londonaicentre-entityschema 1.1.0

Clinical entity extraction schema for MESA

Entityschema

Schema package for clinical entity extraction from NHS medical documents.

Structure

📁 entityschema
├── examples/            # Training examples showing document input and structured output
├── schema.py            # Pydantic model for specifying expected output structure
├── prompt_builder.py    # Prompt builder for data generation and inference
├── prompt_datagen.txt   # Prompt template with example (for training data generation)
├── prompt_main.txt      # Prompt template without example (for inference/deployment)
└── py.typed             # Type checking marker

Usage

from entityschema.prompt_builder import PromptBuilder

# Initialize builder
builder = PromptBuilder()

# Build data generation prompt (with example)
datagen_prompt = builder.build_datagen_prompt()

# Build main/inference prompt (without example)
main_prompt = builder.build_main_prompt()

Schema

Type	Values
EntityType	gastroenteritis, c_difficile_enterocolitis, amoebic_infection, amoebic_liver_disease, pulmonary_tuberculosis, extrapulmonary_tuberculosis, miliary_tuberculosis, meningitis, meningococcal_meningitis, streptococcal_meningitis, viral_meningitis, encephalitis, viral_encephalitis, brain_abscess, spinal_abscess, liver_abscess, perianal_abscess, discitis, osteomyelitis, sepsis, meningococcal_septicaemia, streptococcal_septicaemia, staph_aureus_septicaemia, gram_negative_septicaemia, catheter_or_line_related_septicaemia, toxic_shock_syndrome, upper_respiratory_tract_infection, sinusitis, pharyngitis_or_tonsillitis, epiglottitis, oropharyngeal_abscess, ludwigs_angina, influenza, lower_respiratory_tract_infection, pneumonia, community_acquired_pneumonia, hospital_acquired_pneumonia, aspiration_pneumonia, viral_pneumonia, lung_abscess, legionnaires_disease, cellulitis, cutaneous_abscess, surgical_wound_infection, necrotising_fasciitis, neurosyphilis, lyme_disease, herpes_simplex_infection, eczema_herpeticum, herpes_zoster_infection, acute_hepatitis_a, acute_hepatitis_b, acute_hepatitis_c, acute_hepatitis_e, chronic_hepatitis_b, chronic_hepatitis_c, symptomatic_hiv_disease, cytomegaloviral_disease, infectious_mononucleosis, candidiasis, candidal_septicaemia, aspergillosis, invasive_pulmonary_aspergillosis, pulmonary_aspergilloma, pneumocystis_pneumonia, malaria, toxoplasmosis, giardiasis, cryptosporidiosis, scabies, pertussis, varicella, measles, croup, bronchiolitis, sars_infection, covid_19_infection, post_covid_19_syndrome, resistance_to_beta_lactam_antibiotics, resistance_to_other_antibiotics, pyrexia_of_unknown_origin, primary_cancer_lung, primary_cancer_breast, primary_cancer_colorectal, primary_cancer_prostate, primary_cancer_skin, primary_cancer_pancreas, primary_cancer_liver_or_biliary, primary_cancer_gi_upper, primary_cancer_kidney_or_bladder, primary_cancer_gynaecological, primary_cancer_testicular, primary_cancer_brain_or_cns, primary_cancer_head_and_neck, primary_cancer_haematological, primary_cancer_hodgkin_lymphoma, primary_cancer_non_hodgkin_lymphoma, primary_cancer_acute_leukaemia, primary_cancer_chronic_leukaemia, primary_cancer_myeloma, cancer_unknown_primary, kaposi_sarcoma, cancer_metastases, benign_neoplasm, early_stage_neoplasm_in_situ, chemotherapy, radiotherapy, anaemia, iron_deficiency_anaemia, pernicious_anaemia, anaemia_of_chronic_disease, haemolytic_anaemia, aplastic_anaemia, sickle_cell_trait, sickle_cell_disease, vaso_occlusive_crisis, thalassaemia, haemophilia, thrombophilia, von_willebrand_disease, thrombocytopenia, immune_thrombocytopenia, heparin_induced_thrombocytopenia, disseminated_intravascular_coagulation, thrombotic_thrombocytopenic_purpura, haemolytic_uraemic_syndrome, antiphospholipid_syndrome, neutropenia, febrile_neutropenia, agranulocytosis, polycythaemia_vera, myelodysplastic_syndrome, myelofibrosis, monoclonal_gammopathy_of_undetermined_significance, common_variable_immunodeficiency, tumour_lysis_syndrome, cytokine_release_syndrome, amyloidosis, anaphylaxis, allergic_reaction_to_drug, hypothyroidism, myxoedema_coma, hyperthyroidism, graves_disease, thyroid_storm, thyroiditis, hashimotos_thyroiditis, sick_euthyroid_syndrome, diabetes_mellitus, type_1_diabetes_mellitus, type_2_diabetes_mellitus, diabetic_ketoacidosis, hyperglycaemia, hyperosmolar_hyperglycaemic_state, diabetic_nephropathy, diabetic_retinopathy, diabetic_peripheral_neuropathy, diabetic_autonomic_neuropathy, diabetic_ulcers, hypoglycaemia, hypoglycaemic_coma, hypoparathyroidism, hyperparathyroidism, acromegaly, hyperprolactinaemia, syndrome_of_inappropriate_adh, hypopituitarism, diabetes_insipidus, cushings_syndrome, hyperaldosteronism, adrenocortical_insufficiency, addisonian_crisis, polycystic_ovarian_syndrome, primary_ovarian_failure, testicular_hypofunction, carcinoid_syndrome, malnutrition, refeeding_syndrome, wernicke_encephalopathy, vitamin_d_deficiency, iron_deficiency, obesity, obesity_hypoventilation, hyperlipidaemia, hypernatraemia, hyponatraemia, hyperkalaemia, hypokalaemia, hypercalcaemia, hypocalcaemia, volume_depletion, fluid_overload, lactic_acidosis, phaeochromocytoma, alcohol_use_disorder, alcohol_withdrawal, delirium_tremens, opioid_use_disorder, opioid_withdrawal, iv_drug_use_disorder, cocaine_use_disorder, cannabis_use_disorder, psychotic_episode, schizophrenia, schizoaffective_disorder, manic_episode, bipolar_affective_disorder, depression, low_mood, suicidal_ideation, anxiety_disorder, post_traumatic_stress_disorder, attention_deficit_hyperactivity_disorder, anorexia_nervosa, bulimia_nervosa, personality_disorder, learning_disability, insomnia, dementia, vascular_dementia, frontotemporal_dementia, lewy_body_dementia, mild_cognitive_impairment, delirium, huntingtons_disease, hereditary_ataxia, motor_neuron_disease, paraneoplastic_neurological_syndrome, parkinsons_disease, secondary_parkinsonism, neuroleptic_malignant_syndrome, serotonin_syndrome, essential_tremor, alzheimers_disease, early_onset_alzheimers_disease, multiple_sclerosis, central_pontine_myelinolysis, epilepsy, status_epilepticus, migraine, cluster_headache_syndrome, trigeminal_neuralgia, bells_palsy, subarachnoid_haemorrhage, cerebral_aneurysm_nonruptured, intracerebral_haemorrhage, ischaemic_stroke, transient_ischaemic_attack, cerebral_venous_sinus_thrombosis, nerve_root_or_plexus_disorder, guillain_barre_syndrome, chronic_inflammatory_demyelinating_polyneuropathy, peripheral_neuropathy, myasthenia_gravis, lambert_eaton_syndrome, muscular_dystrophy, myopathy, critical_illness_myopathy, cerebral_palsy, hemiplegia, paraplegia_or_tetraplegia, locked_in_syndrome, hydrocephalus, normal_pressure_hydrocephalus, raised_intracranial_pressure, hypoxic_anoxic_brain_injury, idiopathic_intracranial_hypertension, encephalopathy, posterior_reversible_encephalopathy_syndrome, compression_of_brain, cerebral_oedema, extradural_haemorrhage, subdural_haemorrhage, spinal_cord_compression, cauda_equina_syndrome, conjunctivitis, disorders_of_sclera, keratitis, uveitis, retinal_detachment, cataract, retinal_vascular_occlusions, retinal_haemorrhage, glaucoma, optic_neuritis, papilloedema, visual_disturbance, blindness, otitis_media, otitis_externa, mastoiditis, vestibular_disorders, hearing_loss, macular_degeneration, dental_condition, rheumatic_fever, essential_hypertension, hypertensive_cardiomyopathy, hypertensive_renal_disease, malignant_hypertension, hypertensive_encephalopathy, secondary_hypertension, angina_pectoris, stable_angina, unstable_angina, acute_myocardial_infarction, silent_myocardial_infarction, non_st_elevation_myocardial_infarction, st_elevation_myocardial_infarction, chronic_ischaemic_heart_disease, coronary_artery_stent_in_situ, dresslers_syndrome, aneurysm_of_heart, pulmonary_embolism, massive_pulmonary_embolism, cor_pulmonale, primary_pulmonary_hypertension, secondary_pulmonary_hypertension, pericarditis, restrictive_pericarditis, pericardial_effusion, cardiac_tamponade, infective_endocarditis, mitral_valve_prolapse, mitral_regurgitation, mitral_stenosis, aortic_regurgitation, aortic_stenosis, tricuspid_regurgitation, tricuspid_stenosis, pulmonary_regurgitation, pulmonary_stenosis, myocarditis, cardiomyopathy, dilated_cardiomyopathy, hypertrophic_cardiomyopathy, takotsubo_cardiomyopathy, sick_sinus_syndrome, heart_block, first_degree_heart_block, second_degree_heart_block, complete_heart_block, trifascicular_block, tachyarrhythmia, supraventricular_tachycardia, wolff_parkinson_white_syndrome, atrial_fibrillation, paroxysmal_atrial_fibrillation, atrial_flutter, ventricular_ectopics, ventricular_tachycardia, ventricular_fibrillation, cardiac_arrest, cardiac_arrest_with_rosc, long_qt_syndrome, brugada_syndrome, pacemaker_in_situ, replacement_heart_valve_in_situ, implantable_cardioverter_defibrillator_in_situ, heart_failure, left_ventricular_failure, right_ventricular_failure, heart_failure_preserved_ef, cardiomegaly, atherosclerosis, carotid_artery_stenosis, renal_artery_stenosis, peripheral_artery_disease, acute_limb_ischaemia, gangrene, mesenteric_ischaemia, ischaemic_colitis, aortic_dissection, aortic_aneurysm, aortic_aneurysm_rupture, hereditary_haemorrhagic_telangiectasia, venous_thromboembolism, deep_vein_thrombosis, peripheral_venous_insufficiency, lymphoedema, hypertension, hypotension, orthostatic_hypotension, drug_induced_hypotension, postural_orthostatic_tachycardia_syndrome, copd, emphysema, copd_infective_exacerbation, copd_non_infective_exacerbation, asthma, status_asthmaticus, bronchiectasis, bronchiectasis_infective_exacerbation, cystic_fibrosis, cystic_fibrosis_infective_exacerbation, occupational_lung_disease, acute_respiratory_distress_syndrome, pulmonary_oedema, pulmonary_haemorrhage, idiopathic_pulmonary_fibrosis, interstitial_lung_disease, pneumothorax, tension_pneumothorax, surgical_emphysema, bronchopleural_fistula, pleural_effusion, haemothorax, empyema, type_1_respiratory_failure, type_2_respiratory_failure, respiratory_arrest, sarcoidosis, obstructive_sleep_apnoea, long_term_oxygen_therapy, gastro_oesophageal_reflux_disease, oesophagitis, barretts_oesophagus, mallory_weiss_tear, hiatus_hernia, gastritis_or_duodenitis, upper_gi_ulcer, gastric_ulcer, duodenal_ulcer, perforated_upper_gi_ulcer, upper_gi_bleed, haematemesis, melaena, lower_gi_bleed, rectal_bleeding, acute_appendicitis, inguinal_or_femoral_hernia, umbilical_hernia, ventral_hernia, crohns_disease, ulcerative_colitis, colitis, proctitis, volvulus, intestinal_obstruction, ileus, acute_diverticulitis, diverticular_disease, irritable_bowel_syndrome, megacolon, bowel_perforation, peritonitis, haemorrhoids, anal_fissure, rectal_prolapse, gilberts_syndrome, fatty_liver, non_alcoholic_fatty_liver, alcoholic_fatty_liver, alcoholic_liver_disease, alcoholic_hepatitis, non_alcoholic_steatohepatitis, autoimmune_hepatitis, acute_liver_failure, subacute_liver_failure, hepatic_fibrosis, hepatic_cirrhosis, chronic_liver_failure, portal_hypertension, hepatic_encephalopathy, hepatorenal_syndrome, portal_vein_thrombosis, budd_chiari_syndrome, variceal_disease, oesophageal_varices, gastric_varices, acute_variceal_bleed, spontaneous_bacterial_peritonitis, primary_biliary_cholangitis, primary_sclerosing_cholangitis, alpha_1_antitrypsin_deficiency, wilsons_disease, haemochromatosis, cholelithiasis, cholecystitis, cholangitis, acute_pancreatitis, chronic_pancreatitis, pancreatic_pseudocyst, achalasia, gastroparesis, intestinal_malabsorption, coeliac_disease, impetigo, pemphigus, pemphigoid, atopic_dermatitis, psoriasis, urticaria, erythema_multiforme, stevens_johnson_syndrome, dress_syndrome, toxic_epidermal_necrolysis, erythema_nodosum, pyoderma_gangrenosum, hidradenitis_suppurativa, skin_ulceration, pressure_ulcer, venous_ulcer, arterial_ulcer, septic_arthritis, prosthetic_joint_infection, reactive_arthropathy, rheumatoid_arthritis, psoriatic_or_enteropathic_arthropathy, juvenile_arthritis, gout, pseudogout, osteoarthritis, vasculitis, polyarteritis_nodosa, granulomatosis_with_polyangiitis, takayasu_arteritis, giant_cell_arteritis, polymyalgia_rheumatica, microscopic_polyangiitis, polymyositis, dermatomyositis, systemic_lupus_erythematosus, systemic_sclerosis, sjogrens_syndrome, behcets_disease, raynauds_phenomenon, hypermobility_syndrome, scoliosis, ankylosing_spondylitis, spondylosis, spinal_stenosis, cervical_disc_disorder, sciatica, fibromyalgia, osteoporosis, pathological_fracture, rickets, adult_osteomalacia, osteonecrosis, pagets_disease_of_bone, chronic_pain_syndrome, nephrotic_syndrome, nephritic_syndrome, microscopic_haematuria, macroscopic_haematuria, glomerulonephritis, minimal_change_disease, membranoproliferative_glomerulonephritis, iga_nephropathy, focal_segmental_glomerulosclerosis, anti_gbm_disease, autosomal_dominant_polycystic_kidney_disease, renal_tubular_acidosis, acute_tubular_necrosis, rhabdomyolysis, tubulointerstitial_nephritis, acute_kidney_injury, acute_renal_replacement_therapy, chronic_kidney_disease, ckd_stage_3, ckd_stage_4, ckd_stage_5, arteriovenous_fistula_in_situ, long_term_haemodialysis, peritoneal_dialysis, contrast_induced_nephropathy, urolithiasis, renal_colic, hydronephrosis, hydroureter, nephrogenic_diabetes_insipidus, renal_ischaemia_or_infarction, urinary_tract_infection, cystitis, pyelonephritis, urosepsis, benign_prostatic_hyperplasia, prostatitis, testicular_torsion, female_pelvic_inflammatory_disease, endometriosis, fibroids, ovarian_torsion, dysmenorrhoea, menorrhagia, uterine_prolapse, pregnant, ectopic_pregnancy, pregnancy_with_abortive_outcome, pregnancy_successful_delivery, pregnancy_pre_existing_hypertension, gestational_hypertension, pre_eclampsia, hellp_syndrome, eclampsia, hyperemesis_gravidarum, pregnancy_pre_existing_diabetes, gestational_diabetes, tuberous_sclerosis, fetal_alcohol_syndrome, marfan_syndrome, down_syndrome, edwards_syndrome, patau_syndrome, turner_syndrome, klinefelter_syndrome, fragile_x_syndrome, congenital_heart_disease, ehlers_danlos_syndrome, tachycardia, bradycardia, palpitations, diaphoresis, night_sweats, cyanosis, pallor, flushing, tachypnoea, dyspnoea, exertional_dyspnoea, orthopnoea, cough, purulent_sputum, epistaxis, haemoptysis, stridor, wheezing, hypoxia, vertigo, dizziness, presyncope, syncope_or_any_collapse, pyrexia, febrile_convulsion, rigors, seizure, lymphadenopathy, peripheral_oedema, polydipsia, chest_pain, pleuritic_pain, abdominal_pain, abdominal_distension_or_bloating, guarding_or_peritonism, upper_abdominal_pain, lower_abdominal_pain, flank_pain, lower_back_pain, thoracic_back_pain, chronic_back_pain, arthralgia, myalgia, headache, meningism, pain, neuropathic_pain, severe_pain, calf_pain_or_swelling, claudication, vomiting, nausea, heartburn, dysphagia, constipation, diarrhoea, faecal_incontinence, jaundice, ascites, absent_bowel_sounds, absent_flatus, change_in_bowel_habit, skin_numbness, hyperaesthesia, pruritus, tremor, rigidity, muscle_cramp_or_spasm, fasciculation, ataxia, ataxic_gait, paralytic_gait, difficulty_in_walking, immobility, frailty, recurrent_falls, loss_of_appetite, abnormal_weight_loss, poor_oral_intake, cachexia, dysuria, urinary_incontinence, urinary_retention, anuria, oliguria, polyuria, confusion_or_disorientation, drowsiness, stupor_difficult_to_rouse, avpu_alert, avpu_voice_response, avpu_pain_response, avpu_unresponsive, auditory_hallucinations, visual_hallucinations, agitation, anger, physical_violence, poor_personal_hygiene, cognitive_decline, speech_disturbance, dysphasia_or_aphasia, dysarthria, anosmia_or_parosmia, joint_effusion, non_specific_malaise, fatigue, general_weakness, muscle_wasting, hypothermia, warm_well_perfused, periarrest_state, acute_fall, thoracic_trauma, abdominal_trauma, intracranial_trauma, concussion, fracture_of_skull_or_facial_bones, fracture_of_cervical_spine, fracture_of_thoracic_spine, fracture_of_rib, flail_chest, fracture_of_lumbar_spine, fracture_of_shoulder_or_humerus, fracture_of_forearm_wrist_or_hand, fracture_of_pelvis, fracture_of_hip_or_neck_of_femur, fracture_of_femoral_shaft, fracture_of_lower_leg_ankle_or_foot, compartment_syndrome, intentional_self_harm, intentional_self_overdose, neglect, physical_abuse_or_assault, burn_or_scald_injury, drowning_or_submersion_injury, medication_side_effect, acute_toxicity_from_medication, acute_toxicity_from_paracetamol, acute_alcohol_intoxication, acute_opioid_intoxication, acute_toxicity_from_cocaine, acute_toxicity_from_benzodiazepines, acute_toxicity_from_antidepressants, carbon_monoxide_poisoning, fabry_disease, gaucher_disease, pompe_disease, mucopolysaccharidosis, porphyria, glycogen_storage_disease, mitochondrial_disease, tracheostomy_in_situ, tracheostomy_malfunction, cvc_or_picc_line_in_situ, oxygen_therapy, high_flow_oxygen_therapy, bi_level_positive_pressure_ventilation, continuous_positive_airway_pressure, invasive_ventilation, peg_or_pej_in_situ, stoma_in_situ, blood_transfusion, transplanted_kidney, transplanted_liver, transplanted_heart, transplanted_stem_cells, transplant_failure_or_rejection, extracorporeal_membrane_oxygenation, multiple_organ_dysfunction_or_failure, graft_versus_host_disease, systemic_inflammatory_response_syndrome, circulatory_failure, cardiogenic_shock, hypovolaemic_shock, distributive_shock, massive_haemorrhage, palliative_care, end_of_life_care, emergency_surgery, emergency_laparotomy, major_open_surgery, minimally_invasive_surgery, upper_gi_endoscopic_therapy, lower_gi_endoscopic_therapy, ureteroscopic_or_cystoscopic_therapy, bronchoscopic_therapy, percutaneous_drain, vascular_interventional_procedure, organ_transplantation, coronary_artery_bypass_graft, percutaneous_coronary_intervention, cardiac_electrophysiology_procedure, transcatheter_valve_procedure, cancer_tumour_resection_or_debulking, major_upper_gi_surgery, major_lower_gi_surgery, major_hpb_surgery, major_thoracic_surgery, major_vascular_surgery, major_neurosurgery, major_cardiac_surgery, major_orthopaedic_surgery, major_urologic_surgery, major_gynaecological_surgery, surgical_or_procedural_complication, social_care_package, residential_or_care_home, temporary_accommodation, no_fixed_abode, living_alone_at_home, living_with_others_at_home, zimmer_or_walker_dependency, wheelchair_dependency, assisted_transfer_bed_to_chair_dependency, bedbound, unemployed, active_smoker, ex_smoker, never_smoked, medically_fit_for_discharge, discharge_pending_social, discharge_pending_placement, discharge_pending_transfer
Assertion	positive, negated, hypothetical, ambiguous
Subject	patient, family_history, mother_or_child_or_foetus, other, ambiguous
Relevance	active, recent, historical, planned, ambiguous

License

This project uses a proprietary license issued by Guy's and St Thomas' NHS Foundation Trust, enabling free (non-commercial) use by NHS organisations. See LICENSE files for details.