ExposoGraph.models

Pydantic data models for nodes, edges, and the knowledge graph container.

Enums

class ExposoGraph.models.NodeType(value)

CARCINOGEN = 'Carcinogen'

ENZYME = 'Enzyme'

GENE = 'Gene'

METABOLITE = 'Metabolite'

DNA_ADDUCT = 'DNA_Adduct'

PATHWAY = 'Pathway'

TISSUE = 'Tissue'

class ExposoGraph.models.EdgeType(value)

ACTIVATES = 'ACTIVATES'

DETOXIFIES = 'DETOXIFIES'

TRANSPORTS = 'TRANSPORTS'

FORMS_ADDUCT = 'FORMS_ADDUCT'

REPAIRS = 'REPAIRS'

PATHWAY = 'PATHWAY'

EXPRESSED_IN = 'EXPRESSED_IN'

INDUCES = 'INDUCES'

INHIBITS = 'INHIBITS'

ENCODES = 'ENCODES'

CUSTOM = 'CUSTOM'

class ExposoGraph.models.CurationStatus(value)

DRAFT = 'Draft'

IN_REVIEW = 'In Review'

REVIEWED = 'Reviewed'

APPROVED = 'Approved'

REJECTED = 'Rejected'

class ExposoGraph.models.CurationConfidence(value)

LOW = 'Low'

MEDIUM = 'Medium'

HIGH = 'High'

class ExposoGraph.models.RecordOrigin(value)

IMPORTED = 'imported'

SEEDED = 'seeded'

USER = 'user'

LLM = 'llm'

class ExposoGraph.models.MatchStatus(value)

UNKNOWN = 'unknown'

CANONICAL = 'canonical'

ALIAS = 'alias'

UNMATCHED = 'unmatched'

CUSTOM = 'custom'

Models

class ExposoGraph.models.ProvenanceRecord(*, source_db=None, record_id=None, evidence=None, pmid=None, tissue=None, citation=None, url=None)

Bases: BaseModel

Parameters:

• source_db (str | None)

• record_id (str | None)

• evidence (str | None)

• pmid (str | None)

• tissue (str | None)

• citation (str | None)

• url (str | None)

model_config: ClassVar[ConfigDict] = {'populate_by_name': True, 'validate_by_alias': True, 'validate_by_name': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class ExposoGraph.models.CurationRecord(*, status=CurationStatus.DRAFT, confidence=None, curator=None, reviewed_by=None, reviewed_at=None, notes=None)

Bases: BaseModel

Parameters:

• status (CurationStatus)

• confidence (CurationConfidence | None)

• curator (str | None)

• reviewed_by (str | None)

• reviewed_at (str | None)

• notes (str | None)

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class ExposoGraph.models.Node(*, id, label, type, detail='', group=None, iarc=None, phase=None, role=None, reactivity=None, source_db=None, evidence=None, pmid=None, tissue=None, variant=None, phenotype=None, activity_score=None, tier=None, origin=RecordOrigin.IMPORTED, match_status=MatchStatus.UNKNOWN, canonical_id=None, canonical_label=None, canonical_namespace=None, custom_type=None, provenance=<factory>, curation=None)

Bases: BaseModel

Parameters:

• id (str)

• label (str)

• type (NodeType)

• detail (str)

• group (str | None)

• iarc (str | None)

• phase (str | None)

• role (str | None)

• reactivity (str | None)

• source_db (str | None)

• evidence (str | None)

• pmid (str | None)

• tissue (str | None)

• variant (str | None)

• phenotype (str | None)

• activity_score (float | None)

• tier (int | None)

• origin (RecordOrigin)

• match_status (MatchStatus)

• canonical_id (str | None)

• canonical_label (str | None)

• canonical_namespace (str | None)

• custom_type (str | None)

• provenance (list[ProvenanceRecord])

• curation (CurationRecord | None)

classmethod generate_id(label)

Derive a safe node ID from a label.

Simple labels (e.g. "CYP1A1") pass through unchanged. Labels containing special characters that are stripped during sanitisation get a short hash suffix to avoid collisions (e.g. "Benzo[a]pyrene" → "Benzo_a_pyrene_a4f2c1").

Parameters:

label (str)

Return type:

str

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class ExposoGraph.models.Edge(*, source, target, type, label=None, carcinogen=None, source_db=None, evidence=None, pmid=None, tissue=None, origin=RecordOrigin.IMPORTED, match_status=MatchStatus.UNKNOWN, canonical_predicate=None, canonical_namespace=None, custom_predicate=None, provenance=<factory>, curation=None)

Bases: BaseModel

Parameters:

• source (str)

• target (str)

• type (EdgeType)

• label (str | None)

• carcinogen (str | None)

• source_db (str | None)

• evidence (str | None)

• pmid (str | None)

• tissue (str | None)

• origin (RecordOrigin)

• match_status (MatchStatus)

• canonical_predicate (str | None)

• canonical_namespace (str | None)

• custom_predicate (str | None)

• provenance (list[ProvenanceRecord])

• curation (CurationRecord | None)

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class ExposoGraph.models.KnowledgeGraph(*, nodes=<factory>, edges=<factory>)

Bases: BaseModel

Parameters:

• nodes (list[Node])

• edges (list[Edge])

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].