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      
///