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
| 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) |
Incomplete properties: gomapman annotations.
Indices
Indices are generated across nodes with the same label to allow faster searching.
In progress
Plant node hierarchy
Families contain all genes associated with the family, across plant species.
Clades are subsets of families, as defined by sequence similarity.
FunctionalCllusters are subsets of (possibly multiple) families, as defined by participation in reactions (i.e. their function).
Of the three layers, only FunctionalClusters can participate in reactions.
Plans - incorporate Clades as "parents" of FunctionalClusters, instead of families
Defined reaction types
The database schema is based on a representations of chemical reactions. In a simple example, the following reaction A + B → C (catalysed by e):
can be represented in the graph database (using only nodes and edges) as follows:
Edges (arrows) and reaction nodes are reaction specific. Nodes other than reactions can take part in multiple reactions.
Using this schematic, the database can contain the following reaction types:
binding/oligomerisation |
|
dissociation |
|
catalysis |
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degradation/secretion |
|
protein deactivation |
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protein activation |
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transcriptional/translational activation |
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transcriptional/translational repression |
|
translocation |
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unknown |
|