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      
///