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 | |||
| /// |