Neglected Tropical Diseases Curation Project

GitHub Epic: https://github.com/monarch-initiative/dismech/issues/220

Overview

Curate the WHO-recognized neglected tropical diseases (NTDs) in the Disorder Mechanisms Knowledge Base, with emphasis on pathogen life cycles, transmission routes, immune evasion, and chronic morbidity mechanisms. The current WHO list includes 21 diseases or disease groups, which maps to 22 KB files when splitting the dengue/chikungunya group.

This is an evergreen project: beyond the WHO core list, "Other" expansion categories capture related diseases that share mechanisms (e.g. other arboviruses, other filarial parasites) and can be unfolded as curation continues.

Goals

Create or enhance NTD YAML files in kb/disorders/
Capture vector/reservoir/host interactions
Annotate phenotypes with HPO terms and treatments with NCIT terms
Provide PMID-supported evidence for core mechanisms

Existing NTD Entries in KB (2)

Disease	File	Status
Dengue	Dengue.yaml	Exists
Echinococcosis (polycystic)	Polycystic_Echinococcosis.yaml	Exists

NTDs to Curate (WHO List, 21 groups)

The WHO list below is used as the project scope. Some WHO groups are split into multiple files for clarity (e.g., dengue + chikungunya).

Bacterial NTDs

Disease	Planned File	Notes	Status
Buruli ulcer	Buruli_Ulcer.yaml	Mycobacterium ulcerans	[x]
Leprosy (Hansen's disease)	Leprosy.yaml	M. leprae/ lepromatosis	[x]
Trachoma	Trachoma.yaml	Chlamydia trachomatis	[x]
Noma (cancrum oris)	Noma.yaml	Added to WHO list in 2023	[x]
Yaws and other endemic treponematoses	Yaws.yaml	Bejel.yaml and Pinta.yaml added	[x]
Other bacterial NTDs	—	e.g. leptospirosis, relapsing fever, bartonellosis	[ ]

Protozoal NTDs

Disease	Planned File	Notes	Status
Chagas disease	Chagas_Disease.yaml	Trypanosoma cruzi	[x]
Human African trypanosomiasis	Human_African_Trypanosomiasis.yaml	T. brucei; stage 1/2	[x]
Leishmaniasis	Leishmaniasis.yaml	Visceral/cutaneous/mucosal	[x]
Other protozoal NTDs	—	e.g. babesiosis, balantidiasis, free-living amoebae	[ ]

Viral NTDs

Disease	Planned File	Notes	Status
Dengue	Dengue.yaml	Existing	[x]
Chikungunya	Chikungunya.yaml	Often paired with dengue in WHO list	[x]
Rabies	Rabies.yaml	Neurotropic lyssavirus	[x]
Other arboviral NTDs	—	e.g. Zika, yellow fever, Rift Valley fever	[ ]

Helminth NTDs

Disease/Group	Planned File	Notes	Status
Dracunculiasis (Guinea-worm disease)	Dracunculiasis.yaml	Eradication focus	[x]
Lymphatic filariasis	Lymphatic_Filariasis.yaml	Wuchereria/Brugia	[x]
Onchocerciasis (river blindness)	Onchocerciasis.yaml	O. volvulus	[x]
Other filarial diseases	—	e.g. loiasis, mansonellosis, Dirofilaria	[ ]
Schistosomiasis	Schistosomiasis.yaml	S. haematobium/mansoni/japonicum	[x]
Soil-transmitted helminthiases	Soil_Transmitted_Helminthiases.yaml	Ascaris, Trichuris, hookworm	[x]
Foodborne trematodiases	Foodborne_Trematodiases.yaml	Clonorchis, Opisthorchis, Fasciola, Paragonimus	[x]
Taeniasis/cysticercosis	Taeniasis_Cysticercosis.yaml	Taenia solium	[x]
Other cestode infections	—	e.g. Hymenolepis, Diphyllobothrium, sparganosis	[ ]
Echinococcosis	Cystic_Echinococcosis.yaml	Cystic form added; polycystic file exists	[x]

Fungal NTDs

Disease/Group	Planned File	Notes	Status
Mycetoma, chromoblastomycosis and other deep mycoses	Mycetoma.yaml	Chromoblastomycosis.yaml added	[x]
Other deep mycoses	—	e.g. sporotrichosis, paracoccidioidomycosis, histoplasmosis	[ ]

Ectoparasites, Other, and Envenoming

Disease/Group	Planned File	Notes	Status
Scabies and other ectoparasitoses	Scabies.yaml	Consider Tungiasis.yaml	[x]
Other ectoparasitoses	—	e.g. tungiasis, myiasis, pediculosis	[ ]
Snakebite envenoming	Snakebite_Envenoming.yaml	Toxin-mediated	[x]
Other envenoming	—	e.g. scorpion stings, spider bites, jellyfish	[ ]

Cross-Cutting Mechanisms to Capture

Vector biology: insect/arthropod vectors, seasonality, geographic range
Reservoirs: zoonotic cycles, domestic/wild animal hosts
Immune evasion: antigenic variation, intracellular persistence, Th1/Th2 skewing
Chronic inflammation: granulomas, fibrosis, lymphatic damage, neuroinvasion
Tissue tropism: skin, CNS, liver, lymphatics, eye, bone
Coinfections and comorbidity: HIV, malnutrition, helminth co-burden
Public health interfaces: WASH, mass drug administration, vector control

Suggested Curation Order

High-burden, high-impact: dengue, schistosomiasis, soil-transmitted helminthiases, lymphatic filariasis
Vector-borne protozoa: leishmaniasis, Chagas, HAT
Skin NTDs: leprosy, Buruli ulcer, yaws, scabies, mycetoma/chromoblastomycosis
Zoonotic and toxin-mediated: rabies, echinococcosis, snakebite
Elimination targets: dracunculiasis, trachoma

STATUS

WHO List NTDs (20/20)

[x] Buruli ulcer
[x] Chagas disease
[x] Chikungunya
[x] Dracunculiasis
[x] Foodborne trematodiases
[x] Human African trypanosomiasis
[x] Leishmaniasis
[x] Leprosy
[x] Lymphatic filariasis
[x] Mycetoma / chromoblastomycosis
[x] Noma
[x] Onchocerciasis
[x] Rabies
[x] Scabies and other ectoparasitoses
[x] Schistosomiasis
[x] Snakebite envenoming
[x] Soil-transmitted helminthiases
[x] Taeniasis/cysticercosis
[x] Trachoma
[x] Yaws and other endemic treponematoses

Existing NTD Diseases (2/2)

[x] Dengue
[x] Echinococcosis (polycystic file exists; cystic form added)

Expansion Categories

[ ] Other bacterial NTDs; e.g. leptospirosis, relapsing fever, bartonellosis
[ ] Other protozoal NTDs; e.g. babesiosis, balantidiasis, free-living amoebae
[ ] Other arboviral NTDs; e.g. Zika, yellow fever, Rift Valley fever
[ ] Other filarial diseases; e.g. loiasis, mansonellosis, Dirofilaria
[ ] Other cestode infections; e.g. Hymenolepis, Diphyllobothrium, sparganosis
[ ] Other deep mycoses; e.g. sporotrichosis, paracoccidioidomycosis, histoplasmosis
[ ] Other ectoparasitoses; e.g. tungiasis, myiasis, pediculosis
[ ] Other envenoming; e.g. scorpion stings, spider bites, jellyfish

NOTES

2026-01-26

Added Schistosomiasis.yaml with PMID-supported evidence for transmission, granulomatous pathology, and praziquantel treatment.
Added Lymphatic_Filariasis.yaml with OPL life-cycle stages and PMID evidence for mosquito transmission, lymphatic pathology, and MDA treatments.
Added Leishmaniasis.yaml with OPL life-cycle stages, sand fly transmission, and clinical form subtypes.
Added Chagas_Disease.yaml with OPL life-cycle stages, triatomine transmission, and cardiomyopathy evidence.
Added Human_African_Trypanosomiasis.yaml with OPL life-cycle stages, tsetse transmission, and staged CNS involvement.
Added Soil_Transmitted_Helminthiases.yaml with species coverage, helminth transmission, and deworming treatments.
Added Onchocerciasis.yaml with black fly transmission, pruritus/ocular disease, and ivermectin therapy.
Added Chikungunya.yaml with Aedes transmission, fever/arthralgia phenotypes, and symptomatic care.
Added Taeniasis_Cysticercosis.yaml with Taenia solium lifecycle context and neurocysticercosis seizure evidence.
Added Rabies.yaml with lyssavirus etiology, bite transmission, and post-exposure prophylaxis.
Added Buruli_Ulcer.yaml with mycolactone-mediated tissue destruction and antimicrobial/surgical treatment notes.
Added Dracunculiasis.yaml with waterborne copepod transmission and Dracunculus medinensis etiology.
Added Trachoma.yaml with conjunctival C. trachomatis infection, scarring, and SAFE strategy antibiotic MDA.
Refreshed Dengue.yaml with updated MONDO term, Aedes vector transmission, and severe plasma leakage pathophysiology.
Added Leprosy.yaml with M. leprae etiology, nasal droplet transmission, neuropathy, and multidrug therapy evidence.
Added Scabies.yaml with Sarcoptes scabiei etiology, contact transmission, pruritus/lesions, and first-line therapy evidence.
Added Snakebite_Envenoming.yaml with venom toxicity, clinical features, and antivenom treatment evidence.
Added Foodborne_Trematodiases.yaml with major liver, lung, and intestinal fluke agents and food-borne transmission evidence.
Added Mycetoma.yaml with fungal/bacterial etiologies and classic subcutaneous swelling evidence.
Added Noma.yaml with polymicrobial necrotizing pathology and gangrenous phenotype evidence.
Added Yaws.yaml with T. pallidum subsp. pertenue etiology, direct-contact transmission, ulcers, and azithromycin therapy evidence.
Added Cystic_Echinococcosis.yaml with E. granulosus etiology, dog-associated transmission, hepatic cysts, and benzimidazole/surgical treatments.
Added Chromoblastomycosis.yaml with common etiologic agents, traumatic inoculation, and verrucous lesion phenotypes.
Added Bejel.yaml with T. pallidum subsp. endemicum etiology evidence.
Added Pinta.yaml with T. carateum etiology evidence.

2026-01-25

Project initialized using WHO's current NTD list (21 diseases/groups).