KEGG Markup Language

Schema

Data types

Types

Name	Description	Pattern
string.type	Simple string type.
url.type	String of url to locate web resource.
keggid.type	KEGG database identifier.
maporg.type	Organism of KEGG pathway.
mapnumber.type	Identifier of KEGG pathway.	^([0-9]+)$
id.type	Identifier of element in pathway.	^([0-9]+)$
entry-type.type	Type of entry in KEGG pathway.	See list of valid entry types.
number.type	Simple digit string type. Must be at least one digit.	^([0-9]+)$
graphics.type	Type of graphics element.	See list of valid graphics types.
graphics-color.type	String of hexadecimal color.	^#([0-9a-fA-F]{6})$
idref.type	Reference to other element identifier of type id.type.	^([0-9]+)$
relation-type.type	Type of relation element.	See list of valid relation types.
subtype-name.type	Subtype name.	See list of valid subtype names.
subtype-value.type	Subtype value.	See list of valid subtype values.
reaction-type.type	Type of reaction.	See list of valid reaction types.

Entry type

Value	Description
ortholog	Ortholog entry (KO entry).
enzyme	Enzyme entry.
reaction	Reaction entry.
gene	Gene product entry (Protein).
group	Protein complex entry.
compound	Compound entry (molecule, glycan).
map	Linked pathway entry.
brite	Brite hierarchy entry.
other	Unclassified type of entry.

Graphics type

Value	Description
rectangle	Gene products and complexes are represented with a rectangle shape.
circle	Molecules, compounds and glycans are represented with a circle shape.
roundrectangle	Linked pathways are represented with a rounded rectangle shape.
line	Reactions and relations are represented with a line.

Relation type

Value	Description
ECrel	Enzyme-enzyme relation.
PPrel	Protein-protein relation.
GErel	Transcription factor and target gene relation.
PCrel	Protein-compound relation.
maplink	Link to other pathway.

Reaction type

Value	Description
reversible	Reversible reaction.
irreversible	Irreversible reaction.

Elements

pathway

The pathway element is the root element in the KGML file. All other elements are children of the element.

Attributes

Name	Description	Type	Required/Optional
name	KEGG id of pathway.	keggid.type	Required
org	KEGG organism identifier.	maporg.type	Required
number	Map number of pathway.	mapnumber.type	Required
title	Title of pathway.	string.type	Optional
image	Url to image of pathway.	url.type	Optional
link	Url to information of pathway.	url.type	Optional

entry

Attributes

Name	Description	Type	Required/Optional
id	Identifier of entry in pathway.	id.type	Required
name	KEGG identifier of entry.	keggid.type	Required
type	Type of entry.	entry_type.type	Required
link	Url to information of this entry.	url.type	Optional
reaction	KEGG identifier of corresponding reaction.	keggid.type	Optional

graphics

Attributes

Name	Description	Type	Required/Optional
name	Label of graphics element.	string.type	Optional
x	X position of graphics element.	number.type	Optional
y	Y position of graphics element.	number.type	Optional
width	Width of graphics element.	number.type	Optional
height	Height of graphics element.	number.type	Optional
coords	Coordinates of a line object in graphics element. Komma-seperated list of numbers (x1,y1,x2,y2).	string.type	Optional
type	Type of graphics element	graphics.type	Optional
fgcolor	Foreground color used by graphics element.	graphics-color.type	Optional
bgcolor	Background color used by graphics element.	graphics-color.type	Optional

component

Attributes

Name	Description	Type	Required/Optional
id	Identifier referencing entry in pathway.	idref.type	Required

relation

Attributes

Name	Description	Type	Required/Optional
entry1	Identifier referencing first entry in pathway.	idref.type	Required
entry2	Identifier referencing second entry in pathway.	idref.type	Required
type	Type of relation.	relation-type.type	Required

subtype

Attributes

Name	Description	Type	Required/Optional
name	Name of subtype.	subtype-name.type	Required
value	Value of subtype.	subtype-value.type	Required

reaction

Attributes

Name	Description	Type	Required/Optional
id	Identifier referencing reaction in pathway.	idref.type	Required
name	KEGG identifier of reaction.	keggid.type	Required
type	Type of reaction.	reaction-type.type	Required

substrate

Attributes

Name	Description	Type	Required/Optional
id	Identifier of substrate.	idref.type	Required
name	KEGG identifier of substrate.	keggid.type	Required

product

Attributes

Name	Description	Type	Required/Optional
id	Identifier of product.	idref.type	Required
name	KEGG identifier of product.	keggid.type	Required

alt

Attributes

Name	Description	Type	Required/Optional
name	Alternative name of parent element as KEGG identifier.	keggid.type	Required