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List of allowed columns for genetic variant overlay data

Note: All terms are case insensitive.

General terms

Column name Description 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 of the elements in different compartments works ONLY for separate (not nested) compartments. Setting a color for elements in a compartment that encloses other compartments does not set the color inside the nested compartments. 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
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

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Available annotators / identifiers

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

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

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