Commit 1705bbfe authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

More taxonomic exceptions

parent 4eef4a91
...@@ -16,42 +16,46 @@ my $ncbi_aa = 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id= ...@@ -16,42 +16,46 @@ my $ncbi_aa = 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=
my $uniprot = 'http://www.uniprot.org/uniprot/'; my $uniprot = 'http://www.uniprot.org/uniprot/';
my $pdb = 'http://www.pdb.org/pdb/explore/explore.do?structureId='; my $pdb = 'http://www.pdb.org/pdb/explore/explore.do?structureId=';
my %species = ( 'alfalfa' => '', my %species = ( 'alfalfa' => '',
'baboon' => '', 'baboon' => '',
'barley' => '', 'barley' => '',
'bovine' => '', 'bovine' => '',
'cat' => '', 'cat' => '',
'chicken' => '', 'chicken' => '',
'dog' => '', 'cow' => '',
'goat' => '', 'dog' => '',
'gorilla' => '', 'duck' => '',
'hiv-1' => '', 'goat' => '',
'hiv1' => '', 'gorilla' => '',
'hiv' => '', 'hiv-1' => '',
'horse' => '', 'hiv1' => '',
'hsv1' => '', 'hiv' => '',
'human' => '', #All in lowercase 'horse' => '',
'maize' => '', 'hsv1' => '',
'mouse' => '', 'human' => '', #All in lowercase
'oat' => '', 'maize' => '',
'pea' => '', 'mouse' => '',
'pig' => '', 'oat' => '',
'porcine' => '', 'pea' => '',
'potato' => '', 'pig' => '',
'pumpkin' => '', 'porcine' => '',
'rabbit' => '', 'potato' => '',
'rat' => '', 'pumpkin' => '',
'rats' => '', 'rabbit' => '',
'rice' => '', 'rat' => '',
'sheep' => '', 'rats' => '',
'soybean' => '', 'rice' => '',
'soybeans' => '', 'salamander' => '',
'spinach' => '', 'salmon' => '',
'sunflower' => '', 'sheep' => '',
'tobacco' => '', 'soybean' => '',
'wheat' => '', 'soybeans' => '',
'yeast' => '', 'spinach' => '',
'zebrafish' => '', 'sunflower' => '',
'tobacco' => '',
'wheat' => '',
'yeast' => '',
'zebrafish' => '',
); );
my %nonSpecies = ( 'mRNA' => '', my %nonSpecies = ( 'mRNA' => '',
'cDNA' => '', 'cDNA' => '',
...@@ -137,6 +141,7 @@ my %Strain = ('biogroup' => '', ...@@ -137,6 +141,7 @@ my %Strain = ('biogroup' => '',
'cv.' => '', 'cv.' => '',
'cv' => '', 'cv' => '',
'f.' => '', #Volvox carteri f. nagariensis = forma 'f.' => '', #Volvox carteri f. nagariensis = forma
'forma' => '',
'genotype' => '', 'genotype' => '',
'group' => '', 'group' => '',
'haplogroup' => '', 'haplogroup' => '',
...@@ -176,16 +181,23 @@ my %large_names = ( 'MNPV' => '', ...@@ -176,16 +181,23 @@ my %large_names = ( 'MNPV' => '',
'virus' => '', #FIXME: Highlight also (... virus \d\w*) 'virus' => '', #FIXME: Highlight also (... virus \d\w*)
); );
my %longer_species_name = ( 'corporis' => '', my %longer_species_name = ( 'andium' => '', #Anas flavirostris andium
'corporis' => '',
'coturnix' => '', #Coturnix coturnix japonica 'coturnix' => '', #Coturnix coturnix japonica
'crecca' => '', #Anas crecca crecca
'domestica' => '', 'domestica' => '',
'domesticus' => '', 'domesticus' => '',
'familiaris' => '', 'familiaris' => '',
'flavirostris' => '', #Anas flavirostris flavirostris
'fretensis' => '', #Anas versicolor fretensis
'gallus' => '', 'gallus' => '',
'gorilla' => '', 'gorilla' => '',
'pseudoobscura' => '', 'pseudoobscura' => '',
'quinquefasciatus' => '', 'quinquefasciatus' => '',
'septentrionalium' => '', #Anas cyanoptera septentrionalium
'Sprague-Dawley' => '', #Rattus norvegicus Sprague-Dawley
'sp.' => '', 'sp.' => '',
'versicolor' => '', #Anas versicolor versicolor
'yoelii' => '', 'yoelii' => '',
'x' => '', 'x' => '',
); );
......
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