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List of allowed columns for generic overlay data


Note: All terms are case insensitive.

General terms

Column name Description Remarks Example
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
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

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Available annotators / identifiers

Below table shows the annotations MINERVA handles. The value is a specific identifier for a specific annotator.

Identifier name [A-K] Identifier name [L-Z]
identifier__3dmet identifier_ligand_expo
identifier_affymetrix_probeset identifier_ligand_gated_ion_channel_database
identifier_amoebadb identifier_lincs_cell
identifier_animal_diversity_web identifier_lincs_protein
identifier_animal_genome_cattle_qtl identifier_lipid_bank
identifier_animal_genome_chicken_qtl identifier_lipid_maps
identifier_animal_genome_pig_qtl identifier_macie
identifier_animal_genome_sheep_qtl identifier_maizegdb_locus
identifier_animal_tfdb_family identifier_massbank
identifier_antibiotic_resistance_genes_database identifier_medlineplus
identifier_antweb identifier_merops_family
identifier_apd identifier_merops_inhibitor
identifier_aphidbase_transcript identifier_merops
identifier_arachnoserver identifier_mesh_2012
identifier_arrayexpress_platform identifier_metabolights
identifier_arxiv identifier_metanetx_chemical
identifier_asap identifier_metanetx_reaction
identifier_aspgd_protein identifier_metlin
identifier_atcc identifier_mgd
identifier_autdb identifier_mged_ontology
identifier_bacmap_biography identifier_mgnify_project
identifier_bdgp_est identifier_mi_r_base_sequence
identifier_bdgp_insertion_db identifier_mi
identifier_beetlebase identifier_microbial_protein_interaction_database
identifier_bgee_gene identifier_microsporidiadb
identifier_bgee_organ identifier_mipmoddb
identifier_bgee_stage identifier_mir_tar_base_mature_sequence
identifier_bigg_metabolite identifier_miriam_registry_resource
identifier_bindingdb identifier_mmrrc
identifier_biocarta_pathway identifier_mod
identifier_biocatalogue identifier_molbase
identifier_biomodels_database identifier_molecular_modeling_database
identifier_bionumbers identifier_mycobank
identifier_bioportal identifier_mycobrowser_leprae
identifier_bioproject identifier_mycobrowser_marinum
identifier_biosystems identifier_mycobrowser_smegmatis
identifier_bitterdb_receptor identifier_mycobrowser_tuberculosis
identifier_bold_taxonomy identifier_napp
identifier_brenda_tissue_ontology identifier_narcis
identifier_broad_fungal_genome_initiative identifier_nasc_code
identifier_bugbase_expt identifier_national_bibliography_number
identifier_bugbase_protocol identifier_national_drug_code
identifier_bykdb identifier_ncbi_protein
identifier_canadian_drug_product_database identifier_neurolex
identifier_caps_db identifier_neuromorpho
identifier_cazy identifier_neurondb
identifier_ccds identifier_niaest
identifier_cell_cycle_ontology identifier_nite_biological_research_center_catalogue
identifier_cell_signaling_technology_antibody identifier_noncode_v3
identifier_cell_signaling_technology_pathways identifier_noncode_v4_gene
identifier_charprot identifier_noncode_v4_transcript
identifier_chebi identifier_nucleardb
identifier_chem_id_plus identifier_obi
identifier_chembl_compound identifier_odor_molecules_database
identifier_chembl_target identifier_olfactory_receptor_database
identifier_chemdb identifier_oma_group
identifier_chemspider identifier_omia
identifier_cldb identifier_omim
identifier_clinical_trials_gov identifier_omit
identifier_clinvar_record identifier_ontology_of_physics_for_biology
identifier_cog identifier_opm
identifier_combine_specifications identifier_orcid
identifier_compulyeast identifier_oridb_saccharomyces
identifier_conoserver identifier_oridb_schizosaccharomyces
identifier_conserved_domain_database identifier_orphanet_rare_disease_ontology
identifier_corum identifier_orthodb
identifier_cpc identifier_oryza_tag_line
identifier_cryptodb identifier_oryzabase_gene
identifier_csa identifier_oryzabase_mutant
identifier_cube_db identifier_oryzabase_stage
identifier_cutdb identifier_oryzabase_strain
identifier_dailymed identifier_p3db_protein
identifier_darc identifier_p3db_site
identifier_database_of_interacting_proteins identifier_paleodb
identifier_datf identifier_panther_node
identifier_db_snp identifier_panther_pathway_component
identifier_dbest identifier_pathway_ontology
identifier_dbg2_introns identifier_pato
identifier_degradome_database identifier_paxdb_organism
identifier_depod identifier_paxdb_protein
identifier_dictybase_est identifier_pazar_transcription_factor
identifier_dictybase_gene identifier_pdb
identifier_disprot identifier_peptideatlas
identifier_doi identifier_pfam
identifier_dommino identifier_pharmgkb_drug
identifier_door identifier_pharmgkb_gene
identifier_dpv identifier_phenol_explorer
identifier_dragondb_allele identifier_phosphopoint_phosphoprotein
identifier_dragondb_dna identifier_phosphosite_residue
identifier_dragondb_protein identifier_phylomedb
identifier_drsc identifier_phytozome_locus
identifier_drugbank identifier_piroplasmadb
identifier_ec identifier_plant_ontology
identifier_echobase identifier_pmc
identifier_eco identifier_pocketome
identifier_ecogene identifier_polbase
identifier_ecoliwiki identifier_pombase
identifier_edam_ontology identifier_pride_project
identifier_eggnog identifier_prosite
identifier_elm identifier_protclustdb
identifier_ena identifier_protein_data_bank_ligand
identifier_ensembl_fungi identifier_proteomicsdb_peptide
identifier_ensembl_metazoa identifier_protonet_cluster
identifier_ensembl_plants identifier_protonet_proteincard
identifier_ensembl_protists identifier_pscdb
identifier_ensembl identifier_pseudomonas_genome_database
identifier_entrez identifier_pubchem_bioassay
identifier_epd identifier_pubmed
identifier_eu_clinical_trials identifier_rat_genome_database_qtl
identifier_european_genome_phenome_archive_dataset identifier_reactome
identifier_european_genome_phenome_archive_study identifier_rebase
identifier_exac_transcript identifier_refseq
identifier_exac_variant identifier_relation_ontology
identifier_f_snp identifier_rgd
identifier_flybase identifier_rice_genome_annotation_project
identifier_foodb_compound identifier_rna_modification_database
identifier_funcbase_human identifier_rouge
identifier_funcbase_mouse identifier_sabio_rk_ec_record
identifier_funcbase_yeast identifier_sabio_rk_kinetic_record
identifier_fungidb identifier_saccharomyces_genome_database_pathways
identifier_gabi identifier_sbo_term
identifier_genatlas identifier_scertf
identifier_gene_wiki identifier_scop
identifier_genecards identifier_seed_compound
identifier_genefarm identifier_seed_reactions
identifier_genetree identifier_sequence_read_archive
identifier_genome_properties identifier_sider_side_effect
identifier_geo identifier_signaling_gateway
identifier_glida_gpcr identifier_snomed_ct
identifier_glida_ligand identifier_sol_genomics_network
identifier_glycomedb identifier_spectral_database_for_organic_compounds
identifier_go_ref identifier_spike
identifier_go identifier_stap
identifier_gold_genome identifier_stitch
identifier_golm_metabolome_database_gc_ms_spectra identifier_string
identifier_golm_metabolome_database_profile identifier_substratedb
identifier_golm_metabolome_database identifier_subtilist
identifier_google_patents identifier_subtiwiki
identifier_gpcrdb identifier_swiss_lipids
identifier_grsdb identifier_swiss_model
identifier_gwas_cenral_marker identifier_t3db
identifier_gwas_cenral_phenotype identifier_tair_gene
identifier_gwas_cenral_study identifier_tair_protein
identifier_h_invdb_locus identifier_tarbase
identifier_h_invdb_protein identifier_taxonomy
identifier_h_invdb_transcript identifier_teddy
identifier_hcvdb identifier_tetrahymena_genome_database
identifier_hgmd identifier_tigrfams
identifier_hgnc_family identifier_tissue_list
identifier_hgnc_symbol identifier_topfind
identifier_hgnc identifier_toxicogenomic_chemical
identifier_hmdb identifier_toxodb
identifier_hogenom identifier_transport_classification_database
identifier_homd_sequence_metainformation identifier_tree_of_life
identifier_homeodomain_research identifier_treefam
identifier_homologene identifier_trichdb
identifier_hovergen identifier_tritrypdb
identifier_hssp identifier_ttd_drug
identifier_huge identifier_ttd_target
identifier_human_disease_ontology identifier_uberon
identifier_human_proteome_map_peptide identifier_ubio_namebank
identifier_human_proteome_map_protein identifier_um_bbd_biotransformation_rule
identifier_icd identifier_unigene
identifier_iceberg_element identifier_unimod
identifier_iceberg_family identifier_uniparc
identifier_ideal identifier_unipathway_reaction
identifier_identifiers_org_terms identifier_uniprot
identifier_imex identifier_unit_ontology
identifier_imgt_hla identifier_unite
identifier_intact_molecule identifier_unknown
identifier_intact identifier_uspto
identifier_interpro identifier_vario
identifier_ird_segment_sequence identifier_vbase2
identifier_isbn identifier_vfdb_gene
identifier_isfinder identifier_vfdb_genus
identifier_issn identifier_virsirna
identifier_iuphar_family identifier_vmh_metabolite
identifier_iuphar_receptor identifier_vmh_reaction
identifier_japan_chemical_substance_dictionary identifier_wikidata
identifier_japan_collection_of_microorganisms identifier_wikigenes
identifier_jax_mice identifier_wikipathways
identifier_jstor identifier_wikipedia
identifier_jws_online identifier_worfdb
identifier_kegg_compound identifier_worm_base_rnai
identifier_kegg_disease identifier_worm_base
identifier_kegg_environ identifier_wormpep
identifier_kegg_genes identifier_xenbase
identifier_kegg_glycan identifier_ydpm
identifier_kegg_orthology identifier_yeast_intron_database_v3
identifier_kegg_pathway identifier_yeast_intron_database_v4_3
identifier_kegg_reaction identifier_yetfasco
identifier_knapsack identifier_yrc_pdr
identifier_zinc

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