Differences

This shows you the differences between two versions of the page.

--- pgd [2011/07/07 15:52] – heidi
+++ pgd [2011/10/12 13:19] – heidi
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 Version 1.0\\
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-PGD (Population Genetics Data) is a file format designed to contain population genetics data. The aim of this format is to facilitate the transfer among several population genetics software packages. PGD plays an important role in the new data format converter PGDSpider.
+PGD (Population Genetics Data) is a file format designed to contain population genetics data. The aim of this format is to facilitate the transfer among several population genetics software packages. PGD plays an important role in the new data format converter PGDSpider.\\
-PGD is written in XML and is therefore independent of any particular computer system and extensible for future needs. The XML structure can easily be processed by computer programs. An additional XSLT style sheet makes it possible to display the data in an understandable and comprehensive way. This XSLT style sheet is delivered within the PGDSpider download.
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+PGD is written in XML and is therefore independent of any particular computer system and extensible for future needs. The XML structure can easily be processed by computer programs. An additional XSLT style sheet makes it possible to display the data in an understandable and comprehensive way. This XSLT style sheet is delivered within the PGDSpider download.\\
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+The PGDSpider distribution also includes an XML Schema (PGD_schema.xsd), which defines the structure of the PGD file. The purpose of an XML Schema is to define the legal building blocks of an XML document and the allowable contents (W3Schools, 2008). The provided XML Schema can be used to validate a PGD file.
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 PGD is able to handle following data types:
   * DNA
-  * UHTS (Ultra High-Throughput Sequencing data)
+  * NGS (Next-Generation Sequencing data)
   * Microsat (coded as number of repeats!)
   * RFLP
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 ==== Header block: ====
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     * Value: Character
     * Character which codes missing values
-  * <gap> (mandatory):
+  * <gap> (optional):
     * Value: Character
     * Character which codes gaps
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   * distanceMatrix: lower triangle with diagonal
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 | **header** (attribute: title) | organism |||  o  |  o  |  o  |
 | | numPop |||  x  |  x  |  x  |
-| | ploidy * //(--> mixed/1/2/...)//|||  x (a5)  |  x (a5)  | |
+| | ploidy * //(--> mixed/1/2/...)//|||  x (a4)  |  x (a4)  | |
 | | missing |||  x  |  x  | |
-| | gap |||  x  |  x  | |
+| | gap |||  o  |  o  | |
 | | gameticPhase //(--> known/unknown)//|||  o  |  o  | |
 | | recessiveData //(--> yes/no)//|||  o  |  o  | |
 ^^^^^^^^^^^
 | **dataDescription** (o) | numLoci |||  x  |  x  | |
-| | dataType * //(--> mixed/DNA/NGS/Microsat/RFLP/AFLP/Standard/Frequency/...)//|||  x (a2)  |  x (a2)  |  x  |
+| | dataType * //(--> mixed/DNA/NGS/Microsat/RFLP/AFLP/Standard/Frequency/...)//|||  x (a1)  |  x (a1)  |  x  |
-| | locus (attribute: id) | locusDataType //(--> DNA/NGS/Microsat/RFLP/AFLP/Standard/Frequency/...)//||  a2  |  a2  | |
+| | locus (attribute: id) | locusDataType //(--> DNA/NGS/Microsat/RFLP/AFLP/Standard/Frequency/...)//||  a1  |  a1  | |
 | || locusChromosome //(--> number/X/Y/W/Z/mtDNA/...)//||  o  |  o  | |
 | || locusLocation ||  o  |  o  | |
 | || locusGenic //(--> coding/noncoding)// ||  o  |  o  | |
 | || locusLength ||  o  |  o  | |
-| || locusLinks ||  o  |  o  | |
+| || locusLinks //(--> URL)// ||  o  |  o  | |
 | || locusComments ||  o  |  o  | |
 ^^^^^^^^^^^
 | **population** (attribute: name) | popSize |||  x  |  x  |  x  |
-| | popGeogCoord * //(lon, lat)//|||  o (a3)  |  o (a3)  |  o  |
+| | popGeogCoord * //(lon, lat)//|||  o (a2)  |  o (a2)  |  o  |
-| | popLingGroup * |||  o (a4)  |  o (a4)  |  o  |
+| | popLingGroup * |||  o (a3)  |  o (a3)  |  o  |
-| | popPloidy * //(--> mixed/1/2/...)//|||  x (a5)  |  x (a5)  | |
+| | popPloidy * //(--> mixed/1/2/...)//|||  a4  |  a4  | |
 | | popLoci *<sup>3</sup> //(locus name, locus name,...) --> all locus of same data type// |||  o  |  o  | |
-| | ind (attribute: name) | indGeogCoord //(lon, lat)//||  o (a3)  |  o (a3)  | |
+| | ind (attribute: name) | indGeogCoord //(lon, lat)//||  o (a2)  |  o (a2)  | |
-| || indLingGroup ||  o (a4)  |  o (a4)  | |
+| || indLingGroup ||  o (a3)  |  o (a3)  | |
-| || indLoci *<sup>4</sup> //(locus name, locus name, ...) --> all locus of same data type// ||  x  |  x  | |
+| || indLoci *<sup>4</sup> //(locus name, locus name, ...) --> all locus of same data type// ||  o  |  o  | |
-| || indPloidy //(-->1/2/...)//||  a5  |  a5  | |
+| || indPloidy //(-->1/2/...)//||  a4  |  a4  | |
 | || indFreq //(absolute Freq)// ||  o  |  o  |  x  |
-| || data *<sup>7</sup> //(locus data, locus data, ...)// ||  x  |  x  | |
+| || data *<sup>5</sup> //(locus data, locus data, ...)// ||  x  |  x  | |
-| || read *<sup>8</sup> | start *<sup>8</sup> | |  x   | |
+| || read *<sup>6</sup> (attribute: id) | start *<sup>6</sup> | |  x   | |
-| ||| length *<sup>8</sup> | |  o  | |
+| ||| length *<sup>6</sup> | |  o  | |
-| ||| data *<sup>8</sup> | |  x  | |
+| ||| data *<sup>6</sup> | |  x  | |
-| ||| quality *<sup>8</sup> | |  o  | |
+| ||| quality *<sup>6</sup> | |  o  | |
 ^^^^^^^^^^^
 | **structure** (attribute: name) (o) | numGroups |||  x  |  x  |  x  |
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 | | matrixLabels //(name, name,...)// |||  x  |  x  |  x  |
 | | matrix //(number (line break)  number, number (line break)...)// |||  x  |  x  |  x  |
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 *<sup>3</sup> data of the same data type (loci) in all individuals\\
 *<sup>4</sup> data of different data types (aligned within each locus)\\
-*<sup>7</sup> non-NGS data\\
+*<sup>5</sup> non-NGS data\\
-*<sup>8</sup> NGS data (Next Generation Sequencing)\\
+*<sup>6</sup> NGS data (Next Generation Sequencing)\\
 x: obligatory\\
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 ===== PGD file examples: =====
-  * aligned data: [[PGD_aligned]]
+  * Data of two loci with Standard data type from four diploid populations: [[PGD_standard]]
-  * alinged data with different data types: [[PGD_aligned_DiffDataTypes]]
+  * Data of two loci with different data types (Standard and DNA) from two diploid populations: [[PGD_diffDataTypes]]
-  * UHTS data with mixed number of repeats: [[PGD_unaligned_mixedReads]]
+  * NGS data of two loci from three haploid populations: [[PGD_NGS]]
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