From 404c56d11bc6558c70803ac25c00bea5cb6bfc9a Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 3 Oct 2024 16:08:01 -0400 Subject: [PATCH 01/10] #1825 define and subclass Illumina sequencer serieses --- src/ontology/templates/devices.tsv | 57 ++++++++++++++++-------------- 1 file changed, 30 insertions(+), 27 deletions(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 12bc32db..212fb103 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -2,7 +2,7 @@ ontology ID label editor preferred term has curation status alternative term def ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has function' some % SPLIT=| C 'has part' some % SPLIT=| C 'part of' some % C is_manufactured_by value % C % SPLIT=| OBI:0000038 chromatography column chromatography column metadata incomplete Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. http://en.wikipedia.org/wiki/Column_chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device ('material separation function' and ('realized in' only 'preparative chromatography')) container OBI:0000041 pump valve switch pump valve switch metadata incomplete A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. OBI OBI Instrument branch FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument device mechanical function -OBI:0000048 chromatography device chromatography device metadata complete chromatography instrument A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a ""mobile phase"" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. http://en.wikipedia.org/wiki/Chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device contain function|environment control function|measure function|material separation function +OBI:0000048 chromatography device chromatography device metadata complete chromatography instrument A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a """"""""mobile phase"""""""" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.""" http://en.wikipedia.org/wiki/Chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device contain function|environment control function|measure function|material separation function OBI:0000049 mass spectrometer mass spectrometer ready for release A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum http://en.wikipedia.org/wiki/Mass_spectrometry LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific Frank Gibson device measure function mass analyzer|ion source|ion detector OBI:0000051 liquid chromatography mass spectrometry platform liquid chromatography mass spectrometry platform metadata incomplete A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. OBI Instrument branch OBI instrument branch device measure function|material separation function chromatography device|mass spectrometer OBI:0000052 microarray platform microarray platform metadata incomplete A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. OBI Instrument branch OBI Instrument branch device environment control function microarray @@ -315,35 +315,35 @@ 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 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: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 Illumina HiSeq 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 Instrument 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 -OBI:0002004 Methylation 450K BeadChip metadata complete Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Naumov, Vladimir A., et al. ""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."" Epigenetics 8.9 (2013): 0-1. PMID: 23867710 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip -OBI:0002005 Methylation 27K BeadChip metadata complete Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Polidoro, Silvia, et al. ""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip -OBI:0002006 1M-Duo Infinium HD BeadChip metadata complete Illumina Human 1M-Duo Infinium HD BeadChip A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. http://www.illumina.com/technology/infinium_hd_assay.ilmn Edwards, Todd L., et al. ""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip -OBI:0002007 SOLiD 3 Plus System metadata complete Applied Biosystems SOLiD 3 Plus System A DNA sequencer 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://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf Vissers, Lisenka ELM, et al. ""A de novo paradigm for mental retardation."" Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg AB SOLiD System Applied Biosystems +OBI:0002004 Methylation 450K BeadChip metadata complete Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Naumov, Vladimir A., et al. """"""""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."""""""" Epigenetics 8.9 (2013): 0-1. PMID: 23867710""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip +OBI:0002005 Methylation 27K BeadChip metadata complete Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Polidoro, Silvia, et al. """"""""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."""""""" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip +OBI:0002006 1M-Duo Infinium HD BeadChip metadata complete Illumina Human 1M-Duo Infinium HD BeadChip A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. http://www.illumina.com/technology/infinium_hd_assay.ilmn Edwards, Todd L., et al. """"""""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."""""""" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip +OBI:0002007 SOLiD 3 Plus System metadata complete Applied Biosystems SOLiD 3 Plus System A DNA sequencer 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://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf Vissers, Lisenka ELM, et al. """"""""A de novo paradigm for mental retardation."""""""" Nature genetics 42.12 (2010): 1109-1112. PMID:21076407""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg AB SOLiD System Applied Biosystems OBI:0002008 Mouse 385K Whole Genome CGH Tiling Array metadata complete Nimblegen Mouse 385K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen -OBI:0002009 Mouse 3x720K Whole Genome CGH Tiling Array metadata complete Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Wartman, Lukas D., et al. ""Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression."" The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen +OBI:0002009 Mouse 3x720K Whole Genome CGH Tiling Array metadata complete Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Wartman, Lukas D., et al. """"""""Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression."""""""" The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen OBI:0002010 Human 3x720K Whole Genome CGH Tiling Array metadata complete Nimblegen Human 3x720K Whole Genome CGH Tiling Array 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 3x720,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen -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 NextSeq 500 Illumina 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 DNA sequencer 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 DNA sequencer Illumina +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 NextSeq 500 Illumina 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 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 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 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: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 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 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 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 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 @@ -352,11 +352,11 @@ OBI:0002195 microtome blade microtome blade ready for release A device that is OBI:0002196 Sakura Low profile Accu-Edge microtome blade Sakura Low profile Accu-Edge microtome blade ready for release A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades Chris Stoeckert, Helena Ellis NCI BBRB microtome blade OBI:0002487 microraft microraft A material separation device also commerically known as Isoraft, that is used to isolate single cells. https://en.wikipedia.org/wiki/Microrafts Stephen A. Fisher, Junhyong Kim, Dan Berrios material separation device 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: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 DNA sequencer 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 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: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 OBI:0002681 glass bottle glass bottle metadata complete A container with a narrow neck that is made of glass. VEuPathDB VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 container contain function OBI:0002682 glass bottle coated with insecticides glass bottle coated with insecticides metadata complete A glass bottle that coated with material designed to control insects. VEuPathDB VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 glass bottle contain function @@ -438,8 +438,8 @@ 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 DNA sequencer Illumina -OBI:0003387 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 DNA sequencer 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 Instrument Illumina +OBI:0003387 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 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 @@ -467,10 +467,13 @@ 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 DNA sequencer 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 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 DNA sequencer 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 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 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 Instrument Illumina +OBI:0003683 Illumina HiSeq 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 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 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 @@ -573,7 +576,7 @@ OBI:0400117 vacuum dryer vacuum dryer ready for release An instrument which rem OBI:0400118 vortexer vortexer ready for release vortex_mixer A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. http://en.wikipedia.org/wiki/Vortex_mixer VWR Genie 2 Trish Whetzel|Melanie Courtot device perturb function OBI:0400119 microarray wash station microarray wash station metadata complete A device that is used to wash Affymetrix-type arrays. MO_626 wash_station ArrayIt(r) Microarray Wash Station Trish Whetzel device environment control function OBI:0400120 temperature control bath temperature control bath metadata complete A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. OBI Instrument branch VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. Daniel Schober|Frank Gibson|Alan Ruttenburg DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). device contain function|environment control function -OBI:0400121 molecular crosslinker molecular crosslinker metadata incomplete molecular crosslinker A device that is able to chemically join two or more molecules. MO ?? cannot be found in MO Stratalinker Trish Whetzel AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other ""crosslinkers"" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. device environment control function|light emission function +OBI:0400121 molecular crosslinker molecular crosslinker metadata incomplete molecular crosslinker A device that is able to chemically join two or more molecules. MO ?? cannot be found in MO Stratalinker Trish Whetzel AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other """"""""crosslinkers"""""""" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly.""" device environment control function|light emission function OBI:0400135 image cytometer image cytometer ready for release An image_cytometer is an instrument for image-based study or measurement of cells. http://web.mit.edu/solab/Research/ImageCytometry.html The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. Melanie Courtot device image acquisition function light source|optical filter|photodetector OBI:0400137 cytometer cytometer ready for release A cytometer is an instrument for counting and/or measuring characteristics of cells. http://medical.merriam-webster.com/medical/cytometer Melanie Courtot device measure function light source|optical filter|photodetector OBI:0400140 gel tank gel tank metadata incomplete electrophoresis box|electrophoresis unit A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. sep:00095 CHEF gel box, slab gel box, capillary electrophoresis Person:Frank Gibson|Person:Kevin Clancy device contain function|environment control function @@ -581,7 +584,7 @@ OBI:0400142 power supply power supply pending final vetting PSU|electrical power OBI:0400143 fluorometer fluorometer ready for release A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. OBI laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 Allyson Lister|Kevin Lister spectrophotometer OBI:0400146 multispectral imaging flow cytometer multispectral imaging flow cytometer ready for release MIFC A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. http://www.amnis.com/ Melanie Courtot device image acquisition function|information processor function flow cytometer OBI:0400147 microarray microarray ready for release A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. PERSON: Chris Stoeckert An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. Daniel Schober assay array -OBI:0400148 DNA microarray DNA microarray metadata incomplete DNA Chip|DNA-array A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. Web:@2008/03/03 Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). ""Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis"". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 PERSON: Daniel Schober|PERSON: Frank Gibson microarray +OBI:0400148 DNA microarray DNA microarray metadata incomplete DNA Chip|DNA-array A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. Web:@2008/03/03 Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). """"""""Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis"""""""". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115""" PERSON: Daniel Schober|PERSON: Frank Gibson microarray OBI:0400149 protein microarray protein microarray metadata complete A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. PERSON: Daniel Schober The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. Daniel Schober microarray OBI:0400153 droplet sorter droplet sorter metadata incomplete A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. OBI Instrument branch OBI Instrument branch device sort function OBI:0400155 water bath water bath metadata complete A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). PERSON: Daniel Schober A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. Daniel Schober temperature control bath From d9ebf02df5c7001c9fc848013446c2a8e5540fe8 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 7 Oct 2024 10:41:44 -0400 Subject: [PATCH 02/10] chromatography device quote reduction --- src/ontology/templates/devices.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 212fb103..f1b593d3 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -2,7 +2,7 @@ ontology ID label editor preferred term has curation status alternative term def ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % C 'has function' some % SPLIT=| C 'has part' some % SPLIT=| C 'part of' some % C is_manufactured_by value % C % SPLIT=| OBI:0000038 chromatography column chromatography column metadata incomplete Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. http://en.wikipedia.org/wiki/Column_chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device ('material separation function' and ('realized in' only 'preparative chromatography')) container OBI:0000041 pump valve switch pump valve switch metadata incomplete A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. OBI OBI Instrument branch FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument device mechanical function -OBI:0000048 chromatography device chromatography device metadata complete chromatography instrument A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a """"""""mobile phase"""""""" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.""" http://en.wikipedia.org/wiki/Chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device contain function|environment control function|measure function|material separation function +OBI:0000048 chromatography device chromatography device metadata complete chromatography instrument A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a ""mobile phase"" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. http://en.wikipedia.org/wiki/Chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device contain function|environment control function|measure function|material separation function OBI:0000049 mass spectrometer mass spectrometer ready for release A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum http://en.wikipedia.org/wiki/Mass_spectrometry LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific Frank Gibson device measure function mass analyzer|ion source|ion detector OBI:0000051 liquid chromatography mass spectrometry platform liquid chromatography mass spectrometry platform metadata incomplete A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. OBI Instrument branch OBI instrument branch device measure function|material separation function chromatography device|mass spectrometer OBI:0000052 microarray platform microarray platform metadata incomplete A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. OBI Instrument branch OBI Instrument branch device environment control function microarray From adfcd605636151c5e8ee76b9309b17f40853dddd Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 7 Oct 2024 10:48:28 -0400 Subject: [PATCH 03/10] DNA microarray quote reduction --- src/ontology/templates/devices.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index f1b593d3..92b4ec9c 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -584,7 +584,7 @@ OBI:0400142 power supply power supply pending final vetting PSU|electrical power OBI:0400143 fluorometer fluorometer ready for release A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. OBI laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 Allyson Lister|Kevin Lister spectrophotometer OBI:0400146 multispectral imaging flow cytometer multispectral imaging flow cytometer ready for release MIFC A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. http://www.amnis.com/ Melanie Courtot device image acquisition function|information processor function flow cytometer OBI:0400147 microarray microarray ready for release A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. PERSON: Chris Stoeckert An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. Daniel Schober assay array -OBI:0400148 DNA microarray DNA microarray metadata incomplete DNA Chip|DNA-array A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. Web:@2008/03/03 Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). """"""""Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis"""""""". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115""" PERSON: Daniel Schober|PERSON: Frank Gibson microarray +OBI:0400148 DNA microarray DNA microarray metadata incomplete DNA Chip|DNA-array A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. Web:@2008/03/03 Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). ""Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis"". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 PERSON: Daniel Schober|PERSON: Frank Gibson microarray OBI:0400149 protein microarray protein microarray metadata complete A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. PERSON: Daniel Schober The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. Daniel Schober microarray OBI:0400153 droplet sorter droplet sorter metadata incomplete A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. OBI Instrument branch OBI Instrument branch device sort function OBI:0400155 water bath water bath metadata complete A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). PERSON: Daniel Schober A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. Daniel Schober temperature control bath From 817ae2cd5a8ffcc380817ff85cfc74c867c1a0f4 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 7 Oct 2024 11:00:43 -0400 Subject: [PATCH 04/10] molecular crosslinker quote reduction --- src/ontology/templates/devices.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 92b4ec9c..89b582a1 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -576,7 +576,7 @@ OBI:0400117 vacuum dryer vacuum dryer ready for release An instrument which rem OBI:0400118 vortexer vortexer ready for release vortex_mixer A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. http://en.wikipedia.org/wiki/Vortex_mixer VWR Genie 2 Trish Whetzel|Melanie Courtot device perturb function OBI:0400119 microarray wash station microarray wash station metadata complete A device that is used to wash Affymetrix-type arrays. MO_626 wash_station ArrayIt(r) Microarray Wash Station Trish Whetzel device environment control function OBI:0400120 temperature control bath temperature control bath metadata complete A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. OBI Instrument branch VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. Daniel Schober|Frank Gibson|Alan Ruttenburg DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). device contain function|environment control function -OBI:0400121 molecular crosslinker molecular crosslinker metadata incomplete molecular crosslinker A device that is able to chemically join two or more molecules. MO ?? cannot be found in MO Stratalinker Trish Whetzel AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other """"""""crosslinkers"""""""" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly.""" device environment control function|light emission function +OBI:0400121 molecular crosslinker molecular crosslinker metadata incomplete molecular crosslinker A device that is able to chemically join two or more molecules. MO ?? cannot be found in MO Stratalinker Trish Whetzel AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other ""crosslinkers"" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. device environment control function|light emission function OBI:0400135 image cytometer image cytometer ready for release An image_cytometer is an instrument for image-based study or measurement of cells. http://web.mit.edu/solab/Research/ImageCytometry.html The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. Melanie Courtot device image acquisition function light source|optical filter|photodetector OBI:0400137 cytometer cytometer ready for release A cytometer is an instrument for counting and/or measuring characteristics of cells. http://medical.merriam-webster.com/medical/cytometer Melanie Courtot device measure function light source|optical filter|photodetector OBI:0400140 gel tank gel tank metadata incomplete electrophoresis box|electrophoresis unit A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. sep:00095 CHEF gel box, slab gel box, capillary electrophoresis Person:Frank Gibson|Person:Kevin Clancy device contain function|environment control function From 5bfe2c83c8c00a84c9ca1245447e03f15ca8321e Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 7 Oct 2024 12:14:31 -0400 Subject: [PATCH 05/10] no more triples+ --- src/ontology/templates/devices.tsv | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 89b582a1..96113131 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -315,20 +315,20 @@ 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 Illumina +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 Illumina HiSeq 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 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 Instrument 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 -OBI:0002004 Methylation 450K BeadChip metadata complete Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Naumov, Vladimir A., et al. """"""""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."""""""" Epigenetics 8.9 (2013): 0-1. PMID: 23867710""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip -OBI:0002005 Methylation 27K BeadChip metadata complete Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Polidoro, Silvia, et al. """"""""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."""""""" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip -OBI:0002006 1M-Duo Infinium HD BeadChip metadata complete Illumina Human 1M-Duo Infinium HD BeadChip A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. http://www.illumina.com/technology/infinium_hd_assay.ilmn Edwards, Todd L., et al. """"""""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."""""""" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip -OBI:0002007 SOLiD 3 Plus System metadata complete Applied Biosystems SOLiD 3 Plus System A DNA sequencer 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://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf Vissers, Lisenka ELM, et al. """"""""A de novo paradigm for mental retardation."""""""" Nature genetics 42.12 (2010): 1109-1112. PMID:21076407""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg AB SOLiD System Applied Biosystems +OBI:0002004 Methylation 450K BeadChip metadata complete Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Naumov, Vladimir A., et al. ""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."" Epigenetics 8.9 (2013): 0-1. PMID: 23867710 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip +OBI:0002005 Methylation 27K BeadChip metadata complete Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Polidoro, Silvia, et al. ""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip +OBI:0002006 1M-Duo Infinium HD BeadChip metadata complete Illumina Human 1M-Duo Infinium HD BeadChip A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. http://www.illumina.com/technology/infinium_hd_assay.ilmn Edwards, Todd L., et al. ""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip +OBI:0002007 SOLiD 3 Plus System metadata complete Applied Biosystems SOLiD 3 Plus System A DNA sequencer 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://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf Vissers, Lisenka ELM, et al. ""A de novo paradigm for mental retardation."" Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg AB SOLiD System Applied Biosystems OBI:0002008 Mouse 385K Whole Genome CGH Tiling Array metadata complete Nimblegen Mouse 385K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen -OBI:0002009 Mouse 3x720K Whole Genome CGH Tiling Array metadata complete Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Wartman, Lukas D., et al. """"""""Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression."""""""" The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584""" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen +OBI:0002009 Mouse 3x720K Whole Genome CGH Tiling Array metadata complete Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Wartman, Lukas D., et al. ""Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression."" The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen OBI:0002010 Human 3x720K Whole Genome CGH Tiling Array metadata complete Nimblegen Human 3x720K Whole Genome CGH Tiling Array 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 3x720,000 features. http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg tiling microarray Nimblegen -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: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 NextSeq 500 Illumina 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 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 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 @@ -352,11 +352,11 @@ OBI:0002195 microtome blade microtome blade ready for release A device that is OBI:0002196 Sakura Low profile Accu-Edge microtome blade Sakura Low profile Accu-Edge microtome blade ready for release A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades Chris Stoeckert, Helena Ellis NCI BBRB microtome blade OBI:0002487 microraft microraft A material separation device also commerically known as Isoraft, that is used to isolate single cells. https://en.wikipedia.org/wiki/Microrafts Stephen A. Fisher, Junhyong Kim, Dan Berrios material separation device 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: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 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: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 OBI:0002681 glass bottle glass bottle metadata complete A container with a narrow neck that is made of glass. VEuPathDB VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 container contain function OBI:0002682 glass bottle coated with insecticides glass bottle coated with insecticides metadata complete A glass bottle that coated with material designed to control insects. VEuPathDB VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 glass bottle contain function From 78978a6aefbf61b83bdbfe3f6740dff225b6b66d Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 7 Oct 2024 12:47:36 -0400 Subject: [PATCH 06/10] add word sereis to Illumina Instrumetn terms --- 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 96113131..a315c381 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 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 Illumina HiSeq 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 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 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 OBI:0002004 Methylation 450K BeadChip metadata complete Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Naumov, Vladimir A., et al. ""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."" Epigenetics 8.9 (2013): 0-1. PMID: 23867710 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip OBI:0002005 Methylation 27K BeadChip metadata complete Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Polidoro, Silvia, et al. ""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip @@ -329,21 +329,21 @@ 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 NextSeq 500 Illumina 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 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 Instrument Illumina +OBI:0002021 NextSeq 500 Illumina 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 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 Illumina HiSeq 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 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 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 @@ -354,7 +354,7 @@ 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 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 @@ -438,8 +438,8 @@ 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 Instrument Illumina -OBI:0003387 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 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 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 @@ -467,13 +467,13 @@ 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 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 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 Instrument Illumina -OBI:0003683 Illumina HiSeq 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 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 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 From 3e7d575ea7ad637344eaea6e5b87de7096667a22 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 7 Oct 2024 12:55:08 -0400 Subject: [PATCH 07/10] add Illumina to labels of Illumina DAN seq. instruments --- src/ontology/templates/devices.tsv | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index a315c381..b19e405d 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -318,7 +318,9 @@ OBI:0001974 Ion 314 Chip v2 Ion 314 Chip v2 Ion PGM 314 Chip|Ion 314 Chip|Ion P 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 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 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 + +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 + OBI:0002004 Methylation 450K BeadChip metadata complete Illumina Infinium Human Methylation 450K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Naumov, Vladimir A., et al. ""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."" Epigenetics 8.9 (2013): 0-1. PMID: 23867710 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip OBI:0002005 Methylation 27K BeadChip metadata complete Illumina Infinium Human Methylation 27K BeadChip A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Polidoro, Silvia, et al. ""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina methylation BeadChip OBI:0002006 1M-Duo Infinium HD BeadChip metadata complete Illumina Human 1M-Duo Infinium HD BeadChip A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. http://www.illumina.com/technology/infinium_hd_assay.ilmn Edwards, Todd L., et al. ""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip @@ -329,7 +331,7 @@ 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 NextSeq 500 Illumina 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: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 @@ -439,7 +441,7 @@ OBI:0003114 Illumina MiniSeq Illumina MiniSeq MiniSeq A small benchtop DNA sequ 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 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: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 From 3680de0010659b49e42560e6e1f62e2079c142c1 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 7 Oct 2024 13:08:26 -0400 Subject: [PATCH 08/10] add 'Illumina' to lable for Genome Analyzer II subclasses --- src/ontology/templates/devices.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index b19e405d..1be21e42 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -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 Illumina +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 @@ -337,7 +337,7 @@ 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 Illumina +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 From e13e50e0a94b15637e16d489ca33339854f1a0a2 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Thu, 10 Oct 2024 11:21:43 -0400 Subject: [PATCH 09/10] 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 From 2ed86d2a6f9219b0da713d386cc8b7825974c0fb Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Mon, 21 Oct 2024 12:12:04 -0400 Subject: [PATCH 10/10] Update devices.owl module --- src/ontology/modules/devices.owl | 139 ++++++++++++++++++++++++++----- 1 file changed, 117 insertions(+), 22 deletions(-) diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index a7760fea..03d99d54 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -6359,14 +6359,20 @@ + + + + + + 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 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. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Genome Analyzer IIx Illumina GA IIx - Illumina Genome Analyzer IIx ENCODE group - Genome Analyzer IIx + Illumina Genome Analyzer IIx @@ -6374,7 +6380,7 @@ - + @@ -6395,7 +6401,7 @@ - + @@ -6427,9 +6433,9 @@ 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. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina MiSeq + MiSeq http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf - MiSeq + Illumina MiSeq @@ -6628,7 +6634,7 @@ - + @@ -6637,9 +6643,9 @@ 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. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina NextSeq 500 + NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html - NextSeq 500 + Illumina NextSeq 500 @@ -6647,7 +6653,7 @@ - + @@ -6750,12 +6756,18 @@ + + + + + + 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. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Genome Analyzer IIe Illumina GA IIe - Illumina Genome Analyzer IIe http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf - Genome Analyzer IIe + Illumina Genome Analyzer IIe @@ -6793,7 +6805,7 @@ - + @@ -6813,7 +6825,7 @@ - + @@ -6913,6 +6925,12 @@ + + + + + + Illumina Genome Analyzer 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. @@ -6927,7 +6945,13 @@ - + + + + + + + Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. @@ -7097,7 +7121,7 @@ - + @@ -8446,7 +8470,7 @@ - + @@ -8470,7 +8494,7 @@ - + @@ -8485,7 +8509,7 @@ https://www.illumina.com/systems/sequencing-platforms/nextseq.html https://github.com/obi-ontology/obi/issues/1546 gEAR - NextSeq 550 + Illumina NextSeq 550 @@ -9126,7 +9150,7 @@ - + @@ -9161,7 +9185,7 @@ - + @@ -9184,7 +9208,7 @@ - + @@ -9204,6 +9228,77 @@ + + + + + + + + + + + https://www.illumina.com/content/dam/illumina-support/documents//products/datasheets/datasheet_hiseq_systems.pdf + + A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq. + 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. + PERSON: Mark Andrew Miller + HiSeq series + PERSON: Mark Andrew Miller + https://github.com/obi-ontology/obi/issues/1825 + Alicia Clum + Illumina HiSeq Series Instrument + + + + + + + + + + + + + + + https://www.cd-genomics.com/blog/nextseq/ + + A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq. + 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. + PERSON: Mark Andrew Miller + NextSeq series + PERSON: Mark Andrew Miller + https://github.com/obi-ontology/obi/issues/1825 + Alicia Clum + Illumina NextSeq Series Instrument + + + + + + + + + + + + + + + + A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq. + 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. + PERSON: Mark Andrew Miller + NovaSeq series + PERSON: Mark Andrew Miller + https://github.com/obi-ontology/obi/issues/1825 + Alicia Clum + Illumina NovaSeq Series Instrument + + + +