SemanticTui

public enum SemanticTui

The major UMLS-related semantic types as decided at the inception of cTAKES. Each semantic type has a single UMLS TUI. Semantic types are collected in Semantic Groups.

T116, "Amino Acid, Peptide, or Protein", DRUG 
T020, "Acquired Abnormality", DISORDER 
T052, "Activity", EVENT 
T100, "Age Group", SUBJECT 
T003, "Alga", ENTITY 
T087, "Amino Acid Sequence", DRUG 
T011, "Amphibian", ENTITY 
T190, "Anatomical Abnormality", DISORDER 
T008, "Animal", ENTITY 
T017, "Anatomical Structure", ANATOMY 
T195, "Antibiotic", DRUG 
T194, "Archaeon", ENTITY 
T123, "Biologically Active Substance", DRUG 
T007, "Bacterium", ENTITY 
T031, "Body Substance", FINDING 
T022, "Body System", ANATOMY 
T053, "Behavior", FINDING 
T038, "Biologic Function", PHENOMENON 
T012, "Bird", ENTITY 
T029, "Body Location or Region", ANATOMY 
T091, "Biomedical Occupation or Discipline", TITLE 
T122, "Biomedical or Dental Material", DRUG 
T023, "Body Part, Organ, or Organ Component", ANATOMY 
T030, "Body Space or Junction", ANATOMY 
T118, "Carbohydrate", DRUG 
T026, "Cell Component", ANATOMY 
T043, "Cell Function", FINDING 
T025, "Cell", ANATOMY 
T019, "Congenital Abnormality", DISORDER 
T103, "Chemical", DRUG 
T120, "Chemical Viewed Functionally", DRUG 
T104, "Chemical Viewed Structurally", DRUG 
T185, "Classification", FINDING 
T201, "Clinical Attribute", CLINICAL_ATTRIBUTE 
T200, "Clinical Drug", DRUG 
T077, "Conceptual Entity", FINDING 
T049, "Cell or Molecular Dysfunction", DISORDER 
T088, "Carbohydrate Sequence", DRUG 
T060, "Diagnostic Procedure", PROCEDURE 
T056, "Daily or Recreational Activity", FINDING 
T047, "Disease or Syndrome", DISORDER 
T203, "Drug Delivery Device", DEVICE 
T065, "Educational Activity", PROCEDURE 
T069, "Environmental Effect of Humans", PHENOMENON 
T111, "Eicosanoid", ENTITY 
T196, "Element, Ion, or Isotope", DRUG 
T050, "Experimental Model of Disease", DISORDER 
T018, "Embryonic Structure", ANATOMY 
T071, "Entity", ENTITY 
T126, "Enzyme", DRUG 
T051, "Event", EVENT 
T099, "Family Group", SUBJECT 
T021, "Fully Formed Anatomical Structure", ANATOMY 
T013, "Fish", ENTITY 
T033, "Finding", FINDING 
T004, "Fungus", ENTITY 
T168, "Food", DRUG 
T169, "Functional Concept", FINDING 
T045, "Genetic Function", FINDING 
T083, "Geographic Area", ENTITY 
T028, "Gene or Genome", FINDING 
T064, "Governmental or Regulatory Activity", EVENT 
T102, "Group Attribute", SUBJECT 
T096, "Group", SUBJECT 
T068, "Human-caused Phenomenon or Process", PHENOMENON 
T093, "Health Care Related Organization", ENTITY 
T058, "Health Care Activity", PROCEDURE 
T131, "Hazardous or Poisonous Substance", DRUG 
T125, "Hormone", DRUG 
T016, "Human", SUBJECT 
T078, "Idea or Concept", FINDING 
T129, "Immunologic Factor", DRUG 
T055, "Individual Behavior", FINDING 
T197, "Inorganic Chemical", DRUG 
T037, "Injury or Poisoning", DISORDER 
T170, "Intellectual Product", FINDING 
T009, "Invertebrate", ENTITY 
T130, "Indicator, Reagent, or Diagnostic Aid", DRUG 
T171, "Language", ENTITY 
T059, "Laboratory Procedure", PROCEDURE 
T034, "Laboratory or Test Result", LAB 
T119, "Lipid", DRUG 
T015, "Mammal", ENTITY 
T063, "Molecular Biology Research Technique", PROCEDURE 
T066, "Machine Activity", PROCEDURE 
T074, "Medical Device", DEVICE 
T041, "Mental Process", FINDING 
T073, "Manufactured Object", DEVICE 
T048, "Mental or Behavioral Dysfunction", DISORDER 
T044, "Molecular Function", FINDING 
T085, "Molecular Sequence", FINDING 
T191, "Neoplastic Process", DISORDER 
T114, "Nucleic Acid, Nucleoside, or Nucleotide", DRUG 
T070, "Natural Phenomenon or Process", PHENOMENON 
T124, "Neuroreactive Substance or Biogenic Amine", DRUG 
T086, "Nucleotide Sequence", FINDING 
T057, "Occupational Activity", EVENT 
T090, "Occupation or Discipline", SUBJECT 
T115, "Organophosphorous Compound", DRUG 
T109, "Organic Chemical", DRUG 
T032, "Organism Attribute", SUBJECT 
T040, "Organism Function", FINDING 
T001, "Organism", ENTITY 
T092, "Organization", ENTITY 
T042, "Organ or * Tissue Function", FINDING 
T046, "Pathologic Function", FINDING 
T072, "Physical Object", ENTITY 
T067, "Phenomenon or Process", PHENOMENON 
T039, "Physiologic Function", FINDING 
T121, "Pharmacologic Substance", DRUG 
T002, "Plant", ENTITY 
T101, "Patient or Disabled Group", SUBJECT 
T098, "Population Group", SUBJECT 
T097, "Professional or Occupational Group", SUBJECT 
T094, "Professional Society", ENTITY 
T080, "Qualitative Concept", MODIFIER 
T081, "Quantitative Concept", LAB_MODIFIER 
T192, "Receptor", FINDING 
T014, "Reptile", ENTITY 
T062, "Research Activity", PROCEDURE 
T075, "Research Device", DEVICE 
T006, "Rickettsia or Chlamydia", DISORDER 
T089, "Regulation or Law", ENTITY 
T167, "Substance", DRUG 
T095, "Self-help or Relief Organization", ENTITY 
T054, "Social Behavior", FINDING 
T184, "Sign or Symptom", FINDING 
T082, "Spatial Concept", MODIFIER 
T110, "Steroid", DRUG 
T024, "Tissue", ANATOMY 
T079, "Temporal Concept", TIME 
T061, "Therapeutic or Preventive Procedure", PROCEDURE 
T005, "Virus", DISORDER 
T127, "Vitamin", DRUG 
T010, "Vertebrate", ENTITY 
T204, "Eukaryote", ENTITY UNKNOWN, "Unknown", SemanticGroup.UNKNOWN

public int getCode()

• Returns: type for UMLS TUI.
  
  

public String getSemanticType()

• Returns: Name for the type.
  
  

public void setGroup( final SemanticGroup group )

Allows a user to override the semantic group associated with a tui. This is useful when differentiating things like chemicals and drugs.

• Parameters:
  • group -
    
    

public SemanticGroup getGroup()

• Returns: semantic group for this type.
  
  

public int getGroupCode()

• Returns: internal cTAKES CONST code for group. These were old constants that shouldn't be used.
  
  

public String getGroupName()

• Returns: Short name for the group for this type. e.g. "Disease" or "Drug".
  
  

public Class<? extends IdentifiedAnnotation> getCtakesClass()

• Returns: the cTAKES java / type system class that represents the group for this type.
  
  

public Function<JCas, ? extends IdentifiedAnnotation> getCreator()

• Returns: A function that can create the java / type system class that represents the group for this type.
  
  

private String getMatchType()

• Returns: name of this type to lowercase and without commas.
  
  

static public SemanticTui getTui( final String semanticType )

• Parameters:
  • semanticType name of a semantic type.
• Returns: Type for the given type name.
  
  

static public SemanticTui getTui( final int code )

• Parameters:
  • code UMLS TUI code of a semantic type, not including "T" prefix.
• Returns: Type for the given TUI.
  
  

static public SemanticTui getTuiFromCode( final String tuiCode )

• Parameters:
  • tuiCode UMLS TUI code of a semantic type, including "T" prefix.
• Returns: Type for the given TUI.
  
  

static public Collection<SemanticTui> getTuis( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation Some annotation.
• Returns: The types appropriate for the annotation. Done using known TUIs for the annotation.
  
  

static public SemanticTui getTui( final UmlsConcept umlsConcept )

• Parameters:
  • umlsConcept Some UMLS concept of a real-world thing.
• Returns: The type appropriate for the concept.
  
  

static public void setGroup( final int tui, final String group )

Allows a user to override the semantic group associated with a tui. This is useful when differentiating things like chemicals and drugs.

• Parameters:
  • tui -
  • group -
    
    

static public void setGroup( final String type, final String group )

Allows a user to override the semantic group associated with a tui. This is useful when differentiating things like chemicals and drugs.

• Parameters:
  • type -
  • group -
    
    

static private String getMatchable( final String text )

• Parameters:
  • text -
• Returns: text to lowercase and without commas.