Masterarbeit, Heidi Lischer

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== PGD: old versions ======

  * root element: <PGD>
  * microsat data are number of repeats
  * nucleotid data: just one loci in one tag (popLoci/ indLoci)! (If more than one loci: repeat the whole ind tag for every loci)
\\
  * stylesheet: {{stylesheet_data-format3.pdf|}}


===== 1. version: =====
\\
|  ^^^^  data type  ^^^^^^
^  block  ^ subtags ^^^ standard ^ DNA ^ SNP ^ Microsattelite ^ RFLP (AFLP) ^ Allel frequency ^
^^^^^^^^^^^
| header (attribute: title) | number_samples |||  x  |  x  |  x  |  x  |  x  |  x  |
| | data_type |||  x  |  x  |  x  |  x  |  x  |  x  |
| | number_loci | number ||  x  |  x  |  x  |  x  |  x  | | 
| || loci (attribute: name) | locations |  o  |  o  |  o  |  o  |  o  | |
| ||| length |  o  |  o  |  o  |  o  |  o  | |
| | missing |||  o  |  o  |  o  |  o  |  o  | |
| | gap |||  o  |  o  |  o  |  o  |  o  | |
| | gametic_phase |||  o  |  o  |  o  |  o  |  o  | |
| | recessive_alleles |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| sample (attribute: name) | size |||  x  |  x  |  x  |  x  |  x  |  x  |
| | id (attribute: name) | frequency ||  x  |  x  |  x  |  x  |  x  |  x  |
| || loci (attribute: name) //(when unaligned)// | position |    |  o  |  o  |    |  o  | |
| ||| genotype/haplotype (a) |    |  x(a)  |  x(a)  |   |  x(a)  | | 
| || genotype/haplotype (a) (attribute: name) //(when aligned)// | |  x  |  x(a)  |  x(a)  |  x  |  x(a)  | |
^^^^^^^^^^^
| structure (attribute: name) | number_groups |||  o  |  o  |  o  |  o  |  o  | |
| | group (attribute: name) //(sample name, sample name)// |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| distance_matrix (attribute: name) | size |||  o  |  o  |  o  |  o  |  o  | |
| | lables |||  o  |  o  |  o  |  o  |  o  | |
| | matrix |||  o  |  o  |  o  |  o  |  o  | |

x: obligatory\\
o: optional\\
a: alternative\\



\\
===== 2. version: =====
\\
|  ^^^^  data type  ^^^^^^
^  block  ^ subtags ^^^ standard ^ DNA ^ SNP ^ Microsattelite ^ RFLP (AFLP) ^ Allel frequency ^
^^^^^^^^^^^
| header (attribute: title) | number_population |||  x  |  x  |  x  |  x  |  x  |  x  |
| | data_type |||  x  |  x  |  x  |  x  |  x  |  x  |
| | number_loci* | number ||  x  |  x  |  x  |  x  |  x  | | 
| || loci (attribute: name) | locations |  o  |  o  |  o  |  o  |  o  | |
| ||| length |  o  |  o  |  o  |  o  |  o  | |
| | missing |||  o  |  o  |  o  |  o  |  o  | |
| | gap |||  o  |  o  |  o  |  o  |  o  | |
| | gametic_phase |||  o  |  o  |  o  |  o  |  o  | |
| | recessive_alleles |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| population (attribute: name) | size |||  x  |  x  |  x  |  x  |  x  |  x  |
| | geographic_coord |||  o  |  o  |  o  |  o  |  o  |  o  |
| | id (attribute: name) (a3) | frequency ||  x  |  x  |  x  |  x  |  x  |  x  |
| || loci (attribute: name) //(when unaligned)// | location |    |  o  |  o  |    |  o  | |
| ||| begin |   |  o  |  o  |   |  o  | |
| ||| length |   |  o  |  o  |   |  o  | |
| ||| genotype/haplotype (a1) |    |  x (a1)  |  x (a1)  |   |  x (a1)  | | 
| || genotype/haplotype (a1) (attribute: name) //(when aligned)// ||  x  |  x (a1)  |  x (a1)  |  x  |  x (a1)  | |
| | ind (attribute: name) (a3) | geographic_coord ||  o  |  o  |  o  |  o  |  o  |  o  |
| || loci (attribute: name) //(when unaligned)// | location |    |  o  |  o  |    |  o  | |
| ||| begin |   |  o  |  o  |   |  o  | |
| ||| length |   |  o  |  o  |   |  o  | |
| ||| genotype/haplotype (a2) |    |  x (a2)  |  x (a2)  |   |  x (a2)  | | 
| || genotype/haplotype (a2) (attribute: name) //(when aligned)// ||  x  |  x (a2)  |  x (a2)  |  x  |  x (a2)  | |
^^^^^^^^^^^ 
| structure (attribute: name) | number_groups |||  o  |  o  |  o  |  o  |  o  | |
| | group (attribute: name) //(sample name, sample name)// |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| distance_matrix (attribute: name) | size |||  o  |  o  |  o  |  o  |  o  | |
| | lables |||  o  |  o  |  o  |  o  |  o  | |
| | matrix |||  o  |  o  |  o  |  o  |  o  | |

* when for all populations the same\\
x: obligatory\\
o: optional\\
a: alternative to\\

\\

===== 3. version: =====
\\
|  ^^^^  data type  ^^^^^^
^  block  ^ subtags ^^^ standard ^ DNA ^ SNP ^ Microsattelite ^ RFLP (AFLP) ^ Allel frequency ^
^^^^^^^^^^^
| **header** (attribute: title) | number_populations |||  x  |  x  |  x  |  x  |  x  |  x  |
| | data_type |||  x  |  x  |  x  |  x  |  x  |  x  |
| | number_loci * | number ||  x  |  x  |  x  |  x  |  x  | | 
| || loci (attribute: name) | location |  o  |  o  |  o  |  o  |  o  | |
| ||| length |  o  |  o  |  o  |  o  |  o  | |
| | gene_copies * |||  x  |  x (a1)  |  x (a1)  |  x  |  x (a1)  | |
| | aligned |||  x  |  x  |  x  |  x  |  x  | |
| | genotypic_data |||  x  |  x  |  x  |  x  |  x  | |
| | missing |||  x  |  x  |  x  |  x  |  x  | |
| | gap |||  x  |  x  |  x  |  x  |  x  | |
| | gametic_phase |||  o  |  o  |  o  |  o  |  o  | |
| | recessive_alleles |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| **population** (attribute: name) | size |||  x  |  x  |  x  |  x  |  x  |  x  |
| | geographic_coord |||  o  |  o  |  o  |  o  |  o  |  o  |
| | linguistic_group |||  o  |  o  |  o  |  o  |  o  |  o  |
| | id (attribute: name) (a3) | frequency ||  x  |  x  |  x  |  x  |  x  |  x  |
| || genotype/haplotype (attribute: name) ||  x  |  x  |  x  |  x  |  x  | |
| | ind (attribute: name) (a3) | geographic_coord ||  o  |  o  |  o  |  o  |  o  | |
| || linguistic_group ||  o  |  o  |  o  |  o  |  o  | |
| || loci (attribute: name) //(when unaligned)// | location |    |  o  |  o  |    |  o  | |
| ||| begin |   |  o  |  o  |   |  o  | |
| ||| length |   |  o  |  o  |   |  o  | |
| ||| gene_copies |   |  x (a1)  |  x (a1)  |   |  x (a1)  | |
| ||| genotype/haplotype (a2) |    |  x (a2)  |  x (a2)  |   |  x (a2)  | | 
| || genotype/haplotype (a2) (attribute: name) //(when aligned)// ||  x  |  x (a2)  |  x (a2)  |  x  |  x (a2)  | |
^^^^^^^^^^^ 
| **structure** (attribute: name) | number_groups |||  o  |  o  |  o  |  o  |  o  |  o  |
| | group (attribute: name) //(sample name, sample name, ...)// |||  o  |  o  |  o  |  o  |  o  |  o  |
^^^^^^^^^^^
| **distance_matrix** (attribute: name) | size |||  o  |  o  |  o  |  o  |  o  |  o  |
| | labels |||  o  |  o  |  o  |  o  |  o  |  o  |
| | matrix //(number (line break)  number, number (line break)...)// |||  o  |  o  |  o  |  o  |  o  |  o  |

* when for all populations the same\\
x: obligatory\\
o: optional\\
a: alternative to\\



\\


===== 4. version: =====
\\
|  ^^^^  data type  ^^^^^^
^  block  ^ subtags ^^^ standard ^ DNA ^ SNP ^ Microsattelite ^ RFLP (AFLP) ^ Allel frequency ^
^^^^^^^^^^^
| **header** (attribute: title) | number_populations |||  x  |  x  |  x  |  x  |  x  |  x  |
| | data_type |||  x  |  x  |  x  |  x  |  x  |  x  |
| | number_loci * | number ||  x  |  x  |  x  |  x  |  x  | | 
| || loci (attribute: name) | location |  o  |  o  |  o  |  o  |  o  | |
| ||| length |  o  |  o  |  o  |  o  |  o  | |
| | number_strains * |||  x  |  x (a1)  |  x (a1)  |  x  |  x (a1)  | |
| | aligned |||  x  |  x  |  x  |  x  |  x  | |
| | genotypic_data |||  x  |  x  |  x  |  x  |  x  | |
| | missing |||  x  |  x  |  x  |  x  |  x  | |
| | gap |||  x  |  x  |  x  |  x  |  x  | |
| | gametic_phase |||  o  |  o  |  o  |  o  |  o  | |
| | recessive_alleles |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| **population** (attribute: name) //aligned// (a2) | size |||  x  |  x  |  x  |  x  |  x  |  x  |
| | geographic_coord * |||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o  |
| | linguistic_group * |||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o  |
| | number_strains * |||  o (a1)  |  o (a1)  |  o (a1)  |  o (a1)  |  o (a1)  | |
| | id (attribute: name) (a3) | frequency ||  x  |  x  |  x  |  x  |  x  |  x  |
| || genotype/haplotype (attribute: name) //(loci, loci,...)// ||  x  |  x  |  x  |  x  |  x  | |
| | ind (attribute: name) (a3) | geographic_coord ||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o  | |
| || linguistic_group ||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  | |
| || number_strains ||  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  | |
| || genotype/haplotype (attribute: name) //(loci, loci,...)// ||  x  |  x  |  x  |  x  |  x  | |
^^^^^^^^^^^ 
| **population** (attribute: name) //unaligned// (a2) | size ||| |  x  |  x  | |  x  | |
| | geographic_coord * ||| |  o (a6)  |  o (a6)  | |  o (a6)  | |
| | linguistic_group * ||| |  o (a7)  |  o (a7)  | |  o (a7)  | |
| | loci_location (attribute: name) * ||| |  o (a8)  |  o (a8)  | |  o (a8)  | |
| | number_strains * ||| |  o (a9)  |  o (a9)  | |  o (a9)  | |
| | ind (attribute: name) | geographic_coord || |  o (a6)*<sup>3</sup>  |  o (a6)*<sup>3</sup>  |  |  o (a6)*<sup>3</sup>  | |
| || linguistic_group || |  o (a7)*<sup>3</sup>  |  o (a7)*<sup>3</sup>  | |  o (a7)*<sup>3</sup>  | |
| || loci_location (attribute: name)*<sup>2</sup> || |  o (a8)*<sup>3</sup>  |  o (a8)*<sup>3</sup>  | |  o (a8)*<sup>3</sup>  | |
| || number_strains || |  x (a9)  |  x (a9)  | |  x (a9)  | |
| || strain (attribute: name) | begin | |  x  |  x  | |  x  | |
| ||| length | |  x  |  x  | |  x  | |
| ||| genotype/haplotype | |  x  |  x  | |  x  | |
^^^^^^^^^^^ 
| **structure** (attribute: name) (o) | number_groups |||  x  |  x  |  x  |  x  |  x  |  x  |
| | group (attribute: name) //(sample name, sample name, ...)// |||  x  |  x  |  x  |  x  |  x  |  x  |
^^^^^^^^^^^
| **distance_matrix** (attribute: name) (o) | size |||  x  |  x  |  x  |  x  |  x  |  x  |
| | labels |||  x  |  x  |  x  |  x  |  x  |  x  |
| | matrix //(number (line break)  number, number (line break)...)// |||  x  |  x  |  x  |  x  |  x  |  x  |

* when for all populations/individuals the same\\
*<sup>2</sup> if it exist --> align DNA over one individual, if it not exist --> align DNA over one population\\
*<sup>3</sup> if for one individual defined, it has to be defined for all individuals\\
x: obligatory\\
o: optional\\
a: alternative to\\


\\


===== 5. version: =====
\\
|  ^^^^  data type  ^^^^^^
^  block  ^ subtags ^^^ standard ^ DNA ^ SNP ^ Microsattelite ^ RFLP (AFLP) ^ Allel frequency ^
^^^^^^^^^^^
| **header** (attribute: title) | nb_pop |||  x  |  x  |  x  |  x  |  x  |  x  |
| | data_type |||  x  |  x  |  x  |  x  |  x  |  x  |
| | loci (o) * | nb ||  x  |  x  |  x  |  x  |  x  | | 
| || locus (attribute: id) | location |  x  |  x  |  x  |  x  |  x  | |
| ||| length |  o  |  o  |  o  |  o  |  o  | |
| ||| links |  o  |  o  |  o  |  o  |  o  | |
| | nb_reads * |||  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  | |
| | aligned |||  x  |  x  |  x  |  x  |  x  | |
| | geno_data |||  x  |  x  |  x  |  x  |  x  | |
| | missing |||  x  |  x  |  x  |  x  |  x  | |
| | gap |||  x  |  x  |  x  |  x  |  x  | |
| | gametic_phase |||  o  |  o  |  o  |  o  |  o  | |
| | recessive_alleles |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| **loci** (o) | nb |||  x  |  x  |  x  |  x  |  x  | |
| | locus (attribute: id) | location ||  x  |  x  |  x  |  x  |  x  | |
| || length ||  o  |  o  |  o  |  o  |  o  | |
| || links ||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| **population** (attribute: name) //aligned, same data type// (a2) | size |||  x  |  x  |  x  |  x  |  x  |  x  |
| | geo_coord * |||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o  |
| | linguistic_group * |||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o  |
| | nb_reads * |||  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  | |
| | loci //(locus, locus,...)// * |||  x  |  x  |  x  |  x  |  x  | |
| | id (attribute: name) (a3) | freq ||  x  |  x  |  x  |  x  |  x  |  x  |
| || geno/hap (attribute: name) //(locus, locus,...)// ||  x  |  x  |  x  |  x  |  x  | |
| | ind (attribute: name) (a3) | geo_coord ||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o  | |
| || linguistic_group ||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  | |
| || nb_reads ||  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  | |
| || geno/hap (attribute: name) //(locus, locus,...)// ||  x  |  x  |  x  |  x  |  x  | |
^^^^^^^^^^^ 
| **population** (attribute: name) //unaligned// (a2) | size ||| |  x  |  x  | |  x  | |
| | geo_coord * ||| |  o (a6)  |  o (a6)  | |  o (a6)  | |
| | linguistic_group * ||| |  o (a7)  |  o (a7)  | |  o (a7)  | |
| | locus (attribute: id)* ||| |  o (a8)  |  o (a8)  | |  o (a8)  | |
| | nb_reads * ||| |  o (a9)  |  o (a9)  | |  o (a9)  | |
| | ind (attribute: name) | geo_coord || |  o (a6)*<sup>3</sup>  |  o (a6)*<sup>3</sup>  |  |  o (a6)*<sup>3</sup>  | |
| || linguistic_group || |  o (a7)*<sup>3</sup>  |  o (a7)*<sup>3</sup>  | |  o (a7)*<sup>3</sup>  | |
| || locus (attribute: id)*<sup>2</sup> || |  o (a8)*<sup>3</sup>  |  o (a8)*<sup>3</sup>  | |  o (a8)*<sup>3</sup>  | |
| || nb_reads || |  x (a9)  |  x (a9)  | |  x (a9)  | |
| || read (attribute: name) | start | |  x  |  x  | |  x  | |
| ||| length | |  x  |  x  | |  x  | |
| ||| geno/hap | |  x  |  x  | |  x  | |
^^^^^^^^^^^ 
| **structure** (attribute: name) (o) | number_groups |||  x  |  x  |  x  |  x  |  x  |  x  |
| | group (attribute: name) //(sample name, sample name, ...)// |||  x  |  x  |  x  |  x  |  x  |  x  |
^^^^^^^^^^^
| **distance_matrix** (attribute: name) (o) | size |||  x  |  x  |  x  |  x  |  x  |  x  |
| | labels |||  x  |  x  |  x  |  x  |  x  |  x  |
| | matrix //(number (line break)  number, number (line break)...)// |||  x  |  x  |  x  |  x  |  x  |  x  |

* when for all populations/individuals the same\\
*<sup>2</sup> if it exist --> align DNA over one individual, if it not exist --> align DNA over one population\\
*<sup>3</sup> if for one individual defined, it has to be defined for all individuals\\

x: obligatory\\
o: optional\\
a: alternative to\\



\\


===== 6. version: =====
\\
|  ^^^^  data type  ^^^^^^
^  block  ^ subtags ^^^ standard ^ DNA ^ SNP ^ Microsattelite ^ RFLP (AFLP) ^ Allel frequency ^
^^^^^^^^^^^
| **header** (attribute: title) | organism |||  o  |  o  |  o  |  o  |  o  |  o  |
| | numPop |||  x  |  x  |  x  |  x  |  x  |  x  |
| | numReads * |||  x  |  x  |  x  |  x  |  x  | |
| | aligned |||  x  |  x  |  x  |  x  |  x  | |
| | missing |||  x  |  x  |  x  |  x  |  x  | |
| | gap |||  x  |  x  |  x  |  x  |  x  | |
| | gameticPhase |||  o  |  o  |  o  |  o  |  o  | |
| | recessiveData |||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| **loci** (o) | lociNum |||  x  |  x  |  x  |  x  |  x  | |
| | lociDataType * |||  x (a10)  |  x (a10)  |  x (a10)  |  x (a10)  |  x (a10)  |  x  |
| | locus (attribute: id) | locusDataType ||  a10  |  a10  |  a10  |  a10  |  a10  | |
| || locusChromosom ||  o  |  o  |  o  |  o  |  o  | |
| || locusLocation ||  o  |  o  |  o  |  o  |  o  | |
| || locusGenic ||  o  |  o  |  o  |  o  |  o  | |
| || locusLength ||  o  |  o  |  o  |  o  |  o  | |
| || locusLinks ||  o  |  o  |  o  |  o  |  o  | |
| || locusComments ||  o  |  o  |  o  |  o  |  o  | |
^^^^^^^^^^^
| **population** (attribute: name) //aligned, same data type// (a2) | popSize |||  x  |  x  |  x  |  x  |  x  |  x  |
| | popGeogCoord * |||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o  |
| | popLingGroup * |||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o  |
| | popNumReads * |||  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  | |
| | popLoci //(locus, locus,...)// * |||  x  |  x  |  x  |  x  |  x  | |
| | ind (attribute: name) (a3) | indGeogCoord ||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o  | |
| || indLingGroup ||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  | |
| || indNumReads ||  a1  |  a1  |  a1  |  a1  |  a1  | |
| || indFreq //(absolute Freq)// ||  o  |  o  |  o  |  o  |  o  |  x  |
| || data //(locus, locus,...)// ||  x  |  x  |  x  |  x  |  x  | |
^^^^^^^^^^^
| **population** (attribute: name) //aligned, diff data type// (a2) | popSize |||  x  |  x  |  x  |  x  |  x  | |
| | popGeogCoord * |||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  | |
| | popLingGroup * |||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  | |
| | popNumReads * |||  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  |  x (a1)  | |
| | ind (attribute: name) (a3) | indGeogCoord ||  o (a4)  |  o (a4)  |  o (a4)  |  o (a4)  |  o  | |
| || indLingGroup ||  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  |  o (a5)  | |
| || indLoci //(locus, locus,...)// ||  x  |  x  |  x  |  x  |  x  | |
| || indNumReads ||  a1  |  a1  |  a1  |  a1  |  a1  | |
| || indFreq //(absolute Freq)// ||  o  |  o  |  o  |  o  |  o  |  x  |
| || data //(locus, locus,...)// ||  x  |  x  |  x  |  x  |  x  | |
^^^^^^^^^^^ 
| **population** (attribute: name) //unaligned// (a2) | popSize ||| |  x  | | | | |
| | popGeogCoord * ||| |  o (a6)  | | | | |
| | popLingGroup * ||| |  o (a7)  | | | | |
| | popNumReads * ||| |  x (a9)  | | | | |
| | popLocus * ||| |  o (a8)  | | | | |
| | ind (attribute: name) | indGeogCoord || |  o (a6)  | | | | |
| || indLingGroup || |  o (a7)  | | | | |
| || indLocus *<sup>2</sup> || |  o (a8)  | | | | |
| || indFreq //(absolute Freq)// || |  o  | | | | |
| || indNumReads || |  a9  | | | | |
| || read | start | |  x (if unalig.)  | | | | |
| ||| length | |  o  | | | | |
| ||| data | |  x  | | | | |
^^^^^^^^^^^ 
| **structure** (attribute: name) (o) | numGroups |||  x  |  x  |  x  |  x  |  x  |  x  |
| | group (attribute: name) //(sample name, sample name, ...)// |||  x  |  x  |  x  |  x  |  x  |  x  |
^^^^^^^^^^^
| **distanceMatrix** (attribute: name) (o) | matrixSize |||  x  |  x  |  x  |  x  |  x  |  x  |
| | matrixLabels //(name, name,...)// |||  x  |  x  |  x  |  x  |  x  |  x  |
| | matrix //(number (line break)  number, number (line break)...)// |||  x  |  x  |  x  |  x  |  x  |  x  |

* when for all populations/individuals the same\\
*<sup>2</sup> if it exist --> align DNA over one individual, if it not exist --> align DNA over one population\\

x: obligatory\\
o: optional\\
a: alternative to\\