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List of allowed columns for generic overlay data#

General terms#

color

Description: The color of the colored element, in the hex format.

Remarks: Color and value exclude each other for an element, do not use these terms together.

Example: #e58ec5

compartment

Description: Narrow coloring to the elements in the compartment.

Remarks: 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.

Example: nucleus

description

Description: The description user provided, it is not displayed by MINERVA.

element_identifier

Description: Color an element by CellDesigner alias id of the element or a reaction id.

Remarks: Interactions coloring and elements by CellDesigner id.

Example: sa81; re423

line_width

Description: The width of the colored interaction. It can be any number {1,2,3….}

Remarks: Interactions coloring only.

Example: 3

map_name

Description: The name of the map or the submap that the coloring is narrow down.

Example: submap1

name

Description: The name of an elements to be colored.

Remarks: Do not use name with identifiers together. One row for one specified group of elements.

Example: h2o; SNCA; fibril

reverse_reaction

Description: Drawing reversed arrows on the colored reaction. Reserved arrows are visible only on the image of map (colored map must be exported as image).

Remarks: Interactions coloring only.

Example: TRUE / FALSE

type

Description: Narrow down coloring of the particular element to its type.

Remarks: Type includes: PROTEIN, GENE, COMPLEX, SIMPLE_MOLECULE, ION, PHENOTYPE, DRUG, RNA, ANTISENSE_RNA, UNKNOWN, DEGRADED.

Example: ion

value

Description: Value of the coloring, the same as in basic overlay, range from [-1,1].

Remarks: Value and color exclude each other for an element, do not use together.

Example: 0.7

identifier

Description: General identifier, any annotation id can be used here.

Remarks: The value is as follows: name of annotator:id

Example: go:GO:1901215; UniProt:O60260; chebi:CHEBI:16908

identifier_[annotator]

Description: Specific identifier, put annotator name in the bracket. The available columns names are displayed below.

Remarks: The value is a specific annotator id.

Example: 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.