From b2ba1b371fa4654445345312a5fd3f677f0e8991 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 3 Oct 2024 12:36:07 -0400 Subject: [PATCH 1/2] manufactured by Illumina edited as CSV in Libre Office. Do not know why ends of other lines changed --- src/ontology/templates/devices.tsv | 36 +++++++++++++++--------------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 576bdddf..e51e9622 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 +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:0002002 Illumina HiSeq 2500 metadata complete HiSeq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf "Spaethling, Jennifer M., and James H. Eberwine. """"Single-cell transcriptomics for drug target discovery."""" Current opinion in pharmacology (2013). pmid:23725882" PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg DNA sequencer Illumina OBI:0002003 MiSeq metadata complete Illumina MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng DNA sequencer Illumina -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 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: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 +OBI:0002027 Genome Analyzer IIe Illumina GA IIe|Illumina Genome Analyzer IIe An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Illumina Genome Analyzer II Illumina OBI:0002046 surface plasmon resonance sensor chip surface plasmon resonance sensor chip pending final vetting sensor chip|biosensor chip|SPR sensor chip A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached OBI ProteOn GLC Sensor Chip #176-5011 Anna Maria Masci device solid support function surface plasmon resonance instrument OBI:0002048 Illumina HiSeq 3000 metadata complete HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html PERSON: Sagar Jain, Richard Scheuermann DNA sequencer Illumina OBI:0002049 Illumina HiSeq 4000 metadata complete HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html PERSON: Sagar Jain, Richard Scheuermann DNA sequencer Illumina OBI:0002088 specimen container specimen container ready for release A container with the function of containing a specimen. Duke Biobank, OBIB COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube Chris Stoeckert For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ equivalent container containing a specimen function OBI:0002089 physical store physical store ready for release A container with an environmental control function. Duke Biobank, OBIB a freezer. a humidity controlled box. Chris Stoeckert For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ equivalent container environment control function OBI:0002109 Human 6x630K CGH Whole Genome Tiling Array ready for release NimbleGen Human 6x630K CGH Whole Genome Tiling Array A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group Term request: https://sourceforge.net/p/obi/obi-terms/791/ tiling microarray Nimblegen -OBI:0002128 Illumina Genome Analyzer Illumina Genome Analyzer pending final vetting Illumina Genome Analyzer I A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Person: Chris Stoeckert, Jason Hilton DNA sequencer -OBI:0002129 Illumina HiSeq X Ten Illumina HiSeq X Ten pending final vetting HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann DNA sequencer +OBI:0002128 Illumina Genome Analyzer Illumina Genome Analyzer pending final vetting Illumina Genome Analyzer I A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Person: Chris Stoeckert, Jason Hilton DNA sequencer Illumina +OBI:0002129 Illumina HiSeq X Ten Illumina HiSeq X Ten pending final vetting HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann DNA sequencer Illumina OBI:0002130 Illumina Infinium Omni5Exome-4 Kit Illumina Infinium Omni5Exome-4 Kit pending final vetting An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html Person: Chris Stoeckert, Jason Hilton Illumina BeadChip OBI:0002131 Illumina Infinium MethylationEPIC v1.0 BeadChip Illumina Infinium MethylationEPIC v1.0 BeadChip pending final vetting An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf Person: Chris Stoeckert, Jason Hilton Illumina methylation BeadChip OBI:0002192 Leica Peloris rapid tissue processor Leica Peloris rapid tissue processor ready for release An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf Chris Stoeckert, Helena Ellis NCI BBRB automatic tissue processor @@ -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: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 @@ -573,7 +573,7 @@ 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 +581,7 @@ 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 781e4babee314c6af189b1c2701b364e6a98c5cc Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Thu, 3 Oct 2024 13:56:43 -0400 Subject: [PATCH 2/2] Restore previous quotation marks --- src/ontology/templates/devices.tsv | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index e51e9622..12bc32db 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 @@ -315,20 +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 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:0002002 Illumina HiSeq 2500 metadata complete HiSeq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg DNA sequencer Illumina OBI:0002003 MiSeq metadata complete Illumina MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng DNA sequencer Illumina -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 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: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 DNA sequencer 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 @@ -573,7 +573,7 @@ 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 +581,7 @@ 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