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Merge pull request #1826 from obi-ontology/1824-add-is_manufactured_b…
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…y-illumina-to-all-illumina-brand-dna-sequencers

Added manufactured by Illumina axioms to src/ontology/templates/devices.tsv
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jamesaoverton authored Oct 3, 2024
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8 changes: 4 additions & 4 deletions src/ontology/templates/devices.tsv
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Expand Up @@ -315,7 +315,7 @@ OBI:0001971 Ion 316 Chip v2 Ion 316 Chip v2 Ion PGM 316 Chip|Ion 316 Chip|Ion P
OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. 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 #775 https://sourceforge.net/p/obi/obi-terms/775/ ion semiconductor chip
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 Genome Analyzer IIx metadata complete Illumina GA IIx|Illumina 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
OBI:0002000 Genome Analyzer IIx metadata complete Illumina GA IIx|Illumina 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 DNA sequencer 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 DNA sequencer Illumina
OBI:0002003 MiSeq metadata complete Illumina 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
Expand All @@ -335,15 +335,15 @@ OBI:0002023 Human Genome U133 Plus 2.0 tiling array HG-U133 Plus 2|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 Genome Analyzer IIe Illumina GA IIe|Illumina 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
OBI:0002027 Genome Analyzer IIe Illumina GA IIe|Illumina 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 DNA sequencer 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 DNA sequencer 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
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 DNA sequencer
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 DNA sequencer 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
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