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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 |
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 |
| identifier_wikipedia | |
| identifier_worm_base |