norm_toolkit 1.0.0__py3-none-any.whl

norm_toolkit/build_umls.py

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+"""
+UMLS database builder for unified normalizer.
+
+This is a convenience wrapper around build_merged_duckdb for UMLS-only builds.
+"""
+
+from __future__ import annotations
+
+from norm_toolkit.build_merged import build_merged_duckdb
+
+
+def build_umls_duckdb(
+    meta_dir: str,
+    db_path: str,
+    threads: int = 20,
+) -> None:
+    """
+    Build UMLS-only DuckDB database with unified schema.
+
+    Args:
+        meta_dir: Directory containing UMLS META RRF files
+        db_path: Output DuckDB database path
+        threads: Number of DuckDB threads to use
+
+    Required RRF files:
+        - MRCONSO.RRF: Concept names and atoms
+        - MRXNS_ENG.RRF: Normalized strings (English)
+        - MRXNW_ENG.RRF: Normalized words (English)
+        - MRSTY.RRF: Semantic types
+        - MRRANK.RRF: Source vocabulary rankings
+        - MRDEF.RRF: Definitions
+
+    This creates a database with the same schema as build_merged_duckdb,
+    but containing only UMLS data.
+    """
+    build_merged_duckdb(
+        db_path=db_path,
+        meta_dir=meta_dir,
+        ontology_dfs=None,
+        threads=threads,
+    )

norm_toolkit/constants.py

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+from enum import StrEnum
+
+import polars as pl
+
+# =============================================================================
+# Database Schema Constants
+# =============================================================================
+
+NS_TABLE = "ns"  # Normalized string index
+NW_TABLE = "nw"  # Normalized word index
+ATOMS_TABLE = "atoms"  # Atom details
+CONCEPTS_TABLE = "concepts"  # Concept metadata
+TYPES_TABLE = "types"  # Semantic types (UMLS only)
+DEFS_TABLE = "defs"  # Definitions
+EDGES_TABLE = "edges"  # Hierarchy edges
+
+# =============================================================================
+# Scoring Constants
+# =============================================================================
+
+RANK_MULTIPLIER = 100
+ISPREF_WEIGHT = 10
+STT_WEIGHT = 5
+TTY_WEIGHT = 1
+EXACT_BUMP = 1000
+
+DEFAULT_PREFER_TTYS = ["MH", "PT", "PN"]
+
+# Polars struct type for normalized hits
+HIT_STRUCT_TYPE = pl.Struct(
+    {
+        "global_identifier": pl.Utf8,
+        "identifier": pl.Utf8,
+        "nstr": pl.Utf8,
+        "name": pl.Utf8,
+        "source": pl.Utf8,
+        "name_type": pl.Utf8,
+        "score": pl.Int64,
+        "total_score": pl.Int64,
+        "match_type": pl.Utf8,
+    }
+)
+
+# Schema for ontology DataFrames (input to build_ontology_duckdb)
+ONTOLOGY_DF_SCHEMA = {
+    "global_identifier": pl.Utf8,
+    "identifier": pl.Utf8,
+    "source": pl.Utf8,
+    "pref_name": pl.Utf8,
+    "description": pl.Utf8,
+    "pref_name_norm": pl.Utf8,
+    "synonyms": pl.List(pl.Utf8),
+    "synonyms_norm": pl.List(pl.Utf8),
+}
+
+# =============================================================================
+# Entity Type Constants
+# =============================================================================
+
+
+class EntityType(StrEnum):
+    PROTEIN_GENEFAMILY = "Protein/GeneFamily"
+    DISEASE = "Disease"
+    CELLTYPE = "CellType"
+    GOTERM = "GOTerm"
+    ANATOMY = "Anatomy"
+    PHENOTYPE = "Phenotype"
+    SMALLMOLECULECLASS = "SmallMoleculeClass"
+    ORGANISM = "Organism"
+    ASSAY_RESULT = "Assay/Result"
+    PATHWAY = "Pathway"
+    CELLLINE = "CellLine"
+    GENE = "Gene"
+    PROTEIN = "Protein"
+    GENEVARIANT = "GeneVariant"
+    SMALLMOLECULE = "SmallMolecule"
+    CLINICALTRIAL = "ClinicalTrial"
+    PEPTIDE = "Peptide"
+    ANTIBODY = "Antibody"
+    RNA = "RNA"
+
+
+UMLS_ENTITY_TYPES = {
+    EntityType.PROTEIN_GENEFAMILY,
+    EntityType.DISEASE,
+    EntityType.CELLTYPE,
+    EntityType.GOTERM,
+    EntityType.ANATOMY,
+    EntityType.PHENOTYPE,
+}
+
+ONT_ENTITY_TYPES = {
+    EntityType.SMALLMOLECULECLASS,
+    EntityType.ORGANISM,
+    EntityType.ASSAY_RESULT,
+    EntityType.PATHWAY,
+    EntityType.CELLLINE,
+}
+
+MANUAL_ENTITY_TYPES = {
+    EntityType.GENE,
+    EntityType.PROTEIN,
+    EntityType.GENEVARIANT,
+    EntityType.SMALLMOLECULE,
+    EntityType.CLINICALTRIAL,
+}
+
+UNK_ENTITY_TYPES = {
+    EntityType.PEPTIDE,
+    EntityType.ANTIBODY,
+    EntityType.RNA,
+}

norm_toolkit/models.py

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+"""
+Data models for unified normalizer.
+
+Provides unified Pydantic models that work for both UMLS and ontology concepts.
+"""
+
+from __future__ import annotations
+
+from pydantic import BaseModel
+
+
+class SemanticType(BaseModel):
+    """Semantic type (UMLS only)."""
+
+    type_id: str  # TUI
+    type_name: str  # STY
+
+
+class ConceptInfo(BaseModel):
+    """
+    Unified concept information.
+
+    Works for both UMLS (CUI) and ontology (global_id) concepts.
+    For ontology databases, semantic_types will be empty.
+    """
+
+    concept_id: str  # CUI or global_id
+    identifier: str | None  # Source-specific ID (CUI for UMLS, e.g. "15377" for CHEBI)
+    source: str | None  # SAB or source
+    preferred_name: str | None
+    name_type: str | None  # TTY or name_type
+    description: str | None
+    def_source: str | None  # Source of definition (UMLS only)
+    synonyms: list[str]
+    semantic_types: list[SemanticType]  # Empty for ontology
+
+
+# Type aliases for backward compatibility
+OntologyConceptInfo = ConceptInfo
+UMLSConceptInfo = ConceptInfo