The MIT License Copyright (c) 2008-2013 the RDML-consortium Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. These elements should be used to annotate samples by setting a property and a value. A property could be sex, the value M or F. Description of the cDNA synthesis method. Enzyme used for reverse transcription. True if RNA was DNAse treated prior cDNA synthesis. For some commercial assays, the primer sequences may be unknown. This element allows to describe commercial assays. The method used to determine the Cq value. Software name and version used to collect and analyze the data. Due to the frequent occurrence of this element, names are kept short. TargetID - A reference to a target. Quantification cycle - The calculated fractional PCR cycle used for downstream quantification. Negative values are used to express following conditions: Not Available: -1.0 Excluded - If present, this entry should not be evaluated. Do not set this element to false if this entry is valid, leave the entire element out instead. It may contain a string with reason for exclusion. Several reasons for exclusion should be seperated by semicolons ";". Amplification data point - The single data points measured during amplification. Melting curve data point - The single data points measured during the melting analysis. End point - Result of an endpoint measurement. Background fluorescence - The y-intercept of the baseline trend based on the estimated background fluorescence. Background fluorescence slope - The slope of the baseline trend based on the estimated background fluorescence. The element should be absent to indicate a slope of 0.0; If this element is present without the bgFluor element it should be ignored. Quantification flourescence - The fluorescence value corresponding to the threshold line. These elements should be used if the same description applies to many samples, targets or experiments. Due to the frequent occurrence of this element, names are kept short. Cycle - The PCR cycle at which data point was collected. Temperature - The temperature in degrees Celsius at the time of measurement. Fluorescence - The fluorescence intensity measured without any correction. The fluorescence intensity must not be baseline corrected. Due to the frequent occurrence of this element, names are kept short. Temperature - The temperature in degrees Celsius of this data point. Fluorescence - The fluorescence intensity measured without any correction. The fluorescence intensity must not be baseline corrected. Information on a dye. Contact details of the experimenter. An experiment can contain several runs. react id within the run must be unique. Documentation references within the run must be unique. Experimenter references within the run must be unique. This step forms a temperature gradient across the PCR block. The high temperature of the gradient in degrees Celsius. The low temperature of the gradient in degrees Celsius. The duration of this step in seconds. The change of the temperature from one cycle to the next: actual highTemperature = highTemperature + (temperatureChange * cycle counter) actual lowTemperature = lowTemperature + (temperatureChange * cycle counter) The change of the duration from one cycle to the next: actual duration = duration + (durationChange * cycle couter) Make a measurement and store it as meltcurve or real-time data. The temperature change from one step to the next in degrees Celsius per second. No value means maximal change rate. A ID must be at least one character and unique. The id should be a human readable short name as it was provided by the user. Label used for pcrFormat. This step waits for the user to open the lid and continues afterwards. It allows to stop the program and to wait for the user to add for example enzymes and continue the program afterwards. The temperature of the previous step is maintained. This step allows to form a loop or to exclude some steps. It allows to jump to a certain "goto" step for "repeat" times. If the "goto" step is higher than the step of the loop, "repeat" must be "0". The step to go to to form the loop. Determines how often the loop is repeated. The first run through the loop is counted as 0, the last loop is "repeat" - 1. The loop is run through exactly "repeat" times. Description of three prime modification (if present). Description of five prime modification (if present). This step allows to pause at a certain temperature. It is typically the last step in an amplification protocol. The temperature in degrees Celsius to maintain during the pause. The format of the run - This allows the software to display the data according to the qPCR instrument run format. Rotor formats always have 1 column; rows correspond to the number of places in the rotor. Values for common formats are: Format | rows | columns | rowLabel | columnLabel -------------------------------------------------------------------------- single-well | 1 | 1 | 123 | 123 48-well plate | 6 | 8 | ABC | 123 96-well plate | 8 | 12 | ABC | 123 384-well plate | 16 | 24 | ABC | 123 1536-well plate | 32 | 48 | ABC | 123 3072-well array | 32 | 96 | A1a1 | A1a1 5184-well chip | 72 | 72 | ABC | 123 32-well rotor | 32 | 1 | 123 | 123 72-well rotor | 72 | 1 | 123 | 123 100-well rotor | 100 | 1 | 123 | 123 free format | -1 | 1 | 123 | 123 If rows are -1 then the software should not try to reconstruct a plate and just display all react data in list (1 column) form. If columns is 1 then the software should not display a column label. The primers used to reverse transcribe the RNA to cDNA. A quantity is always defined by its value and its unit. The unit the quantity cop - copies per microliter fold - fold change dil - dilution (10 would mean 1:10 dilution) nMol - nanomol per microliter ng - nanogram per microliter other - other unit (must be linear, no exponents or logarithms allowed) This element can be used to assign a publisher and id to the RDML file. An MD5Hash calculated over the complete file after removing all rdmlIDTypes and all whitespaces between elements. A reaction is an independent chemical reaction corresponding for example to a well in a 96 well plate, a capillary in a rotor, a through-hole on an array, etc. SampleID - A reference to a sample. The cycle (cyc) within the amplification curve datapoints) (adp) must be unique. The temperature (tmp) within the melting curve datapoints (mdp) must be unique. The ID of this reaction Schemas : - rotor : assign IDs according to the position of the sample on the rotor (1 for the 1st sample, 2 for the 2nd, ...) - plate (96/384/1536 well) : the IDs are assigned in a row-first/column-second manner. For each row, the samples are numbered according to the increasing column number. At the end of a row, the numbering starts at the first column of the next row. An example for this type of plate can be found below : 1 2 3 4 5 6 7 8 9 10 11 12 ___________________________________________________ A | 1 2 3 4 5 6 7 8 9 10 11 12 B | 13 14 15 16 17 18 19 20 21 22 23 24 C | 25 26 27 28 28 30 31 32 33 34 35 36 D | ... 1 2 3 4 5 6 7 8 9 10 11 12 ___________________________________________________ 1 | 1 2 3 4 5 6 7 8 9 10 11 12 2 | 13 14 15 16 17 18 19 20 21 22 23 24 3 | 25 26 27 28 28 30 31 32 33 34 35 36 4 | ... - multi-array plate (BioTrove) : the IDs are assigned in a row-first/column-second manner, ignoring the organisation of sub-arrays. For each row, the samples are numbered according to the increasing column number. At the end of a row, the the next row. An example for this type of plate can be found below : 1 | 2 | 3 | ... -------------------------------------------------------------------- | | 1 2 3 4 | 5 6 7 8 | 9 10 11 12 | ... ____________________________________________________________________ | a | 1 2 3 4 | 5 6 7 8 | 9 10 11 12 | ... A | b | 49 50 51 52 | 53 54 55 56 | 57 58 59 60 | ... | c | 97 98 99 100 | 101 102 103 104 | 105 106 107 108 | ... | d | 145 146 147 148 | 149 150 151 152 | 153 154 155 156 | ... -------------------------------------------------------------------- | a | 193 194 195 196 | 197 198 199 200 | 201 202 203 204 | ... B | b | 241 242 243 244 | 245 246 247 248 | 249 250 251 252 | ... | c | ... | ... | ... | ... A run is a set of reactions performed in one "run", for example one plate, one rotor, one array, one chip. Description of the instrument used to aquire the data. Description of the software used to analyze/collect the data. Description of method used to determine the background. Description of method used to calculate the quantification cycle. The program used to aquire the data. Date and time stamp when the data was aquired. The target ID (tar->@id) within the data element must be unique. A sample is a defined template solution. Dilutions of the same material differ in concentration and are considered different samples. A technical replicate samples should contain the same name (reactions are performed on the same material), and biological replicates should contain different names (the nucleic acids derived from the different biological replicates are not the same). Serial dilutions in a standard curve must have a different name. True if this sample is used as inter run calibrator. Quantity - The reference quantity of this sample. It should be only used if the sample is part of a standard curve. The provided value will be used to quantify unknown samples in absolute quantification assays. Only the use of true numbers is valid like 1, 10, 100, 1000 or 1, 0.1, 0.01, 0.001. The use of exponents is not valid like 1, 2, 3, 4 or -1, -2, -3, -4 because it will not be interpreted as 10E1, 10E2, 10E3, 10E4 or 10E-1, 10E-2, 10E-3, 10E-4. True if this sample is used as calibrator sample. unkn - unknown sample ntc - non template control nac - no amplification control std - standard sample ntp - no target present nrt - minusRT pos - positive control opt - optical calibrator sample All the IUPAC codes : A Adenine C Cytosine G Guanine T (or U) Thymine (or Uracil) R A or G Y C or T S G or C W A or T K G or T M A or C B C or G or T D A or G or T H A or C or T V A or C or G N any base The incremental number of the step. First step should be nr = 1 and then increment each step by + 1. A target is a defined PCR reaction. PCR reactions for the same gene which differ in primer sequences are considered different targets. Amplification efficiency should be given as the fold-increase of DNA per cycle (the base of the exponential function), for example 1.95 for 95% efficiency. The standard error of the value provided in "amplificationEfficiency" should be given. The detection limit is given in copies per microliter. DyeID - A reference to a dye. ref - reference target toi - target of interest This step keeps a constant temperature on the heat block. The temperature of the step in degrees Celsius. The duration of this step in seconds. The change of the temperature from one cycle to the next: actual temperature = temperature + (temperatureChange * cycle counter) The change of the duration from one cycle to the next: actual duration = duration + (durationChange * cycle counter) Indicates to make a measurement and store it as meltcurve or real-time data. The allowed temperature change from one step to the next in degrees Celsius per second. No value means maximal change rate. Concentration of the template in nanogram per microliter in the final reaction mix. A cycling program for PCR or to amplify cDNA. The temperature in degrees Celsius of the lid during cycling. Reference to the person who made or uses this protocol. The steps a protocol runs through to amplify DNA. Reference to an external database, for example "GenBank". The ID of the entry within the external database, for example "AJ832138". The date and time stamp of the creation of this file. The date and time stamp of the last update of this file. xRefs within the sample types must be unique. Documentation references within the sample types must be unique. xRefs within the sample types must be unique. Documentation references within the target types must be unique. step nr within the thermalCyclingConditions must be unique. Documentation references within the thermalCyclingConditions types must be unique. Experimenter references within the thermalCyclingConditions types must be unique. run IDs within the experiment types must be unique. Documentation references within the experiment types must be unique.