test is designed to identify, detect, or characterize. This may include the full binomial name (Genus species) or a higher taxonomic rank (e.g., genus, family) when species-level identification is not applicable. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. ww_surv_target_1 WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102052 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details 1 assay_target_details_1 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present