JOURNAL SUBMISSION FORM

Title: Atlas of Genetics and Cytogenetics in Oncology and Haematology
URL: http://AtlasGeneticsOncology.org

I- Editor and Publisher

Editor-in-Chief: Jean-Loup Huret, Genetics, University Hospital of Poitiers; Database Director: Philippe Dessen, UMR 1170 INSERM, Gustave Roussy.

Second Editor handling manuscripts: Gajanan V Sherbet, Institute for Molecular Medicine at Huntington Beach California.

Contact Address: Jean-Loup Huret, MD, PhD, 10 rue des Treilles, Masseuil, F-86190 Quinçay, France / Gajanan Sherbet, School of Electrical Electronic and Computer Engineering University of Newcastle upon Tyne, UK

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.

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; Poitiers University Fundation; 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 in ".html".

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 journal publishes articles online one at a time rather than collecting articles for release as an "issue". We can nonetheless determine "issues" by chronology: months and years, see http://atlasgeneticsoncology.org/Recent.html and the archives, from 1997 (vol.1), to 2017 (vol.21): 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 21, 2017, June issue, 9 articles, no page numbers since all online (see " 2017 - Vol 21 " i.e. http://atlasgeneticsoncology.org/DatabaseArchives/2017.html). A selection of articles published over the past few years are listed below: http://atlasgeneticsoncology.org/Tumors/GastricTumOverviewID5410.htmlhttp://atlasgeneticsoncology.org/Tumors/DuctCarcBreastID5593.htmlhttp://atlasgeneticsoncology.org/Tumors/GliomaOverviewID5763.html http://atlasgeneticsoncology.org/Tumors/OralMelanomaID6647.html http://atlasgeneticsoncology.org/Tumors/EndometStromalSarcYWHAE-NUTM2ID6649.html and recent papers: Genes: http://atlasgeneticsoncology.org/Genes/ALCAMID616ch3q13.html http://atlasgeneticsoncology.org/Genes/PGRID41700ch11q22.html http://atlasgeneticsoncology.org/Genes/WDR48ID53058ch3p22.html ; Leukemias: http://atlasgeneticsoncology.org/Anomalies/dup1qALLID1049.html http://atlasgeneticsoncology.org/Anomalies/MyeloLymphoPDGFRBID1745.html http://atlasgeneticsoncology.org/Anomalies/MixedPhenoALID1748.html ; Solid tumors: http://atlasgeneticsoncology.org/Tumors/ALKrenalCellCarcID6279.html http://atlasgeneticsoncology.org/Tumors/MaleBreastID6242.html ; Cancer-prone diseases: http://atlasgeneticsoncology.org/Kprones/DownSyndromeID10048.html ; Deep Insights: http://atlasgeneticsoncology.org/Deep/LINE1inCancerID20146.html

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 are at the following URL: http://atlasgeneticsoncology.org/Collab/AtlasMetadata.txt with:TITLE/DATE AUTHORS/AFFILIATION/COUNTRY/CITATION /ABSTRACT/KEYWORDS / ATLAS_ID/CLASS(Section)/URL /PUBLICATION/PUBLISHER/ISSN/LANGUAGE

III- Editorial policies

Editorial policies can be found at the following address: http://atlasgeneticsoncology.org/BackpageAuthors.htmlwith more detailed pages:

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

TEMPLATES

TEMPLATE for GENES

Field Syntax Comment
BEGIN_HEADER    
FILENAME  <Symbol>IDxxxch<location>.txt  
CLASSE GENE fixed  
ID  A number (in the catalog) Atlas ID
LOCUSID  number Entrez ID
TRI_PAR_CHROMOSOME chrom number (X Y, 1-22)  
TRANSLOC     
FUSION_GENE     
CATEGORY from a list of categories  
END_HEADER    
     
BEGIN_AUTHOR    
CREATED   DATE date AUTHORS authors DATE YYYY-MM AUTHORS FirstName LastName, .. separated by ","
CITATION  LastName Firstname Initial,  separated by ","
AUTHOR_AFFILIATION (address, town, country, e-mail) ;   
UPDATED   DATE date AUTHORS authors same syntax  
CITATION   multiple of 3 lines in order of date
AUTHOR_AFFILIATION    
END_AUTHOR    
     
BEGIN_ABSTRACT    
ABSTRACT    One line. Several lines with repeated Field
KEYWORDS    separation by ;
END_ABSTRACT    
     
BEGIN_IDENTITY_GENE    
NAME  <symbol> (description)  
ALIAS  1 alias by line .  repeatable
HGNC  HGNC symbol  
LOCATION  chromosomal band (as hg38 in UCSC)  
LOCATION_BASE_PAIR  coordonates   
LOCAL_ORDER     
IMAGE  reference to a jpg, png .. Image The images are saved in a sub directory Images
IMAGE_LEGEND     
IMAGE_FISH     
IMAGE_FISH_LEGEND     
NOTE     
END_IDENTITY_GENE    
     
BEGIN_DNA_DESCRIPTION    
NOTE     
IMAGE     
IMAGE_LEGEND     
IMAGE_2     
IMAGE_2_LEGEND    
LINK_IMAGE     
LINK_IMAGE_LEGEND     
DESCRIPTION  txt  
TRANSCRIPTION  txt  
PSEUDOGENE  txt  
END_DNA_DESCRIPTION    
     
BEGIN_PROTEIN_DESCRIPTION    
NOTE  txt  
IMAGE     
IMAGE_LEGEND     
DESCRIPTION  txt  
IMAGE_2     
IMAGE_2_LEGEND     
EXPRESSION  txt  
IMAGE_3     
IMAGE_3_LEGEND     
LOCALISATION  txt  
IMAGE_4     
IMAGE_4_LEGEND     
FUNCTION  txt  
IMAGE_5     
IMAGE_5_LEGEND     
HOMOLOGY     
IMAGE_6     
IMAGE_6_LEGEND     
IMAGE_7     
IMAGE_7_LEGEND     
END_PROTEIN_DESCRIPTION    
     
BEGIN_MUTATIONS     
NOTE  txt  
IMAGE     
IMAGE_LEGEND     
IMAGE_2    
IMAGE_2_LEGEND    
IMAGE_3    
IMAGE_3_LEGEND    
IMAGE_VIGNETTE    
IMAGE_VIGNETTE_LEGEND    
GERMINAL txt  
SOMATIC txt  
EPIGENETICS txt  
END_MUTATIONS    
     
BEGIN_IMPLICATED_IN     
TOP_NOTE    
     
BEGIN_ENTITY repeatable bloc  
ENTITY_NAME   <CC: TXT: Breast cancer ID: 5018>  
NOTE  txt  
DISEASE  txt  
PROGNOSIS  txt  
CYTOGENETICS  txt  
HYBRID_GENE  txt  
HYBRID_GENE_IMAGE     
HYBRID_GENE_IMAGE_LEGEND     
FUSION_PROTEIN  txt  
FUSION_PROTEIN_IMAGE     
FUSION_PROTEIN_IMAGE_LEGEND     
ONCOGENESIS  txt  
END_ENTITY    
     
END_IMPLICATED_IN    
     
BEGIN_BREAKPOINTS     
IMAGE_PARTNERS     
IMAGE_PARTNERS_LEGEND     
IMAGE     
IMAGE_LEGEND     
NOTE  txt  
END_BREAKPOINTS    
     
BEGIN_TO_BE_NOTED     
NOTE  txt  
IMAGE     
IMAGE_LEGEND     
END_TO_BE_NOTED    
     
BEGIN_EXTERNAL_LINKS     
HUGO     
GENECARD     
GDBID     
LOCUSLINK  Entrez Symbol The only Field required
GENBANK    All the other Fields are fullfilled by a script and parallel informations
UNIGENE    defined in genes_gc.txt and genes_gn.txt
SWISSPROT     
HGMD     
OMIM     
ORPHANET     
REGISTRY     
ASSOCIATIONS     
PROBES     
DATABASES     
NOTE    
END_EXTERNAL_LINKS    
     
BEGIN_FULL_BIBLIOGRAPHY    
     
BEGIN_REF repeatable bloc Actually references are ordered by fisrt author
TITLE   References are regenerated from PubMed by PMID value
AUTHORS    
REFERENCE    
PMID    
END_REF    
     
END_FULL_BIBLIOGRAPHY    
///    

 

II- TEMPLATE for LEUKEMIAS

Field Syntax Comment Example
BEGIN_HEADER      
FILENAME <Transloc>IDxxx.txt      
CLASSE CHROM_CLIN fixed    
ID       
STATUS      
TRI_PAR_CHROMOSOME      
TRI_CHROM      Examples: 01;19 for t(1;19); 16;00 for inv(16); 99;00 for "NA" (no chrom. Assigned)
TRANSLOC      Example: t(11;19)(q13;p13) FSTL3/CCND1
FUSION_GENE     Example: FSTL3/CCND1
CLASS_DISEASE one or several values; one value per line MPD, and/or  MDS, t-AML, AML, B-ALL, T-ALL, NHL  
ICD-O3_TOPO      C420,C421,C424
ICD-O3_MORPH      
END_HEADER      
       
BEGIN_AUTHOR      
CREATED   DATE date AUTHORS authors      
CITATION       
AUTHOR_AFFILIATION      
UPDATED   DATE date AUTHORS authors      
CITATION      
AUTHOR_AFFILIATION      
END_AUTHOR      
       
BEGIN_ABSTRACT      
ABSTRACT       
KEYWORDS       
END_ABSTRACT      
       
BEGIN_IDENTITY_CHROM_CLIN      
NAME       
ALIAS       
NOTE       
IMAGE       
IMAGE_LEGEND       
END_IDENTITY_CHROM_CLIN      
       
BEGIN_CLINICS_AND_PATHOLOGY      
NOTED      
       
BEGIN_DISEASE       
DISEASE       
NOTE       
PHENOTYPE_STEM_CELL_ORIGIN       
EMBRYONIC_ORIGIN       
ETIOLOGY       
EPIDEMIOLOGY       
CLINICS       
CLINICS_IMAGE       
CLINICS_IMAGE_LEGEND       
CYTOLOGY_IMAGE       
CYTOLOGY_IMAGE_LEGEND       
CYTOLOGY       
PATHOLOGY       
PATHOLOGY_IMAGE       
PATHOLOGY_IMAGE_LEGEND       
PATHOLOGY_IMAGE_2       
PATHOLOGY_IMAGE_2_LEGEND       
PATHOLOGY_IMAGE_3       
PATHOLOGY_IMAGE_3_LEGEND       
PATHOLOGY_IMAGE_4      
PATHOLOGY_IMAGE_4_LEGEND       
PATHOLOGY_IMAGE_5      
PATHOLOGY_IMAGE_5_LEGEND       
PATHOLOGY_IMAGE_6       
PATHOLOGY_IMAGE_6_LEGEND       
PATHOLOGY_IMAGE_7      
PATHOLOGY_IMAGE_7_LEGEND      
PATHOLOGY_IMAGE_8      
PATHOLOGY_IMAGE_8_LEGEND       
PATHOLOGY_IMAGE_9       
PATHOLOGY_IMAGE_9_LEGEND       
PATHOLOGY_IMAGE_10      
PATHOLOGY_IMAGE_10_LEGEND      
PATHOLOGY_IMAGE_11      
PATHOLOGY_IMAGE_11_LEGEND       
PATHOLOGY_IMAGE_12       
PATHOLOGY_IMAGE_12_LEGEND       
OTHER_FEATURES       
OTHER_FEATURES_IMAGE      
OTHER_FEATURES_IMAGE_LEGEND      
CYTOGENETICS       
GENES       
TREATMENT       
EVOLUTION       
PROGNOSIS       
END_DISEASE      
       
END_CLINICS_AND_PATHOLOGY      
       
BEGIN_GENETICS      
NOTE       
GENETICS_IMAGE       
GENETICS_IMAGE_LEGEND       
GENETICS_IMAGE_2       
GENETICS_IMAGE_2_LEGEND       
GENETICS_IMAGE_3       
GENETICS_IMAGE_3_LEGEND       
END_GENETICS      
       
BEGIN_CYTOGENET      
NOTE       
CYTOGENETICS_MORPHOLOGICAL_IMAGE       
CYTOGENETICS_MORPHOLOGICAL_IMAGE_LEGEND       
CYTOGENETICS_MORPHOLOGICAL       
CYTOGENETICS_MOLECULAR       
CYTOGENETICS_MOLECULAR_IMAGE       
CYTOGENETICS_MOLECULAR_IMAGE_LEGEND       
PROBES       
ADDITIONAL_ANOMALIES       
VARIANTS       
END_CYTOGENET      
       
BEGIN_GENES_AND_PROTEINS      
NOTE       
COMPLEMENTATION_GROUPS       
       
BEGIN_GENE_SHORT      
GENE_NAME       
ID      
LOCATION       
NOTE       
DNA_RNA_DESCRIPTION       
IMAGE       
IMAGE_LEGEND       
PROTEIN_DESCRIPTION       
GERMINAL_MUTATIONS       
SOMATIC_MUTATIONS       
END_GENE_SHORT      
       
END_GENES_AND_PROTEINS      
       
BEGIN_RESULT_OF_THE_CHROMOSOMAL_ANOMALY      
BEGIN_HYBRID_GENE      
NOTE       
HYBRID_GENE_IMAGE       
HYBRID_GENE_IMAGE_LEGEND       
DESCRIPTION       
TRANSCRIPT       
DETECTION_PROTOCOLE       
END_HYBRID_GENE      
       
BEGIN_FUSION_PROTEIN      
NOTE       
FUSION_PROTEIN_IMAGE       
FUSION_PROTEIN_IMAGE_LEGEND       
DESCRIPTION       
EXPRESSION_LOCALISATION       
ONCOGENESIS       
END_FUSION_PROTEIN      
       
END_RESULT_OF_THE_CHROMOSOMAL_ANOMALY      
       
BEGIN_TO_BE_NOTED      
NOTE      
IMAGE       
IMAGE_LEGEND       
CASE_REPORT      
END_TO_BE_NOTED      
       
BEGIN_EXTERNAL_LINKS      
PROBES       
DATABASES       
NOTE       
END_EXTERNAL_LINKS      
       
BEGIN_FULL_BIBLIOGRAPHY      
       
BEGIN_REF      
TITLE      
AUTHORS      
REFERENCE      
PMID      
END_REF      
       
END_FULL_BIBLIOGRAPHY      
///      

 

III- TEMPLATE for SOLID TUMORS

Field Syntax
BEGIN_HEADER  
FILENAME   
CLASSE TUMOUR fixed
ID   
TRI_PAR_CHROMOSOME  
TRI_CHROM   
TRANSLOC  
FUSION_GENE   
ICD-O3_TOPO  
ICD-O3_MORPH  
END_HEADER  
   
BEGIN_AUTHOR  
CREATED   DATE date AUTHORS authors  
CITATION   
AUTHOR_AFFILIATION  
UPDATED   DATE date AUTHORS authors  
CITATION  
AUTHOR_AFFILIATION  
END_AUTHOR  
   
BEGIN_ABSTRACT  
ABSTRACT   
KEYWORDS   
END_ABSTRACT  
   
BEGIN_IDENTITY_TUMOUR   
NAME   
ALIAS   
PHYLUM_COMPLETE  
PHYLUM_TISSUE_ORGAN  
PHYLUM_DISEASE  
NOTE   
IMAGE   
IMAGE_LEGEND   
END_IDENTITY_TUMOUR  
   
BEGIN_CLASSIFICATION  
NOTE   
IMAGE   
IMAGE_LEGEND  
CLASSIFICATION  
END_CLASSIFICATION  
   
BEGIN_CLINICS_AND_PATHOLOGY  
NOTE  
   
BEGIN_DISEASE   
DISEASE   
NOTE   
PHENOTYPE_STEM_CELL_ORIGIN   
EMBRYONIC_ORIGIN   
ETIOLOGY   
EPIDEMIOLOGY   
CLINICS   
CLINICS_IMAGE   
CLINICS_IMAGE_LEGEND   
CYTOLOGY_IMAGE   
CYTOLOGY_IMAGE_LEGEND   
CYTOLOGY   
PATHOLOGY   
PATHOLOGY_IMAGE   
PATHOLOGY_IMAGE_LEGEND   
PATHOLOGY_IMAGE_2   
PATHOLOGY_IMAGE_2_LEGEND   
PATHOLOGY_IMAGE_3   
PATHOLOGY_IMAGE_3_LEGEND   
OTHER_FEATURES   
OTHER_FEATURES_IMAGE  
OTHER_FEATURES_IMAGE_LEGEND  
CYTOGENETICS   
GENES   
TREATMENT   
EVOLUTION   
PROGNOSIS   
END_DISEASE  
   
END_CLINICS_AND_PATHOLOGY  
   
BEGIN_GENETICS  
NOTE   
GENETICS_IMAGE   
GENETICS_IMAGE_LEGEND   
GENETICS_IMAGE_2   
GENETICS_IMAGE_2_LEGEND   
GENETICS_IMAGE_3   
GENETICS_IMAGE_3_LEGEND   
END_GENETICS  
   
BEGIN_CYTOGENET  
NOTE   
CYTOGENETICS_MORPHOLOGICAL_IMAGE   
CYTOGENETICS_MORPHOLOGICAL_IMAGE_LEGEND   
CYTOGENETICS_MORPHOLOGICAL   
CYTOGENETICS_MOLECULAR   
CYTOGENETICS_MOLECULAR_IMAGE   
CYTOGENETICS_MOLECULAR_IMAGE_LEGEND   
PROBES   
ADDITIONAL_ANOMALIES   
VARIANTS   
END_CYTOGENET  
   
BEGIN_GENES_AND_PROTEINS  
NOTE   
COMPLEMENTATION_GROUPS   
   
BEGIN_GENE_SHORT  
GENE_NAME   
ID  
LOCATION   
NOTE   
DNA_RNA_DESCRIPTION   
IMAGE   
IMAGE_LEGEND   
PROTEIN_DESCRIPTION   
GERMINAL_MUTATIONS   
SOMATIC_MUTATIONS   
END_GENE_SHORT  
   
END_GENES_AND_PROTEINS  
   
BEGIN_RESULT_OF_THE_CHROMOSOMAL_ANOMALY  
BEGIN_HYBRID_GENE  
NOTE   
HYBRID_GENE_IMAGE   
HYBRID_GENE_IMAGE_LEGEND   
DESCRIPTION   
TRANSCRIPT   
DETECTION_PROTOCOLE   
END_HYBRID_GENE  
   
BEGIN_FUSION_PROTEIN  
NOTE   
FUSION_PROTEIN_IMAGE   
FUSION_PROTEIN_IMAGE_LEGEND   
DESCRIPTION   
EXPRESSION_LOCALISATION   
ONCOGENESIS   
END_FUSION_PROTEIN  
   
END_RESULT_OF_THE_CHROMOSOMAL_ANOMALY  
   
BEGIN_TO_BE_NOTED  
NOTE   
IMAGE   
IMAGE_LEGEND   
END_TO_BE_NOTED  
   
BEGIN_EXTERNAL_LINKS  
PROBES   
DATABASES   
NOTE   
END_EXTERNAL_LINKS  
   
BEGIN_FULL_BIBLIOGRAPHY  
   
BEGIN_REF  
TITLE  
AUTHORS  
REFERENCE  
PMID  
END_REF  
   
END_FULL_BIBLIOGRAPHY  
///  

 

IV- TEMPLATE for CANCER-PRONE DISEASES

Field Syntax Comment Example
BEGIN_HEADER      
FILENAME      
CLASSE K_PRONE fixed    
ID    Atlas_ID  
TRI_PAR_CHROMOSOME      
LOCATION       
GENES_INVOLVED      
OMIM      
END_HEADER      
       
BEGIN_AUTHOR      
CREATED   DATE date AUTHORS authors      
CITATION       
AUTHOR_AFFILIATION      
UPDATED   DATE date AUTHORS authors      
CITATION      
AUTHOR_AFFILIATION      
END_AUTHOR      
       
BEGIN_ABSTRACT      
ABSTRACT       
KEYWORDS       
END_ABSTRACT      
       
BEGIN_IDENTITY_K_PRONE      
NAME       
ALIAS       
NOTE       
INHERITANCE       
IMAGE       
IMAGE_LEGEND       
END_IDENTITY_K_PRONE       
       
BEGIN_CLINICS      
NOTE       
PHENOTYPE_AND_CLINICS       
IMAGE_1       
IMAGE_1_LEGEND       
IMAGE_2       
IMAGE_2_LEGEND       
DIFFERENTIAL_DIAGNOSIS       
IMAGE_3       
IMAGE_3_LEGEND       
NEOPLASTIC_RISK       
TREATMENT       
EVOLUTION       
PROGNOSIS       
END_CLINICS      
       
BEGIN_CYTOGENETICS      
NOTE       
INBORN_CONDITION       
IMAGE       
IMAGE_LEGEND       
ACQUIRED_CONDITION       
ACQUIRED_CONDITION_IMAGE       
ACQUIRED_CONDITION_IMAGE_LEGEND       
END_CYTOGENETICS      
       
BEGIN_OTHER_FINDINGS      
NOTE       
END_OTHER_FINDINGS      
       
BEGIN_GENES_AND_PROTEINS      
NOTE       
COMPLEMENTATION_GROUPS       
       
BEGIN_GENE      
GENE_NAME      <CC: TXT: BRCA1 ID: 11111>
ID     11111
LOCATION      25q23.4
NOTE       
END_GENE       
       
BEGIN_DNA_DESCRIPTION      
NOTE       
IMAGE       
IMAGE_LEGEND       
DNA_DESCRIPTION       
TRANSCRIPTION       
PSEUDOGENE       
END_DNA_DESCRIPTION      
       
BEGIN_PROTEIN_DESCRIPTION      
NOTE       
IMAGE       
IMAGE_LEGEND       
DESCRIPTION       
EXPRESSION       
LOCALISATION       
FUNCTION       
HOMOLOGY       
END_PROTEIN_DESCRIPTION      
       
BEGIN_MUTATIONS       
NOTE       
IMAGE       
IMAGE_LEGEND       
GERMINAL       
SOMATIC       
EPIGENETICS       
END_MUTATIONS      
       
END_GENES_AND_PROTEINS      
       
BEGIN_TO_BE_NOTED       
NOTE       
IMAGE       
IMAGE_LEGEND       
CASE_REPORT       
END_TO_BE_NOTED      
       
BEGIN_EXTERNAL_LINKS      
HGMD      
OMIM      
ORPHANET      
REGISTRY      
ASSOCIATIONS      
DATABASES      
NOTE       
END_EXTERNAL_LINKS      
       
BEGIN_FULL_BIBLIOGRAPHY      
       
BEGIN_REF      
TITLE      
AUTHORS      
REFERENCE      
PMID      
END_REF      
       
END_FULL_BIBLIOGRAPHY      
///      

# ##################################################
# 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

The Atlas website structure
http://atlasgeneticsoncology.org

Philippe Dessen (Database Director) This email address is being protected from spambots. You need JavaScript enabled to view it.
Jean Loup Huret (Editor) This email address is being protected from spambots. You need JavaScript enabled to view it.
May 2018

 

 


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:


NAME

STATUS

AUTHORS

ID Atlas

ICD-O3_MORPH

ICD-O3_TOPO

05;00§ tri 5/NHL or chronic Lympho

FOR SALE

 

 

 

C421,C424

05;00§ MDS with isolated del (5q)

DONE

XX

1134

9986/3

C421,C424

05;00§ del(5)(q32q33) TNIP1/PDGFRB

Reserved

XXXX

1773

 

C421,C424

… about 1,000 items/lines

 

 

 

 

 

99;99§ Extraosseous plasmacytoma

Reserved

XXXXXX

1718

734/3

C421,C424

99;99§ Florid follicular hyperplasia PTLD

Reserved

XXX

1788

 

C421,C424

AUTHOR

e-mail

"Translocation"

DEADLINE

COMMENTS

XXX

XXX@xx

Florid follicular hyperplasia PTLD

DONE

3rd paper (leuk.) + 1 paper (gene)

XXXX

XXXX@xxxx

del(5)(q32q33) TNIP1/PDGFRB

?????

Reminder 2017/06/26; 2017/03/21"Yes, will have this to you shortly"; Reminder 2016/11/19; Reminder 2016/06/17; 2016/01/17 no deadline ("soon"); 2015/10/14: OK

XXXXX

XXXXX@xxxx

del(X)(p22p22) (P2RY8/CRLF2)

16/03/2017

Spontaneous proposal

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:


Item

Internal hyperlink toward

1 Gene

n1 Leukemias

 

n2 Solid tumors

 

n3 Cancer-prone

 

 

1 Leukemia

n4 Genes

 

n5 Cancer-prone

 

 

1 Solid tumor

n6 Genes

 

n7 Cancer-prone

 

 

1 Cancer-prone

n8 Genes

 

n9 Leukemias
n10 Solid tumors

Examples:

Item

Hyperlinks toward

Gene

NUP214

Leukemia

t(6;9)(p23;q34) DEK/NUP214

 

 

Leukemia

t(9;9)(q34;q34) SET/NUP214

 

 

Leukemia

T cell ALL

 

 

Solid Tumor

Lung Adenocar. t(9;9)(q34;q34) PRRC2B/NUP214

 

 

 

 

Gene

KIT

Leukemia

trisomy 4

 

 

Solid Tumor

Melanoma

 

 

Cancer Prone

Piebaldism

 

 

 

 

Leukemia

t(6;9)(p23;q34) DEK/NUP214

Gene

NUP214

 

 

Gene

DEK

 

 

 

 

Cancer Prone

Tuberous sclerosis

Gene

TSC1

 

 

Gene

TSC2

 

 

Solid Tumor

Renal carcinoma

 

 

Solid Tumor

Ependymomas

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.