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List of allowed columns for genetic variant overlay data

Please note that all terms are case insensitive.

General terms

Column name Description Important remarks Example
allele_frequency The relative frequency of this variant; it will be visualized by the height of the bar in the genome browser popup optional, range:[0,1]. Visualises a frequency as the height of the variant marker, proportional to the value. 0.3750000
alternative_DNA The variant of the DNA.   A; T
amino_acid_change MolArt, optional. The change in the protein-coding region associated with this variant. Allows to visualize the mutation in the protein structure in MolArt. PRKN:NC_000006.11:g.162683694G>A:p.A92V
chromosome Number of the chromosome. The same information as column Contig chr3; chrY; 3; scaffold10102
color The color of the colored element, in the hex format. Color and value exclude each other for an element, do not use these terms together. #e58ec5
compartment Narrow coloring to the elements in the compartment. Coloring compartments works ONLY for separate (not nested) compartments. Setting a color for elements in a compartment that encloses other compartments sets the color in the nested compartments as well. nucleus
Contig Number of the chromosome. The same function as column chromosome chr3; chrY; 3; scaffold10102
description The description user provided, it is not displayed by MINERVA.    
gene_name The name of the gene variant.    
map_name The name of the map or the submap that the coloring is narrow down.   submap1
original_DNA The reference DNA.   G; T
position The location of the variant in the genome.   161709831
references PubMed publications id.   20171212
variant_identifier The indicator of a mutation, the mutation and it’s position   rs55654276
identifier General identifier, any annotation id can be used here. The value is as follows: name of annotator:id go:GO:1901215; UniProt:O60260; chebi:CHEBI:16908
identifier_[annotator] Specific identifier, put annotator name in the bracket. The available columns names are displayed below. The value is a specific annotator id. GO:1901215; O60260; CHEBI:16908

Available annotators / identifiers

Below there is the list with annotations that MINERVA uses. The value is a specific identifier for a specific annotator.

Column name
identifier_BiGG_compartment identifier_DrugBank_target_v4 identifier_mgd identifier_sgd
identifier_BiGG_metabolite identifier_ec identifier_mi_r_base_mature_sequence identifier_stitch
identifier_BiGG_reactions identifier_Ensembl identifier_mi_r_base_sequence identifier_string
identifier_biomodels_database identifier_Ensembl_plants identifier_miR_tar_base_mature_sequence identifier_TAIR_locus
identifier_brenda identifier_Entrez identifier_obi identifier_taxonomy
identifier_cas identifier_go identifier_OMIM identifier_toxicogenomic_chemical
identifier_CAZy identifier_HGNC identifier_panther identifier_unigene
identifier_ccds identifier_HGNC_symbol identifier_PDB identifier_UniProt
identifier_chebi identifier_hmdb identifier_pfam identifier_UniProt_isoform
identifier_ChEMBL_compound identifier_interpro identifier_pharm identifier_unknown
identifier_ChEMBL_target identifier_KEGG_compound identifier_pubchem identifier_vmh_metabolite
identifier_chemspider identifier_KEGG_genes identifier_pubchem_substance identifier_vmh_reaction
identifier_clinical_trials_gov identifier_KEGG_orthology identifier_PubMed identifier_wikidata
identifier_cog identifier_KEGG_pathway identifier_Reactome identifier_wikipathways
identifier_doi identifier_KEGG_reaction identifier_RefSeq identifier_wikipedia
identifier_DrugBank identifier_mesh_2012 identifier_rhea identifier_worm_base