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List of allowed columns for generic overlay data

Please note that all terms are case insensitive.

General terms

Column name Description Remarks Example of usage
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
description The description user provided, it is not displayed by MINERVA.    
element_identifier Color an element by CellDesigner alias id of the element or a reaction id. Interactions coloring and elements by CellDesigner id. sa81; re423
line_width The width of the colored interaction. It can be any number {1,2,3….} Interactions coloring only. 3
map_name The name of the map or the submap that the coloring is narrow down.   submap1
name The name of an elements to be colored. Do not use name with identifiers together. One row for one specified group of elements. h2o; SNCA; fibril
reverse_reaction Drawing reversed arrows on the colored reaction. Reserved arrows are visible only on the image of map (colored map must be exported as image). Interactions coloring only. TRUE / FALSE
type Narrow down coloring of the particular element to its type. Type includes: PROTEIN, GENE, COMPLEX, SIMPLE_MOLECULE, ION, PHENOTYPE, DRUG, RNA, ANTISENSE_RNA, UNKNOWN, DEGRADED. ion
value Value of the coloring, the same as in basic overlay, range from [-1,1]. Value and color exclude each other for an element, do not use together.  
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