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

www www at source.lon-capa.org
Tue Sep 13 15:45:04 EDT 2011


www		Tue Sep 13 19:45:04 2011 EDT

  Modified files:              
    /modules/gerd/harvesting	problem_taxonomy.pl seq_taxonomy.pl 
                            	taxonomy.dat 
  Log:
  Probably about as far as one gets from using the sequences
  
  
-------------- next part --------------
Index: modules/gerd/harvesting/problem_taxonomy.pl
diff -u modules/gerd/harvesting/problem_taxonomy.pl:1.2 modules/gerd/harvesting/problem_taxonomy.pl:1.3
--- modules/gerd/harvesting/problem_taxonomy.pl:1.2	Sat Sep 10 03:19:01 2011
+++ modules/gerd/harvesting/problem_taxonomy.pl	Tue Sep 13 19:45:04 2011
@@ -1,5 +1,7 @@
 use strict;
 
+# Read the sequence taxonomy
+
 my %st=();
 open(IN,'seq_taxonomy.dat');
 while (my $line=<IN>) {
@@ -20,43 +22,44 @@
 }
 close(IN);
 
-# Debug/learning only
-my @urlkey=();
-
-open(IN,'resource.dat');
-while (my $line=<IN>) {
-   my @entries=split(/\t/,$line);
-   $entries[4]=~s/^\/res\/\w+\/\w+\///;
-   $entries[4]=~s/\.\w+$//;
-   my %poskeys=();
-   foreach my $poskey (split(/[^A-Za-z]+/,$entries[4])) {
-      if (length($poskey)>3) {
-         $poskeys{lc($poskey)}=1;
-      }
-   }
-   $urlkey[$entries[0]]=join(',',keys(%poskeys));
-
-}
-close(IN);
-
-
-my @keywords=();
-
-my $keystr='';
-my ($id,$key)=(1,'');
-open(IN,'keywords.dat');
-while (my $line=<IN>) {
-   my $oid=$id;
-   chomp($line);
-   ($id,$key)=split(/\t/,$line);
-   if ($id!=$oid) {
-      $keystr=~s/^\,//;
-      $keywords[$oid]=$keystr;
-      $keystr=$urlkey[$id];
-   }
-   $keystr.=','.lc($key);
-}
-close(IN);
+#my @urlkey=();
+#my @url=();
+#
+#open(IN,'resource.dat');
+#while (my $line=<IN>) {
+#   my @entries=split(/\t/,$line);
+#   $url[$entries[0]]=$entries[4];
+#   $entries[4]=~s/^\/res\/\w+\/\w+\///;
+#   $entries[4]=~s/\.\w+$//;
+#   my %poskeys=();
+#   foreach my $poskey (split(/[^A-Za-z]+/,$entries[4])) {
+#      if (length($poskey)>3) {
+#         $poskeys{lc($poskey)}=1;
+#      }
+#   }
+#   $urlkey[$entries[0]]=join(',',keys(%poskeys));
+#
+#}
+#close(IN);
+
+
+#my @keywords=();
+#
+#my $keystr='';
+#my ($id,$key)=(1,'');
+#open(IN,'keywords.dat');
+#while (my $line=<IN>) {
+#   my $oid=$id;
+#   chomp($line);
+#   ($id,$key)=split(/\t/,$line);
+#   if ($id!=$oid) {
+#      $keystr=~s/^\,//;
+#      $keywords[$oid]=$keystr;
+#      $keystr=$urlkey[$id];
+#   }
+#   $keystr.=','.lc($key);
+#}
+#close(IN);
 
 for (my $i=0; $i<=$#taxo; $i++) {
    my %taxh=();
@@ -73,5 +76,8 @@
    }
    $taxout=~s/^\,//;
    print $i."\t".$taxout."\n";
-   if ($j>1) { print "KEYS: $i $keywords[$i]\n"; }
+#   if (($j>1) || ($j==0)) { 
+#      print "KEYS: $i $keywords[$i]\n"; 
+#      print "URL: $i $url[$i]\n";
+#   }
 }
Index: modules/gerd/harvesting/seq_taxonomy.pl
diff -u modules/gerd/harvesting/seq_taxonomy.pl:1.5 modules/gerd/harvesting/seq_taxonomy.pl:1.6
--- modules/gerd/harvesting/seq_taxonomy.pl:1.5	Tue Sep 13 13:47:47 2011
+++ modules/gerd/harvesting/seq_taxonomy.pl	Tue Sep 13 19:45:04 2011
@@ -19,9 +19,9 @@
    }
    $catidx{$cat}=$i;
 # Debug
-   print ">-----$cats[$i]\n";
-   print "is: $iss[$i]\n";
-   print "is not: $isnots[$i]\n";
+#   print ">-----$cats[$i]\n";
+#   print "is: $iss[$i]\n";
+#   print "is not: $isnots[$i]\n";
 #
    $i++;
 }
@@ -33,7 +33,7 @@
    chomp($line);
    my ($seq,$subs,$keys)=split(/\t/,$line);
 
-   print "-------$subs $keys\n";
+#   print "-------$subs $keys\n";
 
    my %keysw=();
    foreach my $keyc (split(/\,/,$keys)) {
Index: modules/gerd/harvesting/taxonomy.dat
diff -u modules/gerd/harvesting/taxonomy.dat:1.6 modules/gerd/harvesting/taxonomy.dat:1.7
--- modules/gerd/harvesting/taxonomy.dat:1.6	Tue Sep 13 13:47:47 2011
+++ modules/gerd/harvesting/taxonomy.dat	Tue Sep 13 19:45:04 2011
@@ -4,10 +4,11 @@
 physics:mechanics:rotationalkinematics	rotation,turn,turning,angular,speed,velocity,acceleration,angle,angles,degree,degrees,radians,displacement,balance	work,force,torque,atom,quantum	
 physics:mechanics:lineardynamics	force,forces,free,diagram,acceleration,mass,newton,weight	torque,angle,angular,charge,magnetic,atom,quantum,work
 physics:mechanics:rotationaldynamics	torque,angular,acceleration,inertia,moment,rolling,rotate,rotation,rotating,rotational,torques	atom,quantum,momentum
+physics:mechanics:gravity	gravity,gravitational,gravitation,universal,newton,mass,field
 physics:mechanics:linearmomentum	momentum,velocity,mass,collision,collisions,elastic,inelastic,impulse	angular,atom,quantum,inertia,torque
 physics:mechanics:angularmomentum	momentum,velocity,angular,inertia,moment,torque	atom,quantum
 physics:mechanics:energy	energy,force,distance,work,potential,kinetic,gravitational,gravity	entropy,charge,atom,quantum,electric
-physics:mechanics:oscillation	period,frequency,resonance,amplitude,harmonic,spring,oscillation,oscillations,vibration,vibrations	wavelength,current
+physics:mechanics:oscillation	period,frequency,resonance,amplitude,harmonic,spring,oscillation,oscillations,vibration,vibrations,hooke,hookes,elongation	wavelength,current
 physics:mechanics:solidsfluids	archimedes,water,air,buoyant,buoyancy,float,floating,fluid,gas,liquid,bernoulli,floats,gravity,sink,sinks,sinking,flow,flows
 physics:mechanics:wave	period,frequency,wavelength,speed,node,antinode,nodes	sound,doppler
 physics:mechanics:sound	sound,frequency,wavelength,speed,doppler,pressure,air,hear,water,longitudinal	magnetic,electric,field
@@ -26,7 +27,7 @@
 physics:electromagnetism:emwaves	emwave,emwaves,magnetic,electric,field,speed,wavelength,frequency,amplitude,color,spectrum,pressure,radiation,intensity,polarization,polarized	lens,interference,sound,air,emf,force,static
 physics:optics:mirrorslenses	light,lens,mirror,lenses,mirrors,converging,focal,concave,convex,virtual,ray,reflection,diffraction,reflected,focus,eye,magnifying,power,incident,incidence,index,refraction,glass,inverted
 physics:optics:opticalinstruments	telescope,microscope,glasses,eyepiece,magnification,focus,light
-physics:optics:interference	slit,pattern,diffraction,interference,grating,maxima,slits,minima	quantum
+physics:optics:interference	slit,pattern,diffraction,interference,grating,maxima,slits,minima,laser	quantum
 physics:modern:relativity	frame,relative,dilation,contraction,time,space,transform,light,observer,speed,relativity,invariant,invariance,momentum,energy	lens,lenses,diffraction,eye,focus,friction
 physics:modern:quantum	spin,quantum,level,energy,black,body,bohr,heisenberg,atom,atoms,electron,electrons,wave,state,states,uncertainty,spectrum,line,photon,emission,absorption,emitted	isotope,nuclear,neutron,neutrons,compound
 physics:modern:nuclear	nucleus,proton,neutron,decay,halflife,atoms,atomic,fission,fusion,decays,protons,neutrons,isotope,radioactive,beta,gamma,activity,nuclear,mass,radiation,activity,alpha
@@ -47,9 +48,10 @@
 chemistry:reactions:rate	rate,time,catalyst,concentration,size,reactant,temperature,activation
 chemistry:reactions:reversible	equilibrium,reversible,keq,lechatelier,concentration,temperature
 chemistry:reactions:equations	balance,balanced,equation,equations,stoichiometry,reactant,reactants,stoichiometric,balancing
+chemistry:reactions:electrochem	anode,cathode,galvanic,electrochemistry,anodic,potential,electrode
 chemistry:matter:solutions	saturated,unsaturated,supersaturated,solution,solutions,concentration,ppm,ppb,molarity,dilute
 chemistry:matter:colloidssuspensions	suspension,colloid,colligative,osmosis,suspended,solution,dispersion,vapor,hypertonic
-chemistry:inorganic:acidsbases	acid,base,acids,bases,arrhenius,hydrogen,ion,water,ph,neutralization	
+chemistry:inorganic:acidsbases	acid,base,acids,bases,arrhenius,hydrogen,ion,water,ph,neutralization,titration	organic
 chemistry:organic:introduction	organic,carbon,hydrogen,oxygen
 chemistry:organic:orbitals	organic,orbital,orbitals,hybridization,bonding
 chemistry:organic:alkanes	organic,carbon,carbons,alkane,alkanes,alkyl
@@ -63,6 +65,7 @@
 chemistry:organic:proteins	organic,carbon,carbons,protein,proteins
 biology:introduction:classification	regio,domain,regnum,kingdom,phylum,division,classis,class,ordo,order,familia,family,genus,species
 biology:introduction:evolution	evolution,darwin,survival,mutation,mutations,genetic,gene,evolutionary,recombination,flow
+biology:cells:structure	volume,function,structure,cell,area,cell,cells,radius,round,solid,spherical,surface,volume,membrane
 biology:cells:organelles	cell,cells,organelle,organelles,eukaryotic,cytoskeleton,prokaryotic,endoplasmic,reticulum,golgi,mitochondria,lysosome
 biology:cells:respiration	cell,cells,respiration,anaerobic,aerobic,cell,metabolism,metabolic,atp,adenosine,triphosphate,catabolic
 biology:cells:photosynthesis	cell,cells,photons,photosynthesis,chloroplast
@@ -70,15 +73,30 @@
 biology:cells:dna	dna,helix,nucleic,acid,base,guanine,cytosine,adenine,thymine
 biology:cells:replitrans	replication,transcription,translation,dna,rna,mrna,chromosomes,chromosome
 biology:cells:regulation	cell,cells,regulation,cycle,gene
+biology:cells:reactions	enzyme,reaction,cell,enzymes,protein,proteins
+biology:anatomy:nervous	brain,nerve,nerves,nervous,system
+biology:anatomy:muscular muscle,muscles,limb
+biology:anatomy:digestive	stomach,food
+biology:anatomy:reproductive	reproduction,reproductive,sex,sexual
+biology:anatomy:lymphatic	lymph,lymphatic
+biology:anatomy:endocrine	endocrine
+biology:anatomy:urinary	urinary,urin
+biology:anatomy:cardiovascular	heart,vessel,cardiovascular
+biology:anatomy:skeletal	bone,bones
 statistics:descriptive:means	mean,standard,deviation,value,proability,number,measure,measurement,median,formula
-mathematics:numbers:fractions	numerator,rational,fraction,fractions,denominator,simplification,simplify,bruch
+mathematics:numbers:classes	rational,complex,irrational,integer,ganz,komplex,komplexe,zahlen,zahl,number,numbers,real
+mathematics:numbers:fractions	numerator,rational,fraction,fractions,denominator,simplification,simplify,bruch,nenner
 mathematics:functions:trigonometric	function,functions,cosine,sine,tangent,sin,cos,period,pi,funktion,sinus,cosinus,tangens
 mathematics:functions:exponential	function,functions,exponent,exponential,power,exp,exponential
 mathematics:functions:logarithmic	function,functions,logarithm,logarithmic,hyperbolic,logarithmus
-mathematics:functions:extrema	function,minimum,maximum,minima,maxima,extrema,local,global,derivative,ableitung
+mathematics:functions:extrema	function,minimum,maximum,minima,maxima,extrema,local,global,derivative,ableitung,derivatives,relative,absolute
 mathematics:calculus:extrema			mathematics:functions:extrema
 mathematics:calculus:series	function,series,expansion,taylor,reihe
-mathematics:calculus:integrals	integral,integrals,stammfunktion,integral,grenze,grenzen
+mathematics:calculus:integrals	integral,integrals,stammfunktion,integral,grenze,grenzen,area,curve
+mathematics:calculus:derivatives	derivative,derivatives,function,funktion,functions,ableitung,ableitungen,steigung,change,slope,convex,concave
+mathematics:calculus:fourier	fourier,frequency,analysis
+mathematics:linalg:matrices	matrix,matrices
+mathematics:linalg:vectors	vector,vectors,length,perpendicular,scalar,product,angle,direction
 geology:climatechange	climate,weather,temperature,temperatures
 geology:deformationmountains	mountain,mountains,strain,stress,pressure,formation,deformation,elevation
 geology:earthhistory	earth,history


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