[LON-CAPA-cvs] cvs: modules /gerd/harvesting finalize.pl taxonomy.dat

[www]

www		Wed Sep 28 01:37:43 2011 EDT

  Modified files:              
    /modules/gerd/harvesting	finalize.pl taxonomy.dat 
  Log:
  UIUC biology taxonomy
  
  
Index: modules/gerd/harvesting/finalize.pl
diff -u modules/gerd/harvesting/finalize.pl:1.3 modules/gerd/harvesting/finalize.pl:1.4
--- modules/gerd/harvesting/finalize.pl:1.3	Thu Sep 15 21:17:48 2011
+++ modules/gerd/harvesting/finalize.pl	Wed Sep 28 01:37:43 2011
@@ -3,6 +3,10 @@
 open(IN,"combined_taxonomy.dat");
 while (my $line=<IN>) {
    chomp($line);
+#  Obsolete
+   $line=~s/\:replitrans/\:replication/g;
+#
+
    my ($idx,$tax)=split(/\t/,$line);
    my %lev1=();
    my %lev2=();
@@ -65,6 +69,7 @@
       }
    }
    if (($win2) && ($win2=~/^$win1/)) { undef($win1); }
+   if (($win3) && ($win3=~/^$win1/)) { undef($win1); }
    if (($win3) && ($win3=~/^$win2/)) { undef($win2); }
    my @winners=();
    foreach my $win ($win1,$win2,$win3) {
Index: modules/gerd/harvesting/taxonomy.dat
diff -u modules/gerd/harvesting/taxonomy.dat:1.10 modules/gerd/harvesting/taxonomy.dat:1.11
--- modules/gerd/harvesting/taxonomy.dat:1.10	Tue Sep 27 12:42:06 2011
+++ modules/gerd/harvesting/taxonomy.dat	Wed Sep 28 01:37:43 2011
@@ -76,17 +76,17 @@
 biology:introduction:domains
 biology:introduction:phylogeny
 biology:introduction:selection
-biology:introduction:scientific_method
+biology:introduction:scientificmethod
 biology:introduction:elements
 biology:introduction:energy
 biology:introduction:bonds
 biology:introduction:water
-biology:introduction:pH
-biology:introduction:organic_chemistry
+biology:introduction:ph
+biology:introduction:organicchemistry
 biology:introduction:carbohydrates
 biology:introduction:lipids
 biology:introduction:proteins
-biology:introduction:nucleic_acids
+biology:introduction:nucleicacids
 biology:introduction:microscopy
 biology:introduction:cells
 biology:cells:structure	volume,function,structure,cell,area,cell,cells,radius,round,solid,spherical,surface,volume,membrane
@@ -107,14 +107,14 @@
 biology:cells:enzymes
 biology:cells:signaling
 biology:cells:mitosis
-biology:cells:cell_cycle
+biology:cells:cellcycle
 biology:cells:meiosis
 biology:cells:bacteria
-biology:cells:protein_structure
-biology:cells:protein_function
+biology:cells:proteinstructure
+biology:cells:proteinfunction
 biology:genetics:genes
 biology:genetics:mendel
-biology:genetics:mendelian_genetics
+biology:genetics:mendeliangenetics
 biology:genetics:inheritance
 biology:genetics:recombination
 biology:genetics:disorders
@@ -125,10 +125,10 @@
 biology:genetics:regulation
 biology:genetics:viruses
 biology:genetics:biotechnology
-biology:genetics:recombinant_dna
+biology:genetics:recombinantdna
 biology:genetics:genomics
 biology:genetics:bioinformatics
-biology:genetics:hardy_weinberg
+biology:genetics:hardyweinberg
 biology:organisms:protists
 biology:organisms:plants
 biology:organisms:fungi
@@ -218,10 +218,21 @@
 ecology:climate
 ecology:biomes
 ecology:populations
-ecology:life_history
+ecology:lifehistory
 ecology:community
 ecology:diversity
 ecology:ecosystems
 ecology:production
 ecology:conservation
 nutrition
+biochemistry:glycolysis
+biochemistry:gluconeogenesis
+biochemistry:pentose_phosphate_pathway
+biochemistry:citric_acid_cycle
+biochemistry:fatty_acid_catabolism
+biochemistry:amino_acid_catabolism
+biochemistry:urea_cycle
+biochemistry:oxidative_phosphorylation
+biochemistry:biosynthesis
+biochemistry:kinetics
+biochemistry:mechanisms