SKM - PSS database schema

Naming conventions

Name format

Node labels: UpperCamelCase
Relationship types: UPPER_SNAKE_CASE
Property keys: snake_case

Edge

Relationship between two nodes

Source

source (start) node of a relationship.

Target

target (end) node of a relationship.

Node labels

A node can have multiple labels. In general, the primary labels have a constraint of a unique name within the label.

Primary Labels

Primary label	Secondary labels (*=optional)	Description
Complex	Node	Complexes that can contain plant, foreign and/or metabolite components
Metabolite	Node, MetaboliteFamily*	Chemical entities
Family	Node, [PlantAbstract \| PlantCoding \| PlantNonCoding]	Gene family (set of all genes within the family)
Clade	Node, [PlantAbstract \| PlantCoding \| PlantNonCoding]	Set of genes defined by sequence similarity
FunctionalCluster	Node, [PlantAbstract \| PlantCoding \| PlantNonCoding]	Set of genes with the same function
Process	Node
ForeignEntity	Node, Foreign	Biological foreign entity, such as a pathogen species
ForeignCoding	Node, Foreign	Protein coding agent of an external factor, such as a pathogen gene
ForeignNonCoding	Node, Foreign	Non-coding agent of an external factor, such as a pathogen gene
ForeignAbstract	Node, Foreign	Undefined or unspecified agent of an external factor, such as a pathogen gene
ForeignAbiotic	Node, Foreign	Abiotic factors (e.g. heat)
Reaction	Node	Reaction node defines a reaction or interaction between entities
Condition		Condition that affects reaction(s)

Secondary Labels

Label	Description
Node	All nodes
MetaboliteFamily	A group of similar chemical entities (e.g. reactive oxygen species)
PlantAbstract	Undefined or unspecified plant gene (e.g. without standard gene identifier)
PlantCoding	Plant gene with protein gene product
PlantNonCoding	Plant gene without protein gene product (e.g miRNA)
Plant	All plant specific nodes (PlantAbstract, PlantCoding, PlantNonCoding)
Foreign	External factors that are neither plant nor metabolite related

Edge types

Each edge only has one type.

Hierarchical related edges

Type	Description	Edge example
COMPONENT_OF	Source node is a component of target node (Complex)	(JAZ) ―[:COMPONENT_OF]→ (JAZ\|DELLA)
TYPE_OF	Source node (Metabolite) is a type of target node (MetaboliteFamily)	(O3) ―[:TYPE_OF]→ (ROS)
AGENT_OF	Source node (Foreign[*]) is an agent of target node (ForeignEntity)	(VPg) ―[:AGENT_OF]→ (potyvirus)
HAS_CLADE	Source node (Family) has child clade target node (Clade)	(AGO) ―[:HAS_CLADE]→ (AHP1,2,3,4,5)
TAKES_PART	Source node (Family) takes part in reactions via target node (FunctionalCluster)	(ACS) ―[:TAKES_PART]→ (ACS6)
CONDITION_INPUT	Source node form part of the condition target node (Condition) defines	(JAZ) ―[:CONDITION_INPUT]→ (NPR1 high & JAZ high)

Reaction related edges

Type	Description	Edge example
ACTIVATES	Source node activates target node (Reaction)	(CYP94) ―[:ACTIVATES]→ (rx00042)
INHIBITS	Source node inhibits target node (Reaction)	(miR6022) ―[:INHIBITS]→ (rx00308)
SUBSTRATE	Source node is a substrate in the reaction, and is consumed/catalysed by reaction	(JA-Ile) ―[:SUBSTRATE]→ (rx00042)
PRODUCT	Target node is a product in the reaction, and is produced/resulted from reaction	(rx00042) ―[:PRODUCT]→ (12-OH-JA-Ile)
TRANSLOCATE_FROM	Source node is translocated from source_compartment by reaction (sister to SUBSTRATE)	(SA) ―[:TRANSLOCATE_FROM]→ (rx00072)
TRANSLOCATE_TO	Target node is translocated to target_compartment by reaction (sister to PRODUCT)	(rx00072) ―[:TRANSLOCATE_TO]→ (SA)

Properties

'-' indicates all nodes and all edges
Property name	Applies to (labels/edge types)	Type	Note
added_by	-	string
creation_date	-	string
name	-	string
components	Complex	list
classification	ForeignEntity	string	Phylogenetic classification
species	ForeignEntity	string
family	FunctionalCluster	string
sequence	FunctionalCluster	string	Only in case of gene not existing in genome model (of GoMapMan)
short_name	FunctionalCluster	string
additional_information	Node	string
curated	Node	bool
external_links	Node	list	unknown, invented:<reason>, or <database>:<database identifier>, where database includes doi, pmid, aracyc, chebi, pubchem, kegg, etc
model_version	Node	string
pathway	Node	string	One of defined pathways
model_status	Node excluding Reaction	string
description	Node, Condition	string
<species>_homologues	Plant	list	list of species specific homologues
species	Plant	list	Subset of defined species
evidence_sentence	Reaction	string
experimental_techniques	Reaction	string
reaction_effect	Reaction	string	activation or inhibition
reaction_mechanism	Reaction	string
species	Reaction	list	Subset of defined species, and "all"
trust_level	Reaction	string	R1;R2;Rx...
reaction_id	Reaction, all reaction related edges	string
reaction_type	Reaction, all reaction related edges	string	One of defined reaction types
source_form	ACTIVATES, INHIBITS, SUBSTRATE, TRANSLOCATE_FROM	string	One of defined node forms
source_location	ACTIVATES, INHIBITS, SUBSTRATE, TRANSLOCATE_FROM	string	One of defined locations
source_organ	ACTIVATES, INHIBITS, SUBSTRATE, TRANSLOCATE_FROM	string	One of defined plant organs (leaf, stem, root)
target_form	PRODUCT, TRANSLOCATE_TO	string	One of defined node forms
target_location	PRODUCT, TRANSLOCATE_TO	string	One of defined locations
target_organ	PRODUCT, TRANSLOCATE_TO	string	One of defined plant organs (leaf, stem, root)