From e13e50e0a94b15637e16d489ca33339854f1a0a2 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Thu, 10 Oct 2024 11:21:43 -0400 Subject: [PATCH] Lowercase 'series instrument' --- src/ontology/templates/devices.tsv | 32 +++++++++++++++--------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 1be21e42..df3f44ca 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -316,8 +316,8 @@ OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion P OBI:0001973 ion semiconductor chip ion semiconductor chip ion chip|ion semiconductor|ion integrated circuit An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. http://www.thefreedictionary.com/Semiconductor+chip PERSON: Sagar Jain Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ ion detector OBI:0001974 Ion 314 Chip v2 Ion 314 Chip v2 Ion PGM 314 Chip|Ion 314 Chip|Ion PGM 314 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ ion semiconductor chip OBI:0002000 Illumina Genome Analyzer IIx metadata complete Illumina GA IIx|Genome Analyzer IIx 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. ENCODE group Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. ""Lane-by-lane sequencing using Illumina's Genome Analyzer II."" BioTechniques 54.5 (2013): 265-269. PMID: 23662897 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Genome Analyzer II Illumina -OBI:0002001 Illumina HiSeq 2000 metadata complete HiSeq 2000 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. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina HiSeq Series Instrument Illumina -OBI:0002002 Illumina HiSeq 2500 metadata complete HiSeq 2500 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. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina HiSeq Series Instrument Illumina +OBI:0002001 Illumina HiSeq 2000 metadata complete HiSeq 2000 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. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina HiSeq series instrument Illumina +OBI:0002002 Illumina HiSeq 2500 metadata complete HiSeq 2500 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. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina HiSeq series instrument Illumina OBI:0002003 Illumina MiSeq metadata complete MiSeq 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. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng DNA sequencer Illumina @@ -331,21 +331,21 @@ OBI:0002010 Human 3x720K Whole Genome CGH Tiling Array metadata complete Nimble OBI:0002011 Human 2.1M Whole-Genome CGH Tiling Array v2.0 metadata complete Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Filges, Isabel, et al. ""Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome."" Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen OBI:0002012 PacBio RS II metadata complete Pacific Biosciences RS II 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. http://www.pacificbiosciences.com/products/ Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg DNA sequencer Pacific Biosciences OBI:0002013 nCounter Human miRNA Expression array metadata complete A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. https://www.nanostring.com/products/mirna-assays/mirna-panels Kolbert, Christopher P., et al. ""Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues."" PloS one 8.1 (2013): e52517. PMID:23382819 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed ""V2"" per https://github.com/obi-ontology/obi/issues/831 on 20180511. assay array NanoString Technologies -OBI:0002021 Illumina NextSeq 500 NextSeq 500 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. http://systems.illumina.com/systems/nextseq-sequencer.html Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina NextSeq Series Instrument Illumina -OBI:0002022 Illumina HiSeq 1000 HiSeq 1000 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. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina HiSeq Series Instrument Illumina +OBI:0002021 Illumina NextSeq 500 NextSeq 500 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. http://systems.illumina.com/systems/nextseq-sequencer.html Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina NextSeq series instrument Illumina +OBI:0002022 Illumina HiSeq 1000 HiSeq 1000 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. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina HiSeq series instrument Illumina OBI:0002023 Human Genome U133 Plus 2.0 tiling array HG-U133 Plus 2|Affymetrix HT Human Genome U133 Plus 2 Array Plate Set|HG-U133 Plus 2 array A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 Person: Venkat Malladi, Chris Stoeckert, Jie Zheng tiling microarray Affymetrix OBI:0002024 SOLiD 4 System Applied Biosystems SOLiD 4 System|SOLiD 4 An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 Person: Venkat Malladi, Chris Stoeckert, Jie Zheng AB SOLiD System Applied Biosystems OBI:0002025 Human Exon 1.0 ST tilling array Affymetrix Human Exon 1.0 St Array|Human Exon 1.0|Human Exon 1.0 ST Array A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 Person: Venkat Malladi, Chris Stoeckert, Jie Zheng tiling microarray Affymetrix OBI:0002026 Human Genome U133 tiling array HG-U133|Affymetrix HT Human Genome U133 Array Plate Set|HG-U133 array A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 Person: Venkat Malladi, Chris Stoeckert, Jie Zheng tiling microarray Affymetrix OBI:0002027 Illumina Genome Analyzer IIe Illumina GA IIe|Genome Analyzer IIe 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 IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina Genome Analyzer II Illumina OBI:0002046 surface plasmon resonance sensor chip surface plasmon resonance sensor chip pending final vetting sensor chip|biosensor chip|SPR sensor chip A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached OBI ProteOn GLC Sensor Chip #176-5011 Anna Maria Masci device solid support function surface plasmon resonance instrument -OBI:0002048 Illumina HiSeq 3000 metadata complete HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html PERSON: Sagar Jain, Richard Scheuermann Illumina HiSeq Series Instrument Illumina -OBI:0002049 Illumina HiSeq 4000 metadata complete HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html PERSON: Sagar Jain, Richard Scheuermann Illumina HiSeq Series Instrument Illumina +OBI:0002048 Illumina HiSeq 3000 metadata complete HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html PERSON: Sagar Jain, Richard Scheuermann Illumina HiSeq series instrument Illumina +OBI:0002049 Illumina HiSeq 4000 metadata complete HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html PERSON: Sagar Jain, Richard Scheuermann Illumina HiSeq series instrument Illumina OBI:0002088 specimen container specimen container ready for release A container with the function of containing a specimen. Duke Biobank, OBIB COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube Chris Stoeckert For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ equivalent container containing a specimen function OBI:0002089 physical store physical store ready for release A container with an environmental control function. Duke Biobank, OBIB a freezer. a humidity controlled box. Chris Stoeckert For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ equivalent container environment control function OBI:0002109 Human 6x630K CGH Whole Genome Tiling Array ready for release NimbleGen Human 6x630K CGH Whole Genome Tiling Array A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group Term request: https://sourceforge.net/p/obi/obi-terms/791/ tiling microarray Nimblegen OBI:0002128 Illumina Genome Analyzer Illumina Genome Analyzer pending final vetting Illumina Genome Analyzer I 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. http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Person: Chris Stoeckert, Jason Hilton DNA sequencer Illumina -OBI:0002129 Illumina HiSeq X Ten Illumina HiSeq X Ten pending final vetting HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann Illumina HiSeq Series Instrument Illumina +OBI:0002129 Illumina HiSeq X Ten Illumina HiSeq X Ten pending final vetting HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann Illumina HiSeq series instrument Illumina OBI:0002130 Illumina Infinium Omni5Exome-4 Kit Illumina Infinium Omni5Exome-4 Kit pending final vetting An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html Person: Chris Stoeckert, Jason Hilton Illumina BeadChip OBI:0002131 Illumina Infinium MethylationEPIC v1.0 BeadChip Illumina Infinium MethylationEPIC v1.0 BeadChip pending final vetting An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf Person: Chris Stoeckert, Jason Hilton Illumina methylation BeadChip OBI:0002192 Leica Peloris rapid tissue processor Leica Peloris rapid tissue processor ready for release An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf Chris Stoeckert, Helena Ellis NCI BBRB automatic tissue processor @@ -356,7 +356,7 @@ OBI:0002487 microraft microraft A material separation device also commerically OBI:0002488 pipette pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. https://en.wikipedia.org/wiki/Pipette Stephen A. Fisher, Junhyong Kim, Dan Berrios device OBI:0002570 nCounter Mouse miRNA Expression array requires discussion A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. https://www.nanostring.com/products/mirna-assays/mirna-panels Kolbert, Christopher P., et al. ""Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues."" PloS one 8.1 (2013): e52517. PMID:23382819 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 assay array NanoString Technologies OBI:0002586 digital acquisition card digital acquisition card DAQ device|digital acquisition and digital generation card The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device). Brenda Farrell, bfarrell@bcm.edu Mark A. Miller device signal conversion function -OBI:0002630 Illumina NovaSeq 6000 Illumina NovaSeq 6000 NovaSeq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. http://www.illumina.com/systems/sequencing-platforms/novaseq.html Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. Dan Berrios Illumina NovaSeq Series Instrument Illumina +OBI:0002630 Illumina NovaSeq 6000 Illumina NovaSeq 6000 NovaSeq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. http://www.illumina.com/systems/sequencing-platforms/novaseq.html Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. Dan Berrios Illumina NovaSeq series instrument Illumina OBI:0002632 PacBio Sequel PacBio Sequel Pacific BioSciences Sequel 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 http://www.pacb.com/products-and-services/pacbio-systems/sequel/ The cDNAs were sequenced on the PacBio Sequel platform. Bonita Lam|Dan Berrios DNA sequencer OBI:0002633 PacBio Sequel II PacBio Sequel II Pacific BioSciences Sequel II 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. http://www.pacb.com/products-and-services/pacbio-systems/sequel/ The cDNAs were sequenced on the PacBio Sequel II platform. Bonita Lam|Dan Berrios DNA sequencer OBI:0002679 vacuum-assisted biopsy needle vacuum-assisted biopsy needle requires discussion A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material. https://www.researchgate.net/publication/330227873 Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source. Damion Dooley https://github.com/obi-ontology/obi/issues/1163 needle transfer function @@ -440,8 +440,8 @@ OBI:0003050 Centers for Disease Control and Prevention gravid trap CDC gravid OBI:0003114 Illumina MiniSeq Illumina MiniSeq MiniSeq A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 PERSON: Bonita Lam DNA sequencer Illumina OBI:0003289 mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1439 device OBI:0003369 assay kit assay kit A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. OBI, VEuPathDB Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1456 device -OBI:0003386 Illumina HiSeq 1500 Illumina HiSeq 1500 HiSeq 1500 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf Jain Aluvathingal|Michelle Giglio|Suvarna Nadendla gEAR https://github.com/obi-ontology/obi/issues/1546 Illumina HiSeq Series Instrument Illumina -OBI:0003387 Illumina NextSeq 550 NextSeq 550 A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. https://www.illumina.com/systems/sequencing-platforms/nextseq.html Jain Aluvathingal|Michelle Giglio|Suvarna Nadendla gEAR https://github.com/obi-ontology/obi/issues/1546 Illumina NextSeq Series Instrument Illumina +OBI:0003386 Illumina HiSeq 1500 Illumina HiSeq 1500 HiSeq 1500 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf Jain Aluvathingal|Michelle Giglio|Suvarna Nadendla gEAR https://github.com/obi-ontology/obi/issues/1546 Illumina HiSeq series instrument Illumina +OBI:0003387 Illumina NextSeq 550 NextSeq 550 A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. https://www.illumina.com/systems/sequencing-platforms/nextseq.html Jain Aluvathingal|Michelle Giglio|Suvarna Nadendla gEAR https://github.com/obi-ontology/obi/issues/1546 Illumina NextSeq series instrument Illumina OBI:0003388 Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays. https://www.agilent.com/cs/library/brochures/IBS-231%20genomics%20catalog%20mech%20FINAL.pdf Jain Aluvathingal|Michelle Giglio|Suvarna Nadendla gEAR https://github.com/obi-ontology/obi/issues/1546 DNA microarray Agilent OBI:0003389 Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays. https://www.agilent.com/cs/library/brochures/5990-6928en_lo.pdf Jain Aluvathingal|Michelle Giglio|Suvarna Nadendla gEAR https://github.com/obi-ontology/obi/issues/1546 DNA microarray Agilent OBI:0003390 Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays. https://www.agilent.com/cs/library/usermanuals/public/G4140-90050_GeneExpression_TwoColor_6.9.pdf Jain Aluvathingal|Michelle Giglio|Suvarna Nadendla gEAR https://github.com/obi-ontology/obi/issues/1546 DNA microarray Agilent @@ -469,13 +469,13 @@ OBI:0003493 SD Bioline Chikungunya IgM capture ELISA kit An assay kit that is OBI:0003494 Advantage Chikungunya IgM Card kit An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA. John Judkins ORCID:0000-0001-6595-0902 assay kit 'J. Mitra' ('capable of' some 'microarray ELISA measuring Chikungunya IgM antibody') OBI:0003550 odor baited CDC light trap human odour baited light trap A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1654 Centers for Disease Control and Prevention light trap OBI:0003551 resting clay pot trap resting clay pot catch A resting arthropod trap that consists of a container composed primarily of clay. John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1651 resting arthropod trap -OBI:0003606 Illumina NextSeq 1000 NextSeq 1000 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. https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html Sebastian Duesing GENEPIO https://github.com/obi-ontology/obi/issues/1711 subclass Illumina NextSeq Series Instrument Illumina +OBI:0003606 Illumina NextSeq 1000 NextSeq 1000 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. https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html Sebastian Duesing GENEPIO https://github.com/obi-ontology/obi/issues/1711 subclass Illumina NextSeq series instrument Illumina OBI:0003650 Illumina Infinium MethylationEPIC v2.0 BeadChip Illumina Infinium MethylationEPIC v2.0 BeadChip An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution. https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html Sebastian Duesing https://github.com/obi-ontology/obi/issues/1665 Illumina methylation BeadChip -OBI:0003663 Illumina NovaSeq X Illumina NovaSeq X NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. The NovaSeq X provides an output of up to 8 Tb (26-52 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass Illumina NovaSeq Series Instrument Illumina -OBI:0003664 Illumina NovaSeq X Plus Illumina NovaSeq X Plus NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. It features a dual-flow cell configuration, allowing to reach an output of up to 16 Tb (52-104 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass Illumina NovaSeq Series Instrument Illumina -OBI:0003683 Illumina HiSeq Series Instrument metadata incomplete HiSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq. PERSON: Mark Andrew Miller https://www.illumina.com/content/dam/illumina-support/documents//products/datasheets/datasheet_hiseq_systems.pdf PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series, including one that was simply called “HiSeq” as the model name. GENEPIO:0100110 ‘Illumina HiSeq’ may refer to a model, not the series. OBI may not have classes for all of the instruments in this series. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina -OBI:0003684 Illumina NextSeq Series Instrument metadata incomplete NextSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq. PERSON: Mark Andrew Miller https://www.cd-genomics.com/blog/nextseq/ PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100126 ’Illumina NextSeq’ refers to the series or a model. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina -OBI:0003685 Illumina NovaSeq Series Instrument metadata incomplete NovaSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq. PERSON: Mark Andrew Miller PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100122 ‘Illumina NovaSeq’ refers to the series or to a model. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina +OBI:0003663 Illumina NovaSeq X Illumina NovaSeq X NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. The NovaSeq X provides an output of up to 8 Tb (26-52 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass Illumina NovaSeq series instrument Illumina +OBI:0003664 Illumina NovaSeq X Plus Illumina NovaSeq X Plus NovaSeq X System|NovaSeq X Series A DNA sequencer with three flow cell types manufactured by Illumina. It features a dual-flow cell configuration, allowing to reach an output of up to 16 Tb (52-104 billion reads per run). The sequencer utilizes XLEAP-SBS chemistry, an advanced version of Illumina's sequencing by synthesis (SBS) technology, which enables faster and more accurate sequencing. https://emea.illumina.com/systems/sequencing-platforms/novaseq-x-plus.html Morgana Barroso Oquendo Morgana Barroso Oquendo https://github.com/obi-ontology/obi/issues/1802 subclass Illumina NovaSeq series instrument Illumina +OBI:0003683 Illumina HiSeq series instrument metadata incomplete HiSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq. PERSON: Mark Andrew Miller https://www.illumina.com/content/dam/illumina-support/documents//products/datasheets/datasheet_hiseq_systems.pdf PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series, including one that was simply called “HiSeq” as the model name. GENEPIO:0100110 ‘Illumina HiSeq’ may refer to a model, not the series. OBI may not have classes for all of the instruments in this series. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina +OBI:0003684 Illumina NextSeq series instrument metadata incomplete NextSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq. PERSON: Mark Andrew Miller https://www.cd-genomics.com/blog/nextseq/ PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100126 ’Illumina NextSeq’ refers to the series or a model. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina +OBI:0003685 Illumina NovaSeq series instrument metadata incomplete NovaSeq series A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq. PERSON: Mark Andrew Miller PERSON: Mark Andrew Miller This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100122 ‘Illumina NovaSeq’ refers to the series or to a model. Alicia Clum https://github.com/obi-ontology/obi/issues/1825 DNA sequencer Illumina OBI:0400005 A10-Analyzer A10-Analyzer ready for release A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400006 A40-MiniFCM A40-MiniFCM ready for release A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. http://www.apogeeflow.com/flow_cytometry_products.htm John Quinn flow cytometer analyzer OBI:0400007 analog-to-digital converter analog-to-digital converter metadata incomplete A2D|A-D An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. http://en.wiktionary.org/wiki/Analog-to-Digital_Converter The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. John Quinn|Melanie Courtot device signal conversion function