Real-time PCR Data Markup Language
Names
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Real-time PCR Data Markup Language
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
RDML
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
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Real-time PCR Data Markup Language
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
RDML
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
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Real-time PCR Data Markup Language
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
RDML
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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The RDML file format is developed by the RDML consortium (http://www.rdml.org) and can be used free of charge. The RDML file format was created to encourage the exchange, publication, revision and re-analysis of raw qPCR data. The core of an RDML file is an experiment, not a PCR run. Therefore all the information is collected which is required to understand an experiment. The structure of the file format was inspired by a database structure. In the file are several master elements, which are then referred to in other parts of the file. This structure allows to reduce the amount of redundant information and encourages the user to provide useful information. The Real-time PCR Data Markup Language (RDML) is a structured and universal data standard for exchanging quantitative PCR (qPCR) data. The data standard should contain sufficient information to understand the experimental setup, re-analyse the data and interpret the results. The data standard is a compressed text file in Extensible Markup Language (XML) and enables transparent exchange of annotated qPCR data between instrument software and third-party data analysis packages, between colleagues and collaborators, and between authors, peer reviewers, journals and readers. To support the public acceptance of this standard, both an on-line RDML file generator is available for end users, as well as RDML software libraries to be used by software developers, enabling import and export of RDML data files.
Description
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The RDML file format is developed by the RDML consortium (http://www.rdml.org) and can be used free of charge. The RDML file format was created to encourage the exchange, publication, revision and re-analysis of raw qPCR data. The core of an RDML file is an experiment, not a PCR run. Therefore all the information is collected which is required to understand an experiment. The structure of the file format was inspired by a database structure. In the file are several master elements, which are then referred to in other parts of the file. This structure allows to reduce the amount of redundant information and encourages the user to provide useful information. The Real-time PCR Data Markup Language (RDML) is a structured and universal data standard for exchanging quantitative PCR (qPCR) data. The data standard should contain sufficient information to understand the experimental setup, re-analyse the data and interpret the results. The data standard is a compressed text file in Extensible Markup Language (XML) and enables transparent exchange of annotated qPCR data between instrument software and third-party data analysis packages, between colleagues and collaborators, and between authors, peer reviewers, journals and readers. To support the public acceptance of this standard, both an on-line RDML file generator is available for end users, as well as RDML software libraries to be used by software developers, enabling import and export of RDML data files.
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
http://www.rdml.org/files.phpWebpage
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http://www.rdml.org/files.php
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence:
Name: Wholecells DB MIT LicenceLicence name
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Wholecells DB MIT Licence
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence URL
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http://www.wholecellsimdb.org/about
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
RDML: structured language and reporting guidelines for real-time quantitative PCR data
PMID: 19223324
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
RDML-Ninja and RDMLdb for standardized exchange of qPCR data
PMID: 26087842
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
RDML: structured language and reporting guidelines for real-time quantitative PCR data
PMID: 19223324
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
RDML-Ninja and RDMLdb for standardized exchange of qPCR data
PMID: 26087842
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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RDML: structured language and reporting guidelines for real-time quantitative PCR data
PubMed citations: 67.
67 articles citing: RDML: structured language and reporting guidelines for real-time quantitative PCR data
CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics. PMID:35690249
Differential Accumulation of Metabolites and Transcripts Related to Flavonoid, Styrylpyrone, and Galactolipid Biosynthesis in Equisetum Species and Tissue Types. PMID:35629907
Molecular Evidence of Orthomyxovirus Presence in Colombian Neotropical Bats. PMID:35558106
A Systematic Approach to Diagnostic Laboratory Software Requirements Analysis. PMID:35447704
Neoplastic synovial lining cells that coexpress podoplanin and CD90 overproduce CSF-1, driving tenosynovial giant cell tumor. PMID:34855235
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data. PMID:34433408
The MicroRNA Landscape of Acute Beta Cell Destruction in Type 1 Diabetic Recipients of Intraportal Islet Grafts. PMID:34359863
Insertion of prpoD_rpoS fragment enhances expression of recombinant protein by dps auto-inducible promoter in Escherichia coli. PMID:34342815
Assessment of common housekeeping genes as reference for gene expression studies using RT-qPCR in mouse choroid plexus. PMID:33558629
Multiple imputation and direct estimation for qPCR data with non-detects. PMID:33243147
Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata. PMID:33150057
Bilberry (Vaccinium myrtillus L.) Extracts Comparative Analysis Regarding Their Phytonutrient Profiles, Antioxidant Capacity along with the In Vivo Rescue Effects Tested on a Drosophila melanogaster High-Sugar Diet Model. PMID:33143302
Cross-sectional study of human coding- and non-coding RNAs in progressive stages of Helicobacter pylori infection. PMID:32901043
AScall - Automatic Allele-Specific qPCR Analysis. PMID:32391349
Filter paper-based spin column method for cost-efficient DNA or RNA purification. PMID:30532193
Genetic expression profile-based screening of genes and pathways associated with papillary thyroid carcinoma. PMID:30344727
Improving the standardization of mRNA measurement by RT-qPCR. PMID:29922589
rdml: A Mathematica package for parsing and importing Real-Time qPCR data. PMID:28606167
A survey of tools for the analysis of quantitative PCR (qPCR) data. PMID:27920994
A novel gene OsAHL1 improves both drought avoidance and drought tolerance in rice. PMID:27453463
Vitellogenin knockdown strongly affects cotton boll weevil egg viability but not the number of eggs laid by females. PMID:27419079
Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses. PMID:27176476
Removal of between-run variation in a multi-plate qPCR experiment. PMID:27077038
Inter-population Differences in Retrogene Loss and Expression in Humans. PMID:26474060
Tissue-Specific Immune Gene Expression in the Migratory Locust, Locusta Migratoria. PMID:26463191
Associations of circulating plasma microRNAs with age, body mass index and sex in a population-based study. PMID:26462558
Systems Medicine: The Application of Systems Biology Approaches for Modern Medical Research and Drug Development. PMID:26357572
Amyloid-β(25-35) Modulates the Expression of GirK and KCNQ Channel Genes in the Hippocampus. PMID:26218288
Transcriptional Response of Human Neurospheres to Helper-Dependent CAV-2 Vectors Involves the Modulation of DNA Damage Response, Microtubule and Centromere Gene Groups. PMID:26207738
RDML-Ninja and RDMLdb for standardized exchange of qPCR data. PMID:26087842
Identification of optimal reference genes for gene expression normalization in a wide cohort of endometrioid endometrial carcinoma tissues. PMID:25473950
In vitro encapsulation of heterologous dsDNA into human parvovirus B19 virus-like particles. PMID:25389040
Identification of most stable endogenous control genes for microRNA quantification in the developing mouse lung. PMID:25368994
Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. PMID:24973947
Detection and quantification of extracellular microRNAs in murine biofluids. PMID:24629058
Comparative assessment of automated nucleic acid sample extraction equipment for biothreat agents. PMID:24452173
Pigmentation in sand pear (Pyrus pyrifolia) fruit: biochemical characterization, gene discovery and expression analysis with exocarp pigmentation mutant. PMID:24445590
Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color. PMID:24400075
RefPrimeCouch--a reference gene primer CouchApp. PMID:24368831
A p53 drug response signature identifies prognostic genes in high-risk neuroblastoma. PMID:24348903
Identification and validation of reference genes for transcript normalization in strawberry (Fragaria × ananassa) defense responses. PMID:23940602
Differentiated neuroprogenitor cells incubated with human or canine adenovirus, or lentiviral vectors have distinct transcriptome profiles. PMID:23922808
Determination of reliable reference genes for multi-generational gene expression analysis on C. elegans exposed to abused drug nicotine. PMID:23681163
Cumulus and granulosa cell markers of oocyte and embryo quality. PMID:23498999
Differential expression of anthocyanin biosynthetic genes and transcription factor PcMYB10 in pears (Pyrus communis L.). PMID:23029391
Human blood RNA stabilization in samples collected and transported for a large biobank. PMID:22988904
Synthetic lethality between Rb, p53 and Dicer or miR-17-92 in retinal progenitors suppresses retinoblastoma formation. PMID:22864477
Primer3--new capabilities and interfaces. PMID:22730293
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
Reference genes for real-time PCR quantification of microRNAs and messenger RNAs in rat models of hepatotoxicity. PMID:22563491
Strand-specific miR-28-5p and miR-28-3p have distinct effects in colorectal cancer cells. PMID:22240480
miRNA expression profiling enables risk stratification in archived and fresh neuroblastoma tumor samples. PMID:22031095
GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR. PMID:21917859
Differential expression of anthocyanin biosynthetic genes in relation to anthocyanin accumulation in the pericarp of Litchi chinensis Sonn. PMID:21559331
Multiplex cDNA quantification method that facilitates the standardization of gene expression data. PMID:21415008
A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification. PMID:21407812
Measurable impact of RNA quality on gene expression results from quantitative PCR. PMID:21317187
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. PMID:21304730
The miR-17-92 microRNA cluster regulates multiple components of the TGF-β pathway in neuroblastoma. PMID:21145484
Modulation of flavonoid biosynthetic pathway genes and anthocyanins due to virus infection in grapevine (Vitis vinifera L.) leaves. PMID:20731850
MicroRNA expression profiling in the prefrontal cortex of individuals affected with schizophrenia and bipolar disorders. PMID:20675101
Transcribed-ultra conserved region expression profiling from low-input total RNA. PMID:20199688
The most likely time and place of introduction of BTV8 into Belgian ruminants. PMID:20195379
Transcribed-Ultra Conserved Region expression is associated with outcome in high-risk neuroblastoma. PMID:20003513
External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data. PMID:19734345
QPCR: Application for real-time PCR data management and analysis. PMID:19712446
A novel and universal method for microRNA RT-qPCR data normalization. PMID:19531210 -
RDML-Ninja and RDMLdb for standardized exchange of qPCR data
PubMed citations: 6.
6 articles citing: RDML-Ninja and RDMLdb for standardized exchange of qPCR data
Hypomethylation of AHRR (cg05575921) Is Related to Smoking Status in the Mexican Mestizo Population. PMID:34440450
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data. PMID:34433408
Salidroside inhibits high-glucose induced proliferation of vascular smooth muscle cells via inhibiting mitochondrial fission and oxidative stress. PMID:28672961
rdml: A Mathematica package for parsing and importing Real-Time qPCR data. PMID:28606167
Removal of between-run variation in a multi-plate qPCR experiment. PMID:27077038
Data on individual PCR efficiency values as quality control for circulating miRNAs. PMID:26568973
Tags:
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
nucleic acid sequence
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
polymerase chain reaction
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
experimental measurement
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
nucleic acid sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
polymerase chain reaction
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: RDML; Real-time PCR Data Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.a4wgws; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
dna experimental measurement gene expression nucleic acid sequence polymerase chain reaction rna
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