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4b988e0 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 | """UMLS semantic type (TUI) codes and definitions (embedded)."""
import re
_TUI_SPLIT = re.compile(r"[;|,/\s]+")
TUI_DEFINITIONS: dict[str, str] = {
"T004": "Fungus",
"T005": "Virus",
"T007": "Bacterium",
"T017": "Anatomical Structure",
"T019": "Congenital Abnormality",
"T021": "Fully Formed Anatomical Structure",
"T022": "Body System",
"T023": "Body Part, Organ, or Organ Component",
"T024": "Tissue",
"T025": "Cell",
"T026": "Cell Component",
"T028": "Gene or Genome",
"T029": "Body Location or Region",
"T030": "Body Space or Junction",
"T031": "Body Substance",
"T032": "Organism Attribute",
"T033": "Finding",
"T034": "Laboratory or Test Result",
"T037": "Injury or Poisoning",
"T038": "Biologic Function",
"T039": "Physiologic Function",
"T040": "Organism Function",
"T041": "Mental Process",
"T042": "Organ or Tissue Function",
"T043": "Cell Function",
"T044": "Molecular Function",
"T045": "Genetic Function",
"T046": "Pathologic Function",
"T047": "Disease or Syndrome",
"T048": "Mental or Behavioral Dysfunction",
"T049": "Cell or Molecular Dysfunction",
"T050": "Experimental Model of Disease",
"T053": "Behavior",
"T055": "Individual Behavior",
"T059": "Laboratory Procedure",
"T060": "Diagnostic Procedure",
"T061": "Therapeutic or Preventive Procedure",
"T067": "Phenomenon or Process",
"T074": "Medical Device",
"T081": "Quantitative Concept",
"T085": "Molecular Sequence",
"T086": "Nucleotide Sequence",
"T087": "Amino Acid Sequence",
"T093": "Health Care Related Organization",
"T094": "Professional Society",
"T114": "Nucleic Acid, Nucleoside, or Nucleotide",
"T116": "Amino Acid, Peptide, or Protein",
"T121": "Pharmacologic Substance",
"T123": "Biologically Active Substance",
"T125": "Hormone",
"T126": "Enzyme",
"T127": "Vitamin",
"T129": "Immunologic Factor",
"T131": "Hazardous or Poisonous Substance",
"T184": "Sign or Symptom",
"T191": "Neoplastic Process",
"T192": "Receptor",
"T195": "Antibiotic",
"T200": "Clinical Drug",
"T201": "Clinical Attribute",
"T203": "Drug Delivery Device",
}
def tui_display(code: str) -> str:
"""Return ``T047 — Disease or Syndrome`` for a single TUI code."""
c = (code or "").strip().upper()
if not c:
return ""
name = TUI_DEFINITIONS.get(c, "")
return f"{c} — {name}" if name else c
def format_tui_list(raw: str, *, compact: bool = False) -> str:
"""Format pipe/semicolon-separated TUI codes with definitions."""
if not raw:
return ""
parts = [p for p in _TUI_SPLIT.split(raw.strip()) if p.strip()]
if not parts:
return ""
if compact and len(parts) == 1:
return tui_display(parts[0])
return "; ".join(tui_display(p) for p in parts)
def tui_codes(raw: str) -> set[str]:
"""Split a raw TUI field into individual codes."""
if not raw:
return set()
out: set[str] = set()
for part in _TUI_SPLIT.split(str(raw).strip()):
code = part.strip().upper()
if code.startswith("T") and len(code) >= 4:
out.add(code)
return out
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