Merge pull request #42 from ldorigo/patch-1

Add a set of available semtypes so users can easily choose the ones they need.

Author: soldni

constants.py

@@ -8,33 +8,137 @@
 
 NEGATIONS = {'none', 'non', 'neither', 'nor', 'no', 'not'}
 
+# The following is a list of all existing semtypes along with their name and some examples. 
+# You can easily select the ones you need by commenting out the lines that are not relevant for your application.
+
 ACCEPTED_SEMTYPES = {
-    'T029',     # Body Location or Region
-    'T023',     # Body Part, Organ, or Organ Component
-    'T031',     # Body Substance
-    'T060',     # Diagnostic Procedure
-    'T047',     # Disease or Syndrome
-    'T074',     # Medical Device
-    'T200',     # Clinical Drug
-    'T203',     # Drug Delivery Device
-    'T033',     # Finding
-    'T184',     # Sign or Symptom
-    'T034',     # Laboratory or Test Result
-    'T058',     # Health Care Activity
-    'T059',     # Laboratory Procedure
-    'T037',     # Injury or Poisoning
-    'T061',     # Therapeutic or Preventive Procedure
-    'T048',     # Mental or Behavioral Dysfunction
-    'T046',     # Pathologic Function
-    'T121',     # Pharmacologic Substance
-    'T201',     # Clinical Attribute
-    'T130',     # Indicator, Reagent, or Diagnostic Aid
-    'T195',     # Antibiotic
-    'T039',     # Physiologic Function
-    'T040',     # Organism Function
-    'T041',     # Mental Process
-    'T170',     # Intellectual Product
-    'T191'      # Neoplastic Process
+    # 'T020', # Acquired Abnormality, ex.: Hemorrhoids; Hernia, Femoral; Cauliflower ear
+    # 'T052', # Activity, ex.: Expeditions; Information Distribution; Social Planning
+    # 'T100', # Age Group, ex.: Adult; Infant, Premature; Adolescent (age group)
+    # 'T087', # Amino Acid Sequence, ex.: Signal Peptides; Homologous Sequences, Amino Acid; Abnormal amino acid
+    # 'T116', # Amino Acid, Peptide, or Protein, ex.: Amino Acids, Cyclic; Glycopeptides; Keratin
+    # 'T011', # Amphibian, ex.: Salamandra; Urodela; Brazilian horned frog
+    # 'T190', # Anatomical Abnormality, ex.: Bronchial Fistula; Foot Deformities; Hyperostosis of skull
+    # 'T017', # Anatomical Structure, ex.: Cadaver; Pharyngostome; Anatomic structures
+    # 'T008', # Animal, ex.: Animals; Animals, Laboratory; Carnivore
+    'T195', # Antibiotic, ex.: Antibiotics; bactericide; Thienamycins
+    # 'T194', # Archaeon, ex.: Thermoproteales; Haloferax volcanii; Methanospirillum
+    # 'T007', # Bacterium, ex.: Acetobacter; Bacillus cereus; Cytophaga
+    # 'T053', # Behavior, ex.: Homing Behavior; Sexuality; Habitat Selection
+    # 'T038', # Biologic Function, ex.: Antibody Formation; Drug resistance; Homeostasis
+    # 'T123', # Biologically Active Substance, ex.: Cytokinins; Pheromone
+    # 'T091', # Biomedical Occupation or Discipline, ex.: Adolescent Medicine; Cellular Neurobiology; Dentistry
+    # 'T122', # Biomedical or Dental Material, ex.: Acrylic Resins; Bone Cements; Dentifrices
+    # 'T012', # Bird, ex.: Serinus; Ducks; Quail
+    'T029', # Body Location or Region, ex.: Forehead; Sublingual Region; Base of skull structure
+    'T023', # Body Part, Organ, or Organ Component, ex.: Aorta; Brain Stem; Structure of neck of femur
+    # 'T030', # Body Space or Junction, ex.: Knee joint; Greater sac of peritoneum; Synapses
+    'T031', # Body Substance, ex.: Amniotic Fluid; saliva; Smegma
+    # 'T022', # Body System, ex.: Endocrine system; Renin-angiotensin system; Reticuloendothelial System
+    # 'T088', # Carbohydrate Sequence, ex.: Carbohydrate Sequence; Abnormal carbohydrate sequence
+    # 'T025', # Cell, ex.: B-Lymphocytes; Dendritic Cells; Fibroblasts
+    # 'T026', # Cell Component, ex.: Axon; Golgi Apparatus; Organelles
+    # 'T043', # Cell Function, ex.: Cell Cycle; Cell division; Phagocytosis
+    # 'T049', # Cell or Molecular Dysfunction, ex.: DNA Damage; Wallerian Degeneration; Atypical squamous metaplasia
+    # 'T103', # Chemical, ex.: Acids; Chemicals; Ionic Liquids
+    # 'T120', # Chemical Viewed Functionally, ex.: Aerosol Propellants; Detergents; Stabilizing Agents
+    # 'T104', # Chemical Viewed Structurally, ex.: Ammonium Compounds; Cations; Sulfur Compounds
+    # 'T185', # Classification, ex.: Anatomy (MeSH Category); Tumor Stage Classification; axis i
+    'T201', # Clinical Attribute, ex.: Bone Density; heart rate; Range of Motion, Articular
+    'T200', # Clinical Drug, ex.: Ranitidine 300 MG Oral Tablet [Zantac]; Aspirin 300 MG Delayed Release Oral
+    # 'T077', # Conceptual Entity, ex.: Geographic Factors; Fractals; Secularism
+    # 'T019', # Congenital Abnormality, ex.: Albinism; Cleft palate with cleft lip; Polydactyly of toes
+    # 'T056', # Daily or Recreational Activity, ex.: Badminton; Dancing; Swimming
+    'T060', # Diagnostic Procedure, ex.: Biopsy; Heart Auscultation; Magnetic Resonance Imaging
+    'T047', # Disease or Syndrome, ex.: Diabetes Mellitus; Drug Allergy; Malabsorption Syndrome
+    'T203', # Drug Delivery Device, ex.: Nordette 21 Day Pack; {7 (Terazosin 1 MG Oral Tablet) / 7 (Terazosin 2 MG
+    # 'T065', # Educational Activity, ex.: Academic Training; Family Planning Training; Preceptorship
+    # 'T196', # Element, Ion, or Isotope, ex.: Carbon; Chromium Isotopes; Radioisotopes
+    # 'T018', # Embryonic Structure, ex.: Blastoderm; Fetus; Neural Crest
+    # 'T071', # Entity, ex.: Gifts, Financial; Image; Product Part
+    # 'T069', # Environmental Effect of Humans, ex.: Air Pollution; Desertification; Bioremediation
+    # 'T126', # Enzyme, ex.: GTP Cyclohydrolase II; enzyme substrate complex; arginine amidase
+    # 'T204', # Eukaryote, ex.: Order Acarina; Bees; Plasmodium malariae
+    # 'T051', # Event, ex.: Anniversaries; Exposure to Mumps virus (event); Device Unattended
+    # 'T050', # Experimental Model of Disease, ex.: Alloxan Diabetes; Liver Cirrhosis, Experimental; Transient Gene Knock-Out
+    # 'T099', # Family Group, ex.: Daughter; Is an only child; Unmarried Fathers
+    'T033', # Finding, ex.: Birth History; Downward displacement of diaphragm; Decreased glucose level
+    # 'T013', # Fish, ex.: Bass; Salmonidae; Whitefish
+    # 'T168', # Food, ex.: Beverages; Egg Yolk (Dietary); Ice Cream
+    # 'T021', # Fully Formed Anatomical Structure, ex.: Entire body as a whole; Female human body; Set of parts of human body
+    # 'T169', # Functional Concept, ex.: Interviewer Effect; Problem Formulation; Endogenous
+    # 'T004', # Fungus, ex.: Aspergillus clavatus; Blastomyces; Neurospora
+    # 'T028', # Gene or Genome, ex.: Alleles; Genome, Human; rRNA Operon
+    # 'T045', # Genetic Function, ex.: Early Gene Transcription; Gene Amplification; RNA Splicing
+    # 'T083', # Geographic Area, ex.: Baltimore; Canada; Far East
+    # 'T064', # Governmental or Regulatory Activity, ex.: Certification; Credentialing; Public Policy
+    # 'T096', # Group, ex.: Focus Groups; jury; teams
+    # 'T102', # Group Attribute, ex.: Family Size; Group Structure; Life Expectancy
+    # 'T131', # Hazardous or Poisonous Substance, ex.: Carcinogens; Fumigant; Mutagens
+    'T058', # Health Care Activity, ex.: ambulatory care services; Clinic Activities; Preventive Health Services
+    # 'T093', # Health Care Related Organization, ex.: Centers for Disease Control and Prevention (U.S.); Halfway Houses;
+    # 'T125', # Hormone, ex.: Enteric Hormones; thymic humoral factor; Prohormone
+    # 'T016', # Human, ex.: Homo sapiens; jean piaget; Member of public
+    # 'T068', # Human-caused Phenomenon or Process, ex.: Baby Boom; Cultural Evolution; Mass Media
+    # 'T078', # Idea or Concept, ex.: Capitalism; Civil Rights; Ethics
+    # 'T129', # Immunologic Factor, ex.: Antigens; Immunologic Factors; Blood group antigen P
+    'T130', # Indicator, Reagent, or Diagnostic Aid, ex.: Fluorescent Dyes; Indicators and Reagents; India ink stain
+    # 'T055', # Individual Behavior, ex.: Assertiveness; Grooming; Risk-Taking
+    'T037', # Injury or Poisoning, ex.: Accidental Falls; Carbon Monoxide Poisoning; Snake Bites
+    # 'T197', # Inorganic Chemical, ex.: Carbonic Acid; aluminum nitride; ferric citrate
+    'T170', # Intellectual Product, ex.: Decision Support Techniques; Information Systems; Literature
+    'T034', # Laboratory or Test Result, ex.: Blood Flow Velocity; Serum Calcium Level; Spinal Fluid Pressure
+    'T059', # Laboratory Procedure, ex.: Blood Protein Electrophoresis; Crystallography; Radioimmunoassay
+    # 'T171', # Language, ex.: Armenian language; braille; Bilingualism
+    # 'T066', # Machine Activity, ex.: Computer Simulation; Equipment Failure; Natural Language Processing
+    # 'T015', # Mammal, ex.: Ursidae Family; Hamsters; Macaca
+    # 'T073', # Manufactured Object, ex.: car seat; Cooking and Eating Utensils; Goggles
+    'T074', # Medical Device, ex.: Bone Screws; Headgear, Orthodontic; Compression Stockings
+    'T048', # Mental or Behavioral Dysfunction, ex.: Agoraphobia; Cyclothymic Disorder; Frigidity
+    'T041', # Mental Process, ex.: Anger; Auditory Fatigue; Avoidance Learning
+    # 'T063', # Molecular Biology Research Technique, ex.: Northern Blotting; Genetic Engineering; In Situ Hybridization
+    # 'T044', # Molecular Function, ex.: Binding, Competitive; Electron Transport; Glycolysis
+    # 'T085', # Molecular Sequence, ex.: Genetic Code; Homologous Sequences; Molecular Sequence
+    # 'T070', # Natural Phenomenon or Process, ex.: Air Movements; Corrosion; Lightning (phenomenon)
+    'T191', # Neoplastic Process, ex.: Abdominal Neoplasms; Bowen's Disease; Polyp in nasopharynx
+    # 'T114', # Nucleic Acid, Nucleoside, or Nucleotide, ex.: Cytosine Nucleotides; Guanine; Oligonucleotides
+    # 'T086', # Nucleotide Sequence, ex.: Base Sequence; Direct Repeat; RNA Sequence
+    # 'T090', # Occupation or Discipline, ex.: Aviation; Craniology; Ecology
+    # 'T057', # Occupational Activity, ex.: Collective Bargaining; Commerce; Containment of Biohazards
+    # 'T042', # Organ or Tissue Function, ex.: Osteogenesis; Renal Circulation; Tooth Calcification
+    # 'T109', # Organic Chemical, ex.: Benzene Derivatives
+    # 'T001', # Organism, ex.: Organism; Infectious agent; Heterotroph
+    # 'T032', # Organism Attribute, ex.: Age; Birth Weight; Eye Color
+    'T040', # Organism Function, ex.: Breeding; Hibernation; Motor Skills
+    # 'T092', # Organization, ex.: Labor Unions; United Nations; Boarding school
+    'T046', # Pathologic Function, ex.: Inflammation; Shock; Thrombosis
+    # 'T101', # Patient or Disabled Group, ex.: Amputees; Institutionalized Child; Mentally Ill Persons
+    'T121', # Pharmacologic Substance, ex.: Antiemetics; Cardiovascular Agents; Alka-Seltzer
+    'T067', # Phenomenon or Process, ex.: Disasters; Motor Traffic Accidents; Depolymerization
+    # 'T072', # Physical Object, ex.: Printed Media; Meteors; Physical object
+    'T039', # Physiologic Function, ex.: Biorhythms; Hearing; Vasodilation
+    # 'T002', # Plant, ex.: Aloe; Pollen; Helianthus species
+    # 'T098', # Population Group, ex.: Asian Americans; Ethnic group; Adult Offenders
+    # 'T097', # Professional or Occupational Group, ex.: Clergy; Demographers; Hospital Volunteers
+    # 'T094', # Professional Society, ex.: American Medical Association; International Council of Nurses; Library
+    # 'T080', # Qualitative Concept, ex.: Clinical Competence; Consumer Satisfaction; Health Status
+    # 'T081', # Quantitative Concept, ex.: Age Distribution; Metric System; Selection Bias
+    # 'T192', # Receptor, ex.: Binding Sites; Lymphocyte antigen CD4 receptor; integrin alpha11beta1
+    # 'T089', # Regulation or Law, ex.: Building Codes; Criminal Law; Health Planning Guidelines
+    # 'T014', # Reptile, ex.: Alligators; Water Mocassin; Genus Python (organism)
+    # 'T062', # Research Activity, ex.: Animal Experimentation; Biomedical Research; Experimental Replication
+    # 'T075', # Research Device, ex.: Electrodes, Enzyme; DNA Microarray Chip; Particle Count and Size Analyzer
+    # 'T095', # Self-help or Relief Organization, ex.: Alcoholics Anonymous; Charities - organization; Red Cross
+    'T184', # Sign or Symptom, ex.: Dyspnea; Nausea; Pain
+    # 'T054', # Social Behavior, ex.: Acculturation; Communication; Interpersonal Relations
+    # 'T082', # Spatial Concept, ex.: Mandibular Rest Position; Lateral; Extrinsic
+    # 'T167', # Substance, ex.: Air (substance); Fossils; Plastics
+    # 'T079', # Temporal Concept, ex.: Birth Intervals; Half-Life; Postoperative Period
+    'T061', # Therapeutic or Preventive Procedure, ex.: Cesarean section; Dermabrasion; Family psychotherapy
+    # 'T024', # Tissue, ex.: Cartilage; Endothelium; Epidermis
+    # 'T010', # Vertebrate, ex.: Vertebrates; Gnathostomata vertebrate; Craniata <chordata>
+    # 'T005', # Virus, ex.: Coliphages; Echovirus; Parvoviridae
+    # 'T127'  # Vitamin, ex.: 5,25-Dihydroxy cholecalciferol; alpha-tocopheryl oxalate; Vitamin A [EPC]
 }
 
 UNICODE_DASHES = {