List of allowed columns for generic overlay data#
- table of content
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 |