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{
"$schema": "http://json-schema.org/draft-06/schema#",
"id": "http://www.indra.bio/schemas/statements.json",
"definitions": {
"ModCondition": {
"type": "object",
"description": "Mutation state of an amino acid position of an Agent.",
"properties": {
"mod_type": {
"type": "string",
"description": "The type of post-translational modification, e.g., 'phosphorylation'. Valid modification types currently include: 'phosphorylation', 'ubiquitination', 'sumoylation', 'hydroxylation', and 'acetylation'. If an invalid modification type is passed an InvalidModTypeError is raised."
},
"residue": {
"type": "string",
"description": "String indicating the modified amino acid, e.g., 'Y' or 'tyrosine'. If None, indicates that the residue at the modification site is unknown or unspecified."
},
"position": {
"type": "string",
"description": "String indicating the position of the modified amino acid, e.g., '202'. If None, indicates that the position is unknown or unspecified."
},
"is_modified": {
"type": "boolean",
"description": "Specifies whether the modification is present or absent. Setting the flag specifies that the Agent with the ModCondition is unmodified at the site."
}
},
"required": ["mod_type", "is_modified"]
},
"MutCondition": {
"type": "object",
"description": "Mutation state of an amino acid position of an Agent.",
"properties": {
"position": {
"type": ["string", "null"],
"description": "Residue position of the mutation in the protein sequence."
},
"residue_from": {
"type": ["string", "null"],
"description": "Wild-type (unmodified) amino acid residue at the given position."
},
"residue_to": {
"type": ["string", "null"],
"description": "Amino acid at the position resulting from the mutation."
}
},
"required": ["position", "residue_from", "residue_to"]
},
"ActivityCondition": {
"type": "object",
"description": "An active or inactive state of a protein.",
"properties": {
"activity_type": {
"type": "string",
"description": "The type of activity, e.g. 'kinase'. The basic, unspecified molecular activity is represented as 'activity'. Examples of other activity types are 'kinase', 'phosphatase', 'catalytic', 'transcription', etc."
},
"is_active": {
"type": "boolean",
"description": "Specifies whether the given activity type is present or absent."
}
},
"required": ["activity_type", "is_active"]
},
"BoundCondition": {
"type": "object",
"description": "Identify Agents bound (or not bound) to a given Agent in a given context.",
"properties": {
"agent": {
"$ref": "#/definitions/Agent"
},
"is_bound": {
"type": "boolean",
"description": "Specifies whether the given Agent is bound or unbound in the current context."
}
},
"required": ["agent", "is_bound"]
},
"Agent": {
"type": "object",
"description": "A molecular entity, e.g., a protein.",
"properties": {
"name": {
"type": "string",
"description": "The name of the agent, preferably a canonicalized name such as an HGNC gene name."
},
"mods": {
"type": "array",
"items": {"$ref": "#/definitions/ModCondition"},
"description": "Modification state of the agent."
},
"mutations": {
"type": "array",
"items": {"$ref": "#/definitions/MutCondition"},
"description": "Amino acid mutations of the agent."
},
"bound_conditions": {
"type": "array",
"items": {"$ref": "#/definitions/BoundCondition"},
"description": "Other agents bound to the agent in this context."
},
"activity": {
"$ref": "#/definitions/ActivityCondition",
"description":"Activity of the agent."
},
"location": {
"type": "string",
"description": "Cellular location of the agent. Must be a valid name (e.g. 'nucleus') or identifier (e.g. 'GO:0005634')for a GO cellular compartment."
},
"db_refs": {
"type": "object",
"description": "Dictionary of database identifiers associated with this agent."
},
"sbo": {
"type": "string",
"description": "Role of this agent in the systems biology ontology"
}
},
"required": ["name", "db_refs"]
},
"Concept": {
"type": "object",
"description": "A concept/entity of interest that is the argument of a Statement",
"properties": {
"name": {
"type": "string",
"description": "The name of the concept, possibly a canonicalized name."
},
"db_refs": {
"type": "object",
"description": "Dictionary of database identifiers associated with this concept."
}
},
"required": ["name", "db_refs"]
},
"Context": {
"type": "object",
"description": "The context in which a given Statement was reported.",
"properties": {
"type": {
"type": "string",
"pattern": "^((bio)|(world))$",
"description": "Either 'world' or 'bio', depending on the type of context being repersented."
}
}
},
"BioContext": {
"type": "object",
"description": "The biological context of a Statement.",
"properties": {
"type": {
"type": "string",
"pattern": "^bio$",
"description": "The type of context, in this case 'bio'."
},
"location": {
"$ref": "#/definitions/RefContext",
"description": "Cellular location, typically a sub-cellular compartment."
},
"cell_line": {
"$ref": "#/definitions/RefContext",
"description": "Cell line context, e.g., a specific cell line, like BT20."
},
"cell_type": {
"$ref": "#/definitions/RefContext",
"description": "Cell type context, broader than a cell line, like macrophage."
},
"organ": {
"$ref": "#/definitions/RefContext",
"description": "Organ context."
},
"disease": {
"$ref": "#/definitions/RefContext",
"description": "Disease context."
},
"species": {
"$ref": "#/definitions/RefContext",
"description": "Species context."
}
}
},
"WorldContext": {
"type": "object",
"description": "The temporal and spatial context of a Statement.",
"properties": {
"type": {
"type": "string",
"pattern": "^world$",
"description": "The type of context, in this case 'world'."
},
"time": {
"$ref": "#/definitions/TimeContext",
"description": "The temporal context of a Statement."
},
"geo_location": {
"$ref": "#/definitions/RefContext",
"description": "The geographical context of a Statement."
}
}
},
"TimeContext": {
"type": "object",
"description": "Represents a temporal context.",
"properties": {
"text": {
"type": "string",
"description": "The text associated with the temporal context."
},
"start": {
"type": "string",
"description": "The start time of the temporal context."
},
"end": {
"type": "string",
"description": "The end time of the temporal context."
},
"duration": {
"type": "string",
"description": "The duration of the temporal context."
}
}
},
"RefContext": {
"type": "object",
"description": "Represents a context identified by name and grounding references.",
"properties": {
"name": {
"type": "string",
"description": "The name associated with the context."
},
"db_refs": {
"type": "object",
"description": "Dictionary of database identifiers associated with this context."
}
}
},
"Evidence": {
"type": "object",
"description": "Container for evidence supporting a given statement.",
"properties": {
"source_api": {
"type": "string",
"description": "String identifying the INDRA API used to capture the statement, e.g., 'trips', 'biopax', 'bel'."
},
"pmid": {
"type": "string",
"description": "String indicating the Pubmed ID of the source of the statement."
},
"source_id": {
"type": "string",
"description": "For statements drawn from databases, ID of the database entity corresponding to the statement."
},
"text": {
"type": "string",
"description": "Natural language text supporting the statement."
},
"annotations": {
"type": "object",
"description": "Dictionary containing additional information on the context of the statement, e.g., species, cell line, tissue type, etc. The entries may vary depending on the source of the information."
},
"epistemics": {
"type": "object",
"description": "A dictionary describing various forms of epistemic certainty associated with the statement."
}
}
},
"Statement": {
"type": "object",
"description": "All statement types, below, may have these fields and 'inherit' from this schema",
"properties": {
"evidence": {
"type": "array",
"items": {
"$ref": "#/definitions/Evidence"
}
},
"id": {
"type": "string",
"description": "Statement UUID"
},
"supports": {
"type": "array",
"items": {
"type": "string"
}
},
"supported_by": {
"type": "array",
"items": {
"type": "string"
}
}
},
"required": ["id"]
},
"Modification": {
"description": "Statement representing the modification of a protein.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^((Phosphorylation)|(Dephosphorylation)|(Ubiquitination)|(Deubiquitination)|(Sumoylation)|(Desumoylation)|(Hydroxylation)|(Dehydroxylation)|(Acetylation)|(Deacetylation)|(Glycosylation)|(Deglycosylation)|(Farnesylation)|(Defarnesylation)|(Geranylgeranylation)|(Degeranylgeranylation)|(Palmitoylation)|(Depalmitoylation)|(Myristoylation)|(Demyristoylation)|(Ribosylation)|(Deribosylation)|(Methylation)|(Demethylation))$",
"description": "The type of the statement"
},
"enz": {
"$ref": "#/definitions/Agent",
"description": "The enzyme involved in the modification."
},
"sub": {
"$ref": "#/definitions/Agent",
"description": "The substrate of the modification."
},
"residue": {
"type": "string",
"description": "The amino acid residue being modified, or None if it is unknown or unspecified."
},
"position": {
"type": "string",
"description": "The position of the modified amino acid, or None if it is unknown or unspecified."
}
},
"required": ["type"]
}
]
},
"SelfModification": {
"description": "Statement representing the self-modification of a protein.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^((Autophosphorylation)|(Transphosphorylation))$",
"description": "The type of the statement"
},
"enz": {
"$ref": "#/definitions/Agent",
"description": "The enzyme involved in the modification."
},
"residue": {
"type": "string",
"description": "The amino acid residue being modified, or None if it is unknown or unspecified."
},
"position": {
"type": "string",
"description": "The position of the modified amino acid, or None if it is unknown or unspecified."
}
},
"required": ["type"]
}
]
},
"RegulateActivity": {
"description": "Regulation of activity (such as activation and inhibition)",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^((Activation)|(Inhibition))$",
"description": "The type of the statement"
},
"subj": {
"$ref": "#/definitions/Agent",
"description": "The agent responsible for the change in activity, i.e., the 'upstream' node."
},
"obj": {
"$ref": "#/definitions/Agent",
"description": "The agent whose activity is influenced by the subject, i.e., the 'downstream' node."
},
"obj_activity": {
"type": "string",
"description": "The activity of the obj Agent that is affected, e.g., its 'kinase' activity."
}
},
"required": ["type"]
}
]
},
"ActiveForm": {
"description": "Specifies conditions causing an Agent to be active or inactive. Types of conditions influencing a specific type of biochemical activity can include modifications, bound Agents, and mutations.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^ActiveForm$",
"description": "The type of the statement"
},
"agent": {
"$ref": "#/definitions/Agent",
"description": "The Agent in a particular active or inactive state. The sets of ModConditions, BoundConditions, and MutConditions on the given Agent instance indicate the relevant conditions."
},
"activity": {
"type": "string",
"description": "The type of activity influenced by the given set of conditions, e.g., 'kinase'."
},
"is_active": {
"type": "boolean",
"description": "Whether the conditions are activating (True) or inactivating (False)."
}
},
"required": ["type", "agent", "activity"]
}
]
},
"Gef": {
"description": "Exchange of GTP for GDP on a small GTPase protein mediated by a GEF. Represents the generic process by which a guanosine exchange factor (GEF) catalyzes nucleotide exchange on a GTPase protein.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^Gef$",
"description": "The type of the statement"
},
"agent": {
"$ref": "#/definitions/Agent",
"description": "The guanosine exchange factor."
},
"ras": {
"$ref": "#/definitions/Agent",
"description": "The GTPase protein."
}
},
"required": ["type"]
}
]
},
"Gap": {
"description": "Acceleration of a GTPase protein's GTP hydrolysis rate by a GAP. Represents the generic process by which a GTPase activating protein (GAP) catalyzes GTP hydrolysis by a particular small GTPase protein.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^Gap$",
"description": "The type of the statement"
},
"gap": {
"$ref": "#/definitions/Agent",
"description": "The GTPase activating protein."
},
"ras": {
"$ref": "#/definitions/Agent",
"description": "The GTPase protein."
}
},
"required": ["type"]
}
]
},
"Complex": {
"description": "A set of proteins observed to be in a complex.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^((Complex)|(Association))$",
"description": "The type of the statement"
},
"members": {
"type": "array",
"items": {
"$ref": "#/definitions/Agent"
}
}
},
"required": ["type"]
}
]
},
"Association": {
"description": "A set of unordered concepts that are associated with each other.",
"allOf": [
{
"$ref": "#/definitions/Complex"
}
]
},
"Translocation": {
"description": "The translocation of a molecular agent from one location to another.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^Translocation$",
"description": "The type of the statement"
},
"agent": {
"$ref": "#/definitions/Agent",
"description": "The agent which translocates."
},
"from_location": {
"type": "string",
"description": "The location from which the agent translocates. This must be a valid GO cellular component name (e.g. 'cytoplasm') or ID (e.g. 'GO:0005737')."
},
"to_location": {
"type": "string",
"description": "The location to which the agent translocates. This must be a valid GO cellular component name or ID."
}
},
"required": ["type", "agent"]
}
]
},
"RegulateAmount": {
"description": "Represents directed, two-element interactions.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^((IncreaseAmount)|(DecreaseAmount))$"
},
"subj": {
"$ref": "#/definitions/Agent",
"description": "The mediating protein"
},
"obj": {
"$ref": "#/definitions/Agent",
"description": "The affected protein"
}
},
"required": ["type"]
}
]
},
"Influence": {
"description": "A causal influence between two events.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^Influence$"
},
"subj": {
"$ref": "#/definitions/Event",
"description": "The event which acts as the influencer."
},
"obj": {
"$ref": "#/definitions/Event",
"description": "The event which acts as the influencee"
}
},
"required": ["type"]
}
]
},
"Event": {
"description": "An event over a concept of interest.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^Event$"
},
"concept": {
"$ref": "#/definitions/Concept",
"description": "The concept which the event happens to."
},
"delta": {
"type": ["object", "null"],
"description": "A dictionary specifying the polarity and adjactives of change in concept."
},
"context": {
"$ref": "#/definitions/Context",
"description": "The context associated with the event"
}
},
"required": ["type", "concept"]
}
]
},
"Conversion": {
"description": "Conversion of molecular species mediated by a controller protein.",
"allOf": [
{
"$ref": "#/definitions/Statement"
},
{
"type": "object",
"properties": {
"type": {
"type": "string",
"pattern": "^Conversion$"
},
"subj": {
"$ref": "#/definitions/Agent",
"description": "The protein mediating the conversion."
},
"obj_from": {
"type": "array",
"items": {
"$ref": "#/definitions/Agent"
},
"description": "The list of molecular species being consumed by the conversion."
},
"obj_to": {
"type": "array",
"items": {
"$ref": "#/definitions/Agent"
},
"description": "The list of molecular species being created by the conversion."
}
},
"required": ["type"]
}
]
}
},
"type": "array",
"items": {
"anyOf": [
{"$ref": "#/definitions/RegulateActivity"},
{"$ref": "#/definitions/Modification"},
{"$ref": "#/definitions/SelfModification"},
{"$ref": "#/definitions/ActiveForm"},
{"$ref": "#/definitions/Gef"},
{"$ref": "#/definitions/Gap"},
{"$ref": "#/definitions/Complex"},
{"$ref": "#/definitions/Association"},
{"$ref": "#/definitions/Translocation"},
{"$ref": "#/definitions/RegulateAmount"},
{"$ref": "#/definitions/Influence"},
{"$ref": "#/definitions/Conversion"},
{"$ref": "#/definitions/Event"}
]
}
}
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