TEMPLATES

TEMPLATE for GENES

II- TEMPLATE for LEUKEMIAS

III- TEMPLATE for SOLID TUMORS

IV- TEMPLATE for CANCER-PRONE DISEASES

# ##################################################
# A. General pipeline for updating the Atlas       #
# ##################################################
# 2017-07-29 Dessen Philippe ( This email address is being protected from spambots. You need JavaScript enabled to view it. )
#
# all scripts are running in $CYT_DIR/Scripts  directory
#
#!/usr/bin/bash
# ===============================================================
# AUTHOR : P. DESSEN
# DATE   : Mon Aug  2 18:27:27 MET DST 1999
# FILE   : maj_full.sh
# GOAL   : Automatic updating of html files from txt files
# RUN :  ./maj_full.sh 2>/dev/null > indexation.log  &
# ===============================================================
cd $CYT_DIR/Scripts
date1=`date`
echo "start " $date1
# I.  Generation of Genes links from Anomalies, Tumors, Kprones
# =============================================================
#  Identification of all links (CC: TXT: ID: > in all txt files

./ident_hyper.pl
 
# Generation of several files
# hyper_Genes0.txt
# hyper_Anomalies.txt
# hyper_Tumors.txt
# hyper_Kprones.txt
# followed by concatenation in ./Scripts/Data/hyper_All.txt
# creation of Data if does exist

./otheranom_gene2.pl

# otheranom_gene2.pl  in Scripts
# creation of an html bloc in Genes html_files
# with relation with Anomalies files
# Generation of  id.html files in the directory
#  ../Genes/AnomLinks/1.html
# 2 distinct extracts
#  1.  genes associated with  a FUSION_GENE in Anom files
#  2.  genes associated with  Anom in hyperlinks <CC: TXT: ID:>
# use the file ./Data/hyper_All.txt
# and the file ./genes_gc.txt (indexation of filename with NAME)

./othertumor_gene2.pl

# othertumor_gene.pl  dans Scripts
# creation of an html bloc in Genes html_files
# with relation with Tumors files
# Generation of  id.html files in the directory
#  ../Genes/TumorsLinks/1.html
# 2 distinct extracts
#  1. genes associated with FUSION_GENE in the  Tumors files
#  2. genes associated with Tumors in hyperlinks <CC: TXT: ID:>

./otherkprone_gene2.pl

# otherkprone_gene2.pl  in Scripts
# creation of an html bloc in Genes html_files
# Generation of  id.html files in the directory
#  ../Genes/KpronesLinks/10001.html
# 2 distinct extractions
#  1. genes associated with SYMBOL dans les fiches  Kprones
#  2. genes associated with Kprones in hyperlinks <CC: TXT: ID:>

./othergene_anom.pl
# othergene_anom.pl id_chrom_clin  in Scripts
# creation of a html bloc html for  Anomalies
# in the directory
# ../Anomalies/GeneLinks/1001.html

./othertransloc_anom.pl

# othertransloc_anom.pl in Scripts
# creation of  a transloc html bloc for  Anomalies
# Validation in first the creation of  the fil
#   ./Data/hyper_translocAll.txt
# with the script  extract_transloc_name.pl
#
# Generation of links files of  transloc files with Anomalies
# File created by extract_transloc_name.pl  from
# ./Data/hyper_translocAll.txt

./othergene_tumor.pl

# othergene_tumor.pl  dans Scripts
# uses the file ./Data/hyper_All.txt
# creation of an html bloc for    Tumors in
#   ../Tumors/GeneLinks/5001.html
# Generation of links of Genes files with Tumors
# File created by extract_gene_name.pl  from
# ./Data/hyper_All.txt
#
require "./miscfct.pl"; # fonctions diverses
require "gereDbid.pl"; # -- pour l'id des genes




./cytatlas
$ ls -ld */*Links
drwxrwxr-x+ 1 phd None 0  1 juil. 09:28 Anomalies/GeneLinks
drwxrwxr-x+ 1 phd None 0  1 juil. 09:24 Genes/AnomLinks
drwxrwxr-x+ 1 phd None 0  1 juil. 09:27 Genes/KproneLinks
drwxrwxr-x+ 1 phd None 0  1 juil. 09:27 Genes/TumorLinks
drwxrwxr-x+ 1 phd None 0  1 juil. 09:28 Tumors/GeneLinks


#
# II. Generation of Genes txt and html files
# ==========================================
rm ../Genes/GC_*.txt
rm -f ../../chromcancer/Genes/GC_*.html

# for the 2 sets of non annotated genes
./gen_genes_gn.sh
./gen_genes_gc.sh
# for the set of experted  genes  (Genes0)

./gen_gene2.sh

# creation of links from GC_annot_genes to AtlasFilename
# This permits to address url either bt AtlasFilename or by
# symolic url "GC_<symbol>.html"

./gen_genes_link.sh
#
# III. indexation
# ===============
./indexation.sh
#
# IV. Generation of all html files
# ================================
# preliminary
# generation of preliminary files LK_xxx.html , TU_xxx.html ..
# for forsale files

./maj_prelim.sh
#
# generation of html cards  files
./gen_anom.sh
./gen_kprone.sh
./gen_tumor.sh
./gen_report.sh
./gen_educ.sh
./gen_deep.sh
#./gen_study.sh

# chromosome pages indexation
./index_bychrom3.pl

# reindexation (second round : not mandatory ?)
./indexation.sh
# regeneration of html cards (after reindexation)
./gen_gene2.sh
./gen_anom.sh
./gen_kprone.sh
./gen_tumor.sh
./gen.educ.sh
./gen_deep.sh
./gen_report.sh

# Management of images
cp_anom_img.sh
cp_deep_img.sh
cp_educ_img.sh
cp_genes_img.sh
cp_kpr_img.sh
cp_report_img.sh
cp_tum_img.sh
date2=`date`
echo "end "  $date2
echo "maj_full.sh "  $date1   $date2
echo "==================================="
#
mail -s "Atlas_IGR__maj_full  " This email address is being protected from spambots. You need JavaScript enabled to view it.   < nohup.out
mail -s "Atlas_IGR__maj_full  " This email address is being protected from spambots. You need JavaScript enabled to view it.   <  indexation.log


# ##################################
# B. Indexation procedure          #
# ##################################

# Use indexation.sh after any modifications on cards to maintain
# updated indexes and links

# indexation.sh

#!/bin/bash
# ==============================================================
# AUTHOR : P.DESSEN
# DATE   :  11.12.99
# FILE   :./indexation.sh
# GOAL   : automatic generation of indexes and catalogs
# ex: ./indexation.sh 2 >/dev/null > indexation_20160306.log &
# to be run in $CYT_DIR/Scripts
# ==============================================================
# ------------------------------------------------
# ATLAS environnement variables
# ------------------------------------------------
# CYT_DIR needs to be defined (in $HOME/cytatlas.sh)
# CYT_DIR='..'
source $HOME/cytatlas.sh
GENE_DIR=$CYT_DIR/Genes
ANOM_DIR=$CYT_DIR/Anomalies
TUMOR_DIR=$CYT_DIR/Tumors
KPRON_DIR=$CYT_DIR/Kprones
REPORT_DIR=$CYT_DIR/Reports
STUDY_DIR=$CYT_DIR/StudyGroup
DEEP_DIR=$CYT_DIR/Deep
EDUC_DIR=$CYT_DIR/Educ
WGENE_DIR=$CYTW_DIR/Genes
WANOM_DIR=$CYTW_DIR/Anomalies
WTUMOR_DIR=$CYTW_DIR/Tumors
WKPRON_DIR=$CYTW_DIR/Kprones
WREPORT_DIR=$CYTW_DIR/Reports
WDEEP_DIR=$CYTW_DIR/Deep
WEDUC_DIR=$CYTW_DIR/Educ
WCOLLAB_DIR=$CYTW_DIR/Collab
SCRIPT_DIR=$CYT_DIR/Scripts
export GENE_DIR ANOM_DIR TUMOR_DIR KPRON_DIR SCRIPT_DIR
export REPORT_DIR STUDY_DIR DEEP_DIR EDUC_DIR
export WGENE_DIR WANOM_DIR WTUMOR_DIR WKPRON_DIR
export WREPORT_DIR WDEEP_DIR  WEDUC_DIR WCOLLAB_DIR
# ----------------------------------------------
echo "--------------------------------------------------------"
echo " Atlas indexation
echo "`date`
echo "--------------------------------------------------------"
DATEIN=`date`
# pretraitment
# Regeneration of GC.txt  files_
echo "Generation of GC_xxx.txt files "
echo "the genes_gc.txt and genes_gn.txt files need to be updated\n"
perl $CYT_DIR/Scripts/gener_gc.pl genes_gc.txt 2>/dev/null
perl $CYT_DIR/Scripts/gener_gc.pl genes_gn.txt 2>/dev/null
ls -l genes_gc.txt
ls -l genes_gn.txt
# ----------------------------------------------------------
# Build of the database of all objects of Atlas
#   ObjDB.txt contains the list
# ----------------------------------------------------------
echo "Build of the database ObjDB.txt"
echo "`date`";
perl $CYT_DIR/Scripts/x_id.pl # build if ObjDB.txt
ls -l ObjDB.txt
# ----------------------------------------------------------
# Build of the Genes : file ObjDB0.txt
perl $CYT_DIR/Scripts/majgene.pl  2>/dev/null       #
ls -l ObjDB0.txt
# ----------------------------------------------------------
# catalog maintains several features of each card
echo "Creation of a catalog"
perl $CYT_DIR/Scripts/catalog.pl   2>/dev/null      #
ls -l catalog
# ----------------------------------------------------------
# reconstruction des index divers
echo "Build of ObjDB1.txt and ObjDB2.txt"
perl $CYT_DIR/Scripts/majfich.pl    2>/dev/null     #
ls -l ObjDB1.txt
ls -l ObjDB2.txt
echo "Build of ObjDB1.html"
perl $CYT_DIR/Scripts/majfich2.pl   2>/dev/null     #
echo "Build of  ObjDB3.txt and ObjDB4.txt"
perl $CYT_DIR/Scripts/majfich3.pl    2>/dev/null     #
ls -l ObjDB3.txt
ls -l ObjDB4.txt
echo "Build of ObjDB5.txt (correlation anom tumor genes) and ObjDB7.txt"
perl $CYT_DIR/Scripts/majfich5.pl  2>/dev/null    
ls -l ObjDB5.txt
# ----------------------------------------------------------
# Generation of tabulated files for catalog and forsale
# catalog_out.txt and forsale_out.txt
perl $CYT_DIR/Scripts/forsale_out.pl forsale  2>/dev/null   # perl $CYT_DIR/Scripts/forsale_out.pl catalog  2>/dev/null   #
ls -l forsale_out.txt
ls -l catalog_out.txt
# ----------------------------------------------------------
# modification of catalog_out.txt depending of the  reserved file
perl $CYT_DIR/Scripts/reserved.pl
# ----------------------------------------------------------
# concatenation  of catalogs (catalog + forsale)
cat $CYT_DIR/Scripts/catalog_out.txt >  catalog_full.txt
cat $CYT_DIR/Scripts/forsale_out.txt >> catalog_full.txt
ls -l catalog_full.txt
# Generation of a expertized Gene file
grep GENE ../../chromcancer/Collab/catalog_out.txt | awk -F\t '{print $3,"\t",$5} ' |grep -v GC_ > gce.txt
# ----------------------------------------------------------
#
echo "=============  End of  rebuild ================"
# ----------------------------------------------------------
# --- Indexations -----
# creation of several indexes for Genes
# index of genes by symbol
# index of objects by  chromosome.
# ----------------------------------------------------------
echo " "
echo " --- Indexation des genes ---"
cd $GENE_DIR
$CYT_DIR/Scripts/index_gene2.pl 2>/dev/null   > $WGENE_DIR/Geneliste.html
ls -l $WGENE_DIR/Geneliste.html
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/index_genes_red.pl
  echo " "
  echo " --- Indexation of Anomalies ---"
$CYT_DIR/Scripts/index_anom2.pl 2>/dev/null    > $WANOM_DIR/Anomliste.html
$CYT_DIR/Scripts/index_lymphoma.pl 2>/dev/null > $WANOM_DIR/Lymphomaliste.html
$CYT_DIR/Scripts/index_myeloid.pl 2>/dev/null  > $WANOM_DIR/Myeloidliste.html
ls -l $WANOM_DIR/Anomliste.html
ls -l $WANOM_DIR/Lymphomaliste.html
ls -l $WANOM_DIR/Myeloidliste.html
  echo " "
  echo " --- Indexation of Tumors ---"
cd $TUMOR_DIR
$CYT_DIR/Scripts/index_tumor2.pl 2>/dev/null  > $WTUMOR_DIR/Tumorliste.html
ls -l $WTUMOR_DIR/Tumorliste.html
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/solid_section.pl 2>/dev/null
  echo " "
  echo " --- Indexation of Kprones ---"
cd $KPRON_DIR
$CYT_DIR/Scripts/index_kprone.pl 2>/dev/null   > $WKPRON_DIR/Kproneliste.html
ls -l $WKPRON_DIR/Kproneliste.html
  echo " "
  echo " --- Indexation of Reports ---"
cd $REPORT_DIR
$CYT_DIR/Scripts/index_report.pl 2>/dev/null   > $WREPORT_DIR/Reportliste.html
ls -l $WREPORT_DIR/Reportliste.html
  echo " --- Indexation of Deep ---"
cd $DEEP_DIR
$CYT_DIR/Scripts/index_deep.pl 2>/dev/null   > $WDEEP_DIR/deeplist.html
ls -l $WDEEP_DIR/deeplist.html
cd $CYT_DIR/Scripts
chmod a+r $CYTW_DIR/Genes/Geneliste.html
chmod a+r $CYTW_DIR/Anomalies/Anomliste.html
chmod a+r $CYTW_DIR/Tumors/Tumorliste.html
chmod a+r $CYTW_DIR/Kprones/Kproneliste.html
chmod a+r $CYTW_DIR/Reports/Reportliste.html
chmod a+r $CYTW_DIR/Deep/deeplist.html
# ----------------------------------------------------------
#
##  echo " "
##  echo "--- Indexation of GeneLink ---"
####     Normally done in  maj_full.sh #####
#### $CYT_DIR/Scripts/ident_hyper.pl
#### $CYT_DIR/Scripts/othergene_anom.pl
#### $CYT_DIR/Scripts/othergene_tumor.pl
#### $CYT_DIR/Scripts/othergene_kprone.pl
#### $CYT_DIR/Scripts/otheranom_gene2.pl
#### $CYT_DIR/Scripts/othertransloc_anom.pl
#### $CYT_DIR/Scripts/othertumor_gene2.pl
#### $CYT_DIR/Scripts/otherkprone_gene2.pl
# ----------------------------------------------------------
#
  echo " "
  echo " ---  Mitelman Files ---"
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/report2mitelman.pl 2> /dev/null
$CYT_DIR/Scripts/report2mitelman2.pl2> /dev/null
$CYT_DIR/Scripts/a0_mitel2jlh.pl > ../../chromcancer/Collab/mitelman_anom.txt
echo ""
# ----------------------------------------------------------
#
#echo " ----- Indexation of Genes GC --- "
#cd $CYT_DIR/Scripts
#perl $CYT_DIR/Scripts/index_genes_gc.sh
# ----------------------------------------------------------
#
  echo " "
  echo " --- Indexation  by chrom ---"
cd $CYT_DIR/Scripts
perl $CYT_DIR/Scripts/index_bychrom3.pl  2> /dev/null
perl $CYT_DIR/Scripts/index_genes_chromg.pl  2>/dev/null  
  echo " "
  echo " --- Creation of th file cytoentities.html ---"
perl $CYT_DIR/Scripts/cytoentities.pl  2> /dev/null
perl $CYT_DIR/Scripts/cytoentities2.pl 2> /dev/null
# ----------------------------------------------------------
### echo " --- Indexation of the file hugo2url.dat ---"
### perl $CYT_DIR/Scripts/hugo2url.pl
# ----------------------------------------------------------
  echo " "
  echo " --- Creation of file GeneExtlnk.txt ---"
perl $CYT_DIR/Scripts/extlnk2.pl Genes 2>/dev/null
  echo " "
  echo " --- Creation of file GeneExtlnk.html ---"
perl $CYT_DIR/Scripts/extlnk3.pl Genes  2>/dev/null
  echo " "
  echo " --- Creation of file GeneLink.txt ---"
perl $CYT_DIR/Scripts/extlnk4.pl Genes
# ----------------------------------------------------------
## indexation des authors
cd $CYT_DIR/Scripts
perl  indxauth.pl 2>/dev/null
ls -l  IndxAuth.txt
perl  indxauth2.pl 2>/dev/null
ls -l indxauth2.pl
ls -l IndxAuth.html
ls -l IndxAuth2.txt
echo "Be careful : the key_date_pays.txt file may be updated...."
ls -l  key_date_pays.txt
echo "Indexation IndxAuth3.txt "
perl  indxauth3.pl 2>/dev/null
ls -l  IndxAuth3.txt
echo "Indexation IndxAuth4.txt "
perl  traitauth.pl 2>/dev/null > ./IndxAuth4.txt
ls -l  IndxAuth4.txt
echo "Indexation IndxAuth5.txt "
perl  indxauth5.pl 2>/dev/null
ls -l  IndxAuth5.txt
echo "Indexation IndxAuth6.txt "
perl  indxauth6.pl 2>/dev/null
ls -l IndxAuth6.txt
echo "Indexation IndxAuth1.txt "
perl  indxauth1.pl 2>/dev/null
ls -l  IndxAuth1.txt
## copies of authors indexes in Collab (Archive)
echo "mv  to ../../chromcancer/Collab "
mv  IndxAuth.txt   $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.txt
mv  IndxAuth.html  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.html
mv  IndxAuth2.txt  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth2.txt
mv  IndxAuth2.html $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.html
mv  IndxAuth3.txt  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth3.txt
mv  IndxAuth4.txt  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth4.txt
mv  IndxAuth5.txt  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth5.txt
mv  IndxAuth6.txt  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth6.txt
mv  IndxAuth1.txt  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth1.txt
mv  IndxAuth1.html  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth1.html
cp -p  key_date_pays.txt   $CYTW_DIR/Collab
# ----------------------------------------------------------
# Generation of Nosology
echo "Reconsruction des  Nosology"
perl $CYT_DIR/Scripts/solid_nosology2.pl 2>/dev/null
ls -l $CYTW_DIR/Tumors/Solid_Nosol*.html
# ----------------------------------------------------------
## indexation des images
echo "Indexation of images"
perl  $CYT_DIR/Scripts/indximg.pl  2>/dev/null
cp -p  $CYT_DIR/Scripts/IndxImg.txt  $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxImg.txt
# ----------------------------------------------------------
### indexation of PMID
echo "Indexation of PMID"
perl  $CYT_DIR/Scripts/parsing_med.pl 2>/dev/null
## indexation of bibliographic references
echo "indexation of bibliographic references"
perl $CYT_DIR/Scripts/parsing_ref.pl 2/dev/null  > ../../chromcancer/Collab/url_ref.txt 
ls -l  ../../chromcancer/Collab/url_ref.txt
## indexation of bibliographic references
echo "indexation of bibliographic references"
perl $CYT_DIR/Scripts/parsing_biblio.pl 2>/dev/null > ../../chromcancer/Collab/parsing_biblio.txt
ls -l ../../chromcancer/Collab/parsing_biblio.txt
# ----------------------------------------------------------
cd $CYT_DIR/Scripts
echo "copies dans ../../chromcancer/Collab"
#  copies in ../../chromcancer/Collab
## copy des ObjDB.txt   dans $CYTW_DIR/Collab/
cp -p ObjDB*.txt  $CYTW_DIR/Collab
## copy of ObjDB1.html   in $CYTW_DIR/Collab/
mv  ObjDB*.html  $CYTW_DIR/Collab
## copy of GeneExtlnk.txt in  $CYTW_DIR/Collab/
mv  GeneExtlnk.txt  $CYTW_DIR/Collab
mv  GeneExtlnk.html  $CYTW_DIR/Collab
##mv  $CYT_DIR/Scripts/GeneLink.txt  $CYTW_DIR/Collab
## copy of cytoentities.html
## copie of tabulated files : forsale et catalog
cp  forsale_out.txt $CYTW_DIR/Collab
cp  catalog_out.txt $CYTW_DIR/Collab
cp  forsale $CYTW_DIR/Collab
cp  catalog $CYTW_DIR/Collab
cp  catalog_full.txt $CYTW_DIR/Collab
## copie du fichier genes_cancer.txt
cp -p genes_gc.txt $CYTW_DIR/Collab
cp -p genes_gn.txt $CYTW_DIR/Collab
cp -p genes_gcr.txt $CYTW_DIR/Collab
## copy of genes non_cancer
cp -p genes_gn.txt $CYTW_DIR/Collab
# copy of parsing_med
cp -p list_refmedline.txt   $CYTW_DIR/Collab
#
chmod  664 $CYTW_DIR/Collab/*.txt
chmod  664 $CYTW_DIR/Collab/*.html
# ----------------------------------------------------------
# generation of the genes atlas file
echo "Generation du fichier gene_atlas.txt "
filtcol genes_gc.txt  45 "<>"  "-"  > $CYTW_DIR/Collab/genes_atlas.txt
ls -l  $CYTW_DIR/Collab/genes_atlas.txt
# ----------------------------------------------------------
# generation of the humprot_atlas.txt file
prtab $CYTW_DIR/Collab/genes_atlas.txt  1 2 10-12 22-23 46 > $CYTW_DIR/Collab/humprot_atlas.txt
echo "generation of the humprot_atlas.txt file"
ls -l $CYTW_DIR/Collab/humprot_atlas.txt
# ----------------------------------------------------------
## copy of Amplicons
echo "copy of amplicons"
cp -p $CYT_DIR/Ampl/*.html   $CYTW_DIR/Ampl
cp -p $CYT_DIR/Ampl/Images/*.jpg   $CYTW_DIR/Ampl/Images
# ----------------------------------------------------------
# Categories
# indexation of images
cd $CYT_DIR/Scripts
echo "indexation of categories "
cd $CYT_DIR/Scripts/Data/Category_editor
./prepcat2.sh
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/indximgcategory.pl 2>/dev/null
$CYT_DIR/Scripts/index_category2.pl 2>/dev/null
ls -l Categories_img.txt
ls -l category_img.txt
ls -l category_lst.txt
cp -p catdeepgene.txt    $CYTW_DIR/Collab/catdeepgene.txt
cp -p Categories_img.txt $CYTW_DIR/Collab/Categories_img.txt
cp -p category_img.txt   $CYTW_DIR/Collab/
cp -p category_lst.txt   $CYTW_DIR/Collab/
# ----------------------------------------------------------
# generation of atlas_statuts
perl $CYT_DIR/Scripts/atlas_status.pl 2> /dev/null
echo "rebuild of Status directories"
ls -l $CYTW_DIR/Status/Status_*html
# ----------------------------------------------------------
# Indexation of ICD
perl $CYT_DIR/Scripts/index_icd_topo.pl  2> /dev/null
perl $CYT_DIR/Scripts/index_icd_morph.pl 2> /dev/null
# ----------------------------------------------------------
# Update of recents files (2 years)
echo "Update of recents files (2 years) "
# lastfiles : Report.html
$CYT_DIR/Scripts/lastfile.pl 2>/dev/null
ls -l $CYTW_DIR/Recent.html
# ----------------------------------------------------------
# Statfiches
echo "statfiches "
$CYT_DIR/Scripts/statfiches.pl 2>/dev/null
ls -l $CYTW_DIR/Collab/StatFiches.html
# ----------------------------------------------------------
# Update of Backpage
# modifBackpage creates a Backpage2.html file
# the addlist file contains new authors
#$CYT_DIR/Scripts/modifBackpage  addlist  
#cp $CYTW_DIR/BackpageAbout.html $CYTW_DIR/BackpageAbout0.html #mv $CYTW_DIR/BackpageAbout2.html $CYTW_DIR/BackpageAbout.html
cp $CYT_DIR/Scripts/listeAuthBPage.txt $CYTW_DIR/Collab/
# ----------------------------------------------------------
# creation of a synthesis file JLH  ObjDB6.txt
echo "creation of ObjDB6.txt "
majfich4.pl 2>/dev/null
ls -l $CYTW_DIR/Collab/ObjDB6.txt
# ----------------------------------------------------------
# List of regular updates (depending of releases)
# creation of chromcancer/cosmic_study.html
# read of ../Standards/COSMIC/cosmic_study.txt
 ./cosmic2html.pl
#
# ICGC : list of projects
# creation of ../../chromcancer/icgc_projects.html
# Lecture de ../TCGA_ICGC/ICGC/cgc_projects.txt
./icgc2html.pl
#
# copies of the Band files
cp $CYT_DIR/Scripts/tmp_allgenes.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/tmp_allanom.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/anom_bandall.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/gene_bandall.txt $CYTW_DIR/Collab
# list of files on archive ( Collab )
echo "list of files on archive $CYTW/Collab "
ls -lt  $CYTW_DIR/Collab
# Update of the data on index.html
# Sun Aug 12 12:09:46 MEST 2007
# Sat Nov 21 10:28:10 MET 2009
# Thu Jul  9 15:36:42 MEST 2015
DATEOUT=`date`
# to be adapted to time/date format (depending of UNIX)
perl -pi.bak -ne 's@\S+ \S+ \d+ \d+:\d+:\d+ MEST 20\d\d@$DATEOUT@' $CYTW_DIR/index.html
rm $CYTW_DIR/index.html.bak
echo "start of indexation $DATEIN"
echo "end of indexation   $DATEOUT"
# ----------------------------------------------------------
# statistics
$CYT_DIR/Scripts/stat_atlas.pl > $CYTW_DIR/stat_atlas.html
#
echo "Do not forgot to update the key_date_pays.txt file"
ls -l key_date_pays.txt
# Update of the MySQL indexation (only on INIST)
# ----------------------------------------------------------
############################################################

JOURNAL SUBMISSION FORM

Title: Atlas of Genetics and Cytogenetics in Oncology and Haematology

Journal: http://irevues.inist.fr/atlasgeneticsoncology

Note: the Journal papers are also available as a Database: http://AtlasGeneticsOncology.org

I- Editor and Publisher

Editors-in-Chief:
Jesús María Hernández Rivas (Molecular Cytogenetics Lab, Dept. of Hematology, University Hospital of Salamanca, Spain    
Paola Dal Cin  Professor, Pathology, Harvard Medical School, Cytogeneticist, Cytogenetics Laboratory, Brigham And Women's Hospital, Boston, MA 02215
Jean-Loup Huret, Honorary Associate Professor of Medical Genetics of the French Universities.

Contact Address: Jean-Loup Huret, MD, PhD, 10 rue des Treilles, Masseuil, F-86190 Quinçay, France.

Email: This email address is being protected from spambots. You need JavaScript enabled to view it. ; This email address is being protected from spambots. You need JavaScript enabled to view it. ; This email address is being protected from spambots. You need JavaScript enabled to view it. ; / This email address is being protected from spambots. You need JavaScript enabled to view it. ; This email address is being protected from spambots. You need JavaScript enabled to view it.

Phone: +33 5 49 60 46 54

Publisher Address: INIST-CNRS, Catherine Morel, 2,Allée du Parc de Brabois, CS 10130, 54519 Vandoeuvre-lès-Nancy France.

Country of origin: France

e-ISSN: ISSN 1768-3262

Publishing Company: ARMGHM, a non-profit organisation, and by the Institute for Scientific and Technical Information of the French National Center for Scientific Research (INIST-CNRS) since 2008.

Funding: see "Activity reports" of the association in charge of the financial side: http://chromosomesincancer.org/en/activity.html

Sponsoring Organizations, Grants and past Grants: Scientific Societies; European funds; French Ministry of Higher Education and Research; French National League against Cancer, etc… see http://atlasgeneticsoncology.org/BackpageAbout.html#GRANTS

II- Publishing Standards

Subject Area: Life Sciences

Publishing Format: electronic format.

Language of Journal: English

Open Access Journal: The Atlas is accessible, free, and may be reproduced under certain conditions (see http://atlasgeneticsoncology.org/BackpageAbout.html#COPYRIGHT and, in this paragraph, the hyperlink toward https://creativecommons.org/licenses/by-nc-nd/2.0/fr/deed.en_GB). Pages can be printed and/or recorded.

No fees for the authors; The Atlas is in open free access for readers, and there are no fees for the authors (the opposite of "predatory open access publishing").

1st Year of Publication: 1997

Issues Frequency: Continuous online: 12 issues per year

Periodicity: The database publishes articles online one at a time and articles are collected for release as "issues" and "volumes" for the Journal, see http://irevues.inist.fr/atlasgeneticsoncology (see also the archives of the database at http://atlasgeneticsoncology.org/DatabaseArchives/DatabaseArchives.html).

Regular and stable publication: The Atlas is a regular and uninterrupted publication since 1997.

Most Recent Issue (Vol, Iss, Yr): As today, Volume 22, 2018, December,  issue 12, 9 articles.

Journal Archives: http://irevues.inist.fr/atlasgeneticsoncology (database archives: http://atlasgeneticsoncology.org/DatabaseArchives/DatabaseArchives.html).

Statistic of Authors by country: http://atlasgeneticsoncology.org/Status/Status_country.html

Bibliographic records: MetaData for bibliographic records of the Atlas Journal are handled by CNRS-INIST are at the following URL: http://irevues.inist.fr/atlasgeneticsoncology and may be uploaded upon request (see also MetaData in the database at; http://atlasgeneticsoncology.org/Collab/AtlasMetadata.txt).

III- Editorial policies

Editorial policies can be found at the following addresses:

Instructions to Authors: http://documents.irevues.inist.fr/bitstream/handle/2042/48486/Instructions-to-authors.pdf

Peer Review: http://documents.irevues.inist.fr/bitstream/handle/2042/56068/Policies-editorial-ethics.pdf

Ethical Publishing Practices: http://documents.irevues.inist.fr/bitstream/handle/2042/56068/Policies-editorial-ethics.pdf

Copyright/sponsorship: http://documents.irevues.inist.fr/bitstream/handle/2042/48487/Copyright-sponsorship.pdf

Editorial content: http://atlasgeneticsoncology.org/Status/Status.html

International focus: Concerning Section Editors and Board members: http://atlasgeneticsoncology.org/BackpageAbout.html#EDITORIAL ; Concerning Authors /papers by country: http://atlasgeneticsoncology.org/Status/Status_country.html ; Concerning internauts/readers: http://chromosomesincancer.org/en/atlas-users.html

IV- Quality of its contents and editorial processes

Aims and Scope of Journal: The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a journal focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases.

Content: The Atlas contains 6 sections, with articles on: 1- Genes, 2- Leukemia entities, 3- Solid tumors, 4- Cancer-prone diseases, 5- 'Deep Insights' (articles dealing with topics in areas related to core subjects in the Atlas) 6- Case reports on hematological malignancies. Papers from sections 1 to 5 are review articles, all of them are commissioned papers. Section 6, case reports, are unsolicited papers.

Number of Reviewers Assigned per Manuscript: Commissioned papers (Review articles): 2 inside reviewers; Case Reports; 1 inside + 3 to 4 outside reviewers.

Percent of Commissioned vs. Unsolicited Manuscripts: 97% (Review articles i.e. all the papers except the Case Reports) vs. 3% (Case Reports)

Acceptance Rate of Unsolicited Manuscripts in last 12 months: accepted without revision: 8%; after revision: 68%; refused: 24%.

Average Time from Acceptance of Manuscript to Publication: 2-3 weeks

Article Types Published: Reviews: about 2650 papers; Research articles: 0 (NO research papers); Case Reports: about 90 papers).

Quality of its contents/Citations: Papers published in the Atlas are cited as such in: Annual Review of Biochemistry (Impact Factor 29,88), Science (29,75), Nature Reviews Cancer (29,54), Cancer Cell (25,29), Nature Cell Biology (19,53), Journal of the National Cancer Institute (14,07), American Journal of Human Genetics (12,30), Molecular Systems Biology (12,13), Genes and Development (12,08), Genome Research (11,34), Trends in Molecular Medicine (11,05), Blood (10,56), Proceedings of the National Academy of Sciences USA (9,43), Trends in Genetics (8,69), Leukemia (8,30), Cancer Res (7,54), Nucleic Acids Research (7,48), Oncogene (7,13), … and many others.
See also the statistics of Atlas users: http://chromosomesincancer.org/en/atlas-users.html
Acknowledgements: http://chromosomesincancer.org/en/acknoledgements-to-the-atlas.html
and "Nominated for award"http://chromosomesincancer.org/en/nominated-for-an-award.html

 

I- Main page: 


II-1.

Foreword 1: There are various types of items developed in the Atlas:
1- Genes (http://atlasgeneticsoncology.org/Genes/XXX )
1-1. Annotated genes (papers/cards written by authors) URLs: http://atlasgeneticsoncology.org/Genes/[name-of-gene]ID[number]ch[location].html (1,493 papers/cards, e.g. http://atlasgeneticsoncology.org/Genes/PGRID41700ch11q22.html); and
1-2. Automated cards on genes (more or less like GeneCards); URLs: http://atlasgeneticsoncology.org/Genes/GC_[name-of-gene].html (28,377 cards);
2- Leukemias 681 annotated papers/cards : http://atlasgeneticsoncology.org/Anomalies/XXX , and 540 "Other Leukemias" (automated cards) : http://atlasgeneticsoncology.org/Anomalies/TL_XXX .
3- Solid tumors 217 annotated papers/card : http://atlasgeneticsoncology.org/Tumors/XXX , and 2,968 "Other Tumors" (automated cards) : http://atlasgeneticsoncology.org/Tumors/TT_XXX .
4- Cancer-prone diseases 114 annotated papers/cards : http://atlasgeneticsoncology.org/Kprones/XXX .
5- Case reports in hematology (http://atlasgeneticsoncology.org/Reports/XXX ) (88 papers/cards)

All these cards are structured from templates (e.g. Submission form for GENES: http://atlasgeneticsoncology.org/Forms/Gene_Form_for_submission.doc) with the addition of a HEADER with tags or tracking devices allowing for indexing of the form in different parts of the data base (e.g. TRI_PAR_CHROMOSOME -> to which chromosome page (red arrow)? CATEGORY-> to which Cell Biology page (red arrow)?); see also: http://atlasgeneticsoncology.org/Collab/catalog and http://chromosomesincancer.org/en/template-for-cards-papers.html ;
- and EXTERNAL LINKS (bottom of each paper/card).
There are also
- Deep Insights (traditional papers) http://atlasgeneticsoncology.org/Deep/XXX (113 Deep)
- Chromosome pages (http://atlasgeneticsoncology.org/Indexbychrom/idxa_[chromosome-number].html e.g. http://atlasgeneticsoncology.org/Indexbychrom/idxa_11.html ) and
- Chromosome band pages (http://atlasgeneticsoncology.org/Bands/[band].html e.g. http://atlasgeneticsoncology.org/Bands/19p13.html ),
- Cell biology pages (http://atlasgeneticsoncology.org/Categories/[category-name] e.g. http://atlasgeneticsoncology.org/Categories/Cell_cycle.html
- ICD-O pages (International Classification of Diseases - Oncology WHO/OMS) e.g. http://atlasgeneticsoncology.org/Tumors/Solid_Nosology.html and http://atlasgeneticsoncology.org/ICD/icd_2016_topo.html
- Atlas status (thesaurus of the Atlas: http://atlasgeneticsoncology.org/Status/Status.html and sub-pages)
- and various other pages (Backpage: http://atlasgeneticsoncology.org/BackpageAbout.html Recent papers http://atlasgeneticsoncology.org/Recent.html , Educational items http://atlasgeneticsoncology.org/GeneticEng.html , Genes partners, International cancer programs etc. (see others on the Main page)

A. Architecture of data:
A1. Text files for cards
Genes0
Anomalies (Leukemias)
Tumors
Kprones (Cancer-prone hereditary diseases)
Reports (Case Reports)
Deep (Deep Insight)
Educ (Educational Items)
The 2 last are defined by a couple of files (.meta + .htm)
A2. Chromosomal location
at the chromosome level
at the chomosomal band level
A3. Functional categories (Cell Biology)
A4 Count/Census of Atlas Items
Statistics on atlas files, see: http://atlasgeneticsoncology.org/Status/Status.html , and http://atlasgeneticsoncology.org/stat_atlas.html
A5. Catalogs and indexes
see in http://atlasgeneticsoncology.org/Collab/
catalog_full.txt (tabulated file with major informations from HEADER and IDENTITY blocs)
ObjDB0.txt  ObjDB2.txt  ObjDB4.txt  ObjDB6.txt  ObjDB.txt
ObjDB1.txt  ObjDB3.txt  ObjDB5.txt  ObjDB7.txt: different files for indexing (might be simplified in a new structure)
A6. External resources

B. Modules for management and development
Module 1: Description of the templates of cards
see: http://atlasgeneticsoncology.org/Collab/Formes.xlsx ,
which correspond to the various submission forms for the authors:
http://atlasgeneticsoncology.org/Forms/Gene_Form_for_submission.doc
http://atlasgeneticsoncology.org/Forms/Leukemia_Form_for_submission.doc
http://atlasgeneticsoncology.org/Forms/Solid_Tumor_Form_for_submission.doc
http://atlasgeneticsoncology.org/Forms/Cancer-Prone_Disease_Form_for_submission.doc

Each card has a unique Atlas ID (present in the filename)
Genes: 1 --> 999 + 40000 --> 80000
Anomalies: 1001 --> 4999
Tumors: 5000 --> 9999
Kprones: 10000 --> 19999
Deep: 20000 --> 29999
Educ: 30000 --> 3999

Organisation of directories
All data is organized in two main directories
1. "cytatlas" (for managment)
2. " chromcancer" (with internet access)

1. cytatlas
./Genes0 (for expert txt)
./Genes (after txt processing)
./Anomalies
./Tumors
./Kprones
./Reports
./Deep
./Educ
Each directory has some other subdirectories for Images, xxLinks …
./Scripts (all bash and perl + references data)

2. chromcancer
./Genes
./Anomalies
./Tumors
./Kprones
./Reports
./Deep
./Educ
(each of the above with subdirectories for Images ..)
./Categories
./Indexbychrom (Chromosomes pages)
./Indexbyalpha
./Bands
./Status
./ICD
./ISCN

The process of scripts is in general made in the ./cytatlas/Scripts
The directory can be installed in a way defined by a general shell script
Cytatlas.sh which defines all the logical variables.

#!/usr/bin/bash
## script cytatlas_cygwin disque D
umask 002
CYT_DIR='/cygdrive/d/ATLAS/cytatlas'
CYTW_DIR='/cygdrive/d/ATLAS/chromcancer'
CYTHTML_DIR='http://genome.igr.fr/chromcancer'
SCRIPT_DIR='$CYT_DIR/Scripts'
PATH=$PATH:$CYT_DIR/Scripts
export CYT_DIR  CYTW_DIR CYTHTML_DIR SCRIPT_DIR PATH

GENE_DIR=$CYT_DIR/Genes
ANOM_DIR=$CYT_DIR/Anomalies
TUMOR_DIR=$CYT_DIR/Tumors
KPRON_DIR=$CYT_DIR/Kprones
REPORT_DIR=$CYT_DIR/Reports
STUDY_DIR=$CYT_DIR/StudyGroup
DEEP_DIR=$CYT_DIR/Deep
EDUC_DIR=$HOME/DATA_DIR/Educ
WGENE_DIR=$CYTW_DIR/Genes
WANOM_DIR=$CYTW_DIR/Anomalies
WTUMOR_DIR=$CYTW_DIR/Tumors
WKPRON_DIR=$CYTW_DIR/Kprones
WREPORT_DIR=$CYTW_DIR/Reports
WDEEP_DIR=$CYTW_DIR/Deep
WEDUC_DIR=$CYTW_DIR/Educ
WCOLLAB_DIR=$CYTW_DIR/Collab
export GENE_DIR ANOM_DIR TUMOR_DIR KPRON_DIR
export REPORT_DIR STUDY_DIR DEEP_DIR EDUC_DIR
export WGENE_DIR WANOM_DIR WTUMOR_DIR WKPRON_DIR
export WREPORT_DIR WDEEP_DIR  WEDUC_DIR WCOLLAB_DIR

alias cyt='cd $CYT_DIR'
alias cytw='cd $CYTW_DIR'
alias cyti='cd $CYT_DIR/Scripts'
echo 'cyt  : $CYT_DIR'
echo 'cyti : $CYT_DIR/Scripts'
echo 'cytw : $CYTW_DIR'
echo 'www  : $CYTHTML_DIR'

Module 2: Editorial management of cards
Foreword 2: Editorial process:
This is an important part, as the Editorial database processing must take it into account. See "Editorial workflow in the Atlas": http://chromosomesincancer.org/en/editorial-workflow.html .
In particular, critically important, Tables are used 1- to identify all/each relevant item (Table 1 herein below); 2- to dialogue with authors (Table 2).
These tables are the today ones used by the editor.
Examples:

Note: Tables used to identify all/each relevant item must be related (bijective type relation) with cards/papers; e.g. 05;00§ MDS with isolated del (5q) / ID 1134 <--> http://atlasgeneticsoncology.org/Anomalies/del5qSoleID1134.html

These tables may not exist per se. They would be integrated in the database of the Atlas (as, so far, some files as catalog, authors lists … on the INIST server. and automatically generated. But the right way will be to use ONLY screens developed ad hoc for editorial management.

Finally, we also have to format the cards/papers into word for the "scientific journal" version (see http://documents.irevues.inist.fr/handle/2042/15655 (e.g. http://documents.irevues.inist.fr/bitstream/handle/2042/62324/10-2014-HSPD1ID40888ch2q33.pdf , equivalent of http://atlasgeneticsoncology.org//Genes/HSPD1ID40888ch2q33.html ) of the Atlas.
A module is being finalized concerning the production of the scientific journal: It is a Web application developed with PHPWord/MySQL/Symfony Framework.

2.1 Actual process of management:
• Reception of a doc file (structured in the ad hoc template.
• Edition in a text file with good fields (validate the presence of a field in the beginning of lines (with eventually multiplicity of the same field)
• Addition of internal links (an expert task)

• Complementary procedure (by scripts)
- Correction of special characters (non compatibility between office Word and hypertext)
- Validation of bibliography with dowloading the short description of PubMed with PMID.
- Reordering biblio with alphabetic order
- Tests of good fields for each line (in good blocs)
- Test of links ( existent Atlas ID).
- Test of logical structure of each bloc (BEGIN.. / END)
- Transformation  in hypertext documents (see further)

2.2 To be developed for a new management:
- On-line templates must be available to the authors who will write directly their paper (e.g. http://atlasgeneticsoncology.org/Forms/Gene_Form_for_submission.doc , corresponding to http://chromosomesincancer.org/en/atlas-templates-for-cards.html ). These templates must be capable of evolution when the Editor(s) in Chief wish to add or delete or modify a tag or even a "BEGIN_END". A password would allow the author to interrupt his writing, save, and come back latter until a last validation.
- A macro-instruction assisting the recognition of an internal hyperlink that the editorial staff member must add before publishing (e.g. ABL: a list of "NAMES" and aliases must help to recognize and propose the hyperlink to ABL1; the editorial member says OK, and the hyperlink to http://atlasgeneticsoncology.org/Genes/ABLID1.html  comes automatically): --> need of a thesaurus (e.g. http://atlasgeneticsoncology.org/Tumors/Solid_Nosology.html
- PMID numbers solely permits to give the full reference
- Special characters are automatically transcribed (e.g. https://text-symbols.com/html/entities-and-descriptions , http://www.symbole-clavier.com , http://alexandre.alapetite.fr/doc-alex/alx_special.html ).

Module 3: Indexations
All the files of Atlas are considered as "objects" and are defined by an Atlas ID.
The standard of the filename of the objects is the following:
- Genes: 2 forms:
<String>ID<number><location>.txt   Ex: ADCYAP1ID43656ch18p11.txt
<String>ID<number>.txt   Ex: AF6ID6.txt
A generic form is built fr an easy links. The filename id defined as:
GC_<symbol>.txt e.g.: GC_ZFP90.txt
- Anomalies (Leukemias)
- Tumors
- Kprones
The filename is as : <string>ID<number>.txt ( ex :t3q21q26TreatRelLeukID1236.txt)
Creation (or Updating) of index or cards
As mentioned in the indexation.sh script (the main indexation performed after some modifications)
Indexation of Cards 1: script indexation.sh (in cytatlas/Scripts)
Used for re-indexation after new files or new data
http://atlasgeneticsoncology.org/Collab/Scripts/indexation.sh
1. Generation of all automatic genes
2. Generation of the main index file for all documents (ObjDB.txt)
3. Generation of some others indexes (ObjDBxx.txt ) (see  in http://atlasgeneticsoncology.org/Collab/)
- ObjDB.txt
- ObjDB0.txt
- ObjDB1.html
- ObjDB1.txt
- ObjDB2.txt
- ObjDB3.txt
- ObjDB4.txt
- ObjDB5.txt
- ObjDB6.txt
- ObjDB7.txt
4. Generation of a catalog (text file with the information from the HEADER, see: http://atlasgeneticsoncology.org/Collab/catalog)
5. Transformation of the catalog (and "for sale" - "to be written" files) in tables with concatenation in a catalog_full.txt file)
6. Indexations of Genes (Geneliste.html), Leukemias (Anomliste.html), etc.
7. Indexation by chromosomes
8. Indexation by authors (different IndxAuthxx.txt / html in Collab) (IndxAuth3.txt is the main index for authors and affiliations)
9. Generation of Categories (several files are maintained before in parallel) for Cell Biology items
10. Generation of status (Genes .. Authors . etc.): http://atlasgeneticsoncology.org/Status/Status.html
11. Generation of Recent (last 2 years documents): http://atlasgeneticsoncology.org/Recent.html
12. Generation of COSMIC projects and TCGA/ICGC projets
13. Statistics (http://atlasgeneticsoncology.org/stat_atlas.html)
Possibility of mysql indexation for some items (query in the home page)

Module 4:  Internal cross links between classes of cards
This section is important and gives a plus at the Atlas with numerous additions of links between cards. These links (Gene -> tumors, Leukemia <- genes …) enrich the quality and the expertise of the Atlas.
An automatic procedure parses all the cards and indexes the location of links (defined as a standard by the pattern ( <: TXT: text ID: AtlasID).
http://atlasgeneticsoncology.org/Collab/Scripts/maj_full.sh
This script has 2 goals: definition of all internal links
and
Generation of all hypertext files (readable on the net)

Map of one set towards another: injectivity/surjectivity:

Examples:

Module 5: Management of external links
Files for annotation of genes:
A parallel management of several databases is regularly made (from NCBI, UCSC, UniProt, Ensembl, HGNC, COSMIC, Mitelman (NCI) …)
All genes defined in the Atlas are based of the update list of gene symbols of human Entrez_genes . A great part of annotations are also associated ones in the ftp files of (ftp.ncbi.nih.gov/gene/DATA/ and /gene/GeneRIF). They are managed by script to lead in 2 tabulated files (genes_gc.txt  and genes_gn.txt ) , the first one for « cancer genes » (some words in description and/or GeneRif in Entrez Gene),
the second for other genes of Entrez_Gene (NCBI). Genes used are limited to   a genome location (hg38)  defined in http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz.
See: for a definition of all the fields keep updated and used in External links of the cards on Genes: External_annotations_genes

Module 6: Statistics
- Topics/Items for the Atlas (genes, leukemias, solid tumors and others):
- Need of Tables (e.g. http://atlasgeneticsoncology.org/Collab/ID-TRANSLOC.txt ) to know what is done, what is done but old, what is reserved to a given author, what needs an author to be found. Allows the addition of new items.