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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 |
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 |