Ontology for Parasite Life Cycle

What is the Ontology for Parasite Lifecycle (OPL)?

OPL models the life cycle stage details of T.cruzi and two related kinetoplastids, Trypanosoma brucei and Leishmania major. In addition, the ontology also models necessary contextual details such as host information, vector information, strain and anatomical location. All the entities in the ontology are linked to each other by explicitly modeled named relationships that will enable software applications to accurately interpret data annotated with this ontology. For example, “Trypanosoma_cruzi→has_vector_organism→triatominae”. The PLO is modeled in the W3C Web Ontology Language (OWL) standard and currently has 41 classes and 5 properties with a description logic expressivity of ALU. OPL(ver 0.1), which was called Parasite Lifecycle Ontology is released through NCBO’s BioPortal repository for public use.

{"openlevels":1,"minExpandLevel":2} Owl:Thing entity continuant dependent_continuant specifically_dependent_continuant realizable_entity role parasite_role human_parasite_role infection_agent_vector_role biological_vector_of_infectious_agent_role host_role definitive_host_role intermediate_host_role independent_continuant material_entity Organism mollusca bulinus oncomelania biomphalaria insect triatominae anopheles Phlebotominae glossina parasite_organism leishmania leishmania_major leishmania_major_amastigote leishmania_major_promastigote leishmania_major_metacyclic_promastigote leishmania_major_procyclic_promastigote trypanosoma trypanosoma_brucei trypanosoma_brucei_epimastigote trypanosoma_brucei_trypomastigote trypanosoma_brucei_metacyclic_trypomastigote trypanosoma_brucei_procyclic_trypomastigote trypanosoma_cruzi trypanosoma_cruzi_amastigote trypanosoma_cruzi_epimastigote trypanosoma_cruzi_trypomastigote trypanosoma_cruzi_metacyclic_trypomastigote plasmodium plasmodium_falciparum plasmodium_falciparum_erythrocytic_schizont plasmodium_falciparum_hepatic_schizont plasmodium_falciparum_macrogamete plasmodium_falciparum_macrogametocyte plasmodium_falciparum_merozoite plasmodium_falciparum_microgamete plasmodium_falciparum_microgametocyte plasmodium_falciparum_exflagellated_microgametocyte plasmodium_falciparum_oocyst plasmodium_falciparum_ookinete plasmodium_falciparum_ring_trophozoite plasmodium_falciparum_sporozoite plasmodium_falciparum_trophozoite plasmodium_falciparum_zygote schistosoma schistosoma_japonicum schistosoma_japonicum_cercaria schistosoma_japonicum_egg schistosoma_japonicum_miracidium schistosoma_japonicum_schistosomulum schistosoma_24_hour_japonicum_schistosomulum schistosoma_3_day_japonicum_schistosomulum schistosoma_3_hour_japonicum_schistosomulum schistosoma_6_day_japonicum_schistosomulum schistosoma_japonicum_sporocyst schistosoma_japonicum_daughter_sporocyst schistosoma_japonicum_mother_sporocyst schistosoma_japonicum_worm schistosoma_japonicum_3_week_worm schistosoma_japonicum_7_week_worm schistosoma_mansoni schistosoma_mansoni_sporocyst schistosoma_mansoni_daughter_sporocyst schistosoma_mansoni_mother_sporocyst schostosoma_mansoni_cercaria schostosoma_mansoni_egg schostosoma_mansoni_miracidium schostosoma_mansoni_schistosomulum schistosoma_mansoni_24_hour_schistosomulum schistosoma_mansoni_3_day_schistosomulum schistosoma_mansoni_3_hour_schistosomulum schistosoma_mansoni_6_day_schistosomulum schistosoma_mansoni_worm schistosoma_mansoni_3_week_worm schistosoma_mansoni_7_week_worm schistosoma_haematobium schistosoma_haematobium_cercarcia schistosoma_haematobium_egg schistosoma_haematobium_miracidium schistosoma_haematobium_schistosomulum schistosoma_haematobium_24_hour_schistosomulum schistosoma_haematobium_3_day_schistosomulum schistosoma_haematobium_3_hour_schistosomulum schistosoma_haematobium_6_day_schistosomulum schistosoma_haematobium_sporocyst schistosoma_haematobium_daughter_sporocyst schistosoma_haematobium_mother_sporocyst schistosoma_haematobium_worm schistosoma_haematobium_3_week_worm schistosoma_haematobium_7_week_worm vertebrate mammal mus_musculus homo_sapiens canis_familiaris anatomical_structure hepatopancreas biomphalaria_hepatopancreas bulinus_hepatopancreas oncomelania_hepatopancreas proboscis Phlebotominae_proboscis cell hepatocyte human_hepatocyte erythrocyte human_erythrocyte macrophage human_macrophage urinary_bladder human_bladder mesenteric_vein human_mesenteric_vein ureter human_ureter intestine human_intestine blood human_blood salivary_gland anopheles_salivary_gland glossina_salivary_gland midgut anopheles_midgut glossina|midgut Phlebotominae_midgut triatominae_midgut hindgut triatominae_hindgut cerebrospinal_fluid human_cerebrospinal_fluid lung human_lung skin_of_body human_skin liver human_liver occurrent proccessual_entity lifecycle_stage amastigote_stage cercaria_stage egg_stage epimastigote_stage gametocyte_stage macrogametocyte_stage microgametocyte_stage exflagellated_microgametocyte_stage hypnozoite_stage macrogamete_stage merozoite_stage microgamete_stage miracidium_stage oocyst_stage ookinete_stage promastigote_stage schistosomulum_stage 24_hour_schistosomulum_stage 3_day_schistosomulum_stage 3_hour_schistosomulum_stage 6_day_schistosomulum_stage schizont_stage erythrocytic_shizont_stage hepatic_shizont_stage sporozoite_stage trophozoite_stage ring_trophozoite_stage trypomastigote_stage bloodstream_trypomastigote_stage metacyclic_trypomastigote_stage procyclic_trypomastigote_stage worm_stage 3_week_worm_stage 7_week_worm_stage zygote_stage parasite_lifecycle_stage leishmania_major_lifecycle_stage leishmania_major_amastigote_stage leishmania_major_promastigote_stage plasmodium_falciparum_lifecycle_stage [[Plasmodium_Falciparum_Gametocyte_Stage|plasmodium_falciparum_gametocyte_stage plasmodium_falciparum_macrogametocyte_stage plasmodium_falciparum_microgametocyte_stage]] plasmodium_falciparum_macrogamete_stage plasmodium_falciparum_merozoite_stage plasmodium_falciparum_microgame_stage plasmodium_falciparum_oocyst_stage plasmodium_falciparum_ookinete_stage plasmodium_falciparum_schizont_stage plasmodium_erythrocytic_falciparum_schizont_stage plasmodium_falciparum_hepatic_schizont_stage plasmodium_falciparum_sporozoite_stage plasmodium_falciparum_trophozoite_stage plasmodium_falciparum_ring_trophozoite_stage plasmodium_falciparum_zygote_stage schistosoma_haematobium_lifecycle_stage schistosoma_haematobium_cercaria_stage schistosoma_haematobium_egg_stage schistosoma_haematobium_miracidium_stage schistosoma_haematobium_schistosomulum_stage schistosoma_haematobium_24_hour_schistosomulum_stage schistosoma_haematobium_3_day_schistosomulum_stage schistosoma_haematobium_3_hour_schistosomulum_stage schistosoma_haematobium_6_day_schistosomulum_stage schistosoma_haematobium_worm_stage schistosoma_haematobium_3_week_worm_stage schistosoma_haematobium_7_week_worm_stage schistosoma_japonicum_lifecycle_stage schistosoma_japonicum_cercaria_stage schistosoma_japonicum_egg_stage schistosoma_japonicum_miracidium_stage schistosoma_japonicum_schistosomulum_stage schistosoma_japonicum_24_hour_schistosomulum_stage schistosoma_japonicum_3_day_schistosomulum_stage schistosoma_japonicum_3_hour_schistosomulum_stage schistosoma_japonicum_6_day_schistosomulum_stage schistosoma_japonicum_worm_stage schistosoma_japonicum_3_week_worm_stage schistosoma_japonicum_7_week_worm_stage schistosoma_mansoni_lifecycle_stage schistosoma_mansoni_cercaria_stage schistosoma_mansoni_egg_stage schistosoma_mansoni_miracidium_stage schistosoma_mansoni_schistosomulum_stage schistosoma_mansoni_24_hour_schistosomulum_stage schistosoma_mansoni_3_day_schistosomulum_stage schistosoma_mansoni_3_hour_schistosomulum_stage schistosoma_mansoni_6_day_schistosomulum_stage schistosoma_mansoni_worm_stage schistosoma_mansoni_3_week_worm_stage schistosoma_mansoni_7_week_worm_stage trypanosoma_brucei_lifecycle_stage trypanosoma_brucei_epimastigote_stage trypanosoma_brucei_trypomastigote_stage trypanosoma_brucei_bloodstream_trypomastigote_stage trypanosoma_brucei_metacyclic_trypomastigote_stage trypanosoma_brucei_Procyclic_trypomastigote_stage trypanosoma_cruzi_lifecycle_stage trypanosoma_cruzi_amastigote_stage trypanosoma_cruzi_epimastigote_stage trypanosoma_cruzi_trypomastigote_stage trypanosoma_cruzi_metacyclic_trypomastigote_stage

Snapshot of class hierarchy of the parasite life cycle ontology using Protege toolkit. Detail of this ontology is available at NCBO BioPortal

List of ontology classes

24 Hour Schistosomulum Stage 3 Day Schistosomulum Stage 3 Hour Schistosomulum Stage 3 Week Worm Stage 6 Day Schistosomulum Stage 7 Week Worm Stage A Amastigote Stage Anatomical Structure Anopheles Anopheles Midgut Anopheles Salivary Gland B Biological Vector of Infections Agent Role Biomphalaria Biomphalaria Hepatopancreas Blood Bloodstream Trypomastigote Stage Bulinus Bulinus Hepatopancreas C Canis familiaris Cell Cercaria Stage Cerebrospinal Fluid Continuant D Definitive Host Role Dependent Contininuant E Egg Stage Entity Epimastigote Stage Erythrocyte Erythrocytic Shizont Stage Exflagellated Microgametocyte Stage G Gametocyte Stage Glossina Glossina Midgut Glossina Salivary Gland H Hepatic Shizont Stage Hepatocyte Hepatopancreas Hindgut Homo sapiens Host Role Human Blood Human Bladder Human Cerebrospinal Fluid Human Erythrocyte Human Hepatocyte Human Intestine Human Liver Human Lung Human Macrophage Human Mesenteric Vein Human Parasite Role Human Skin Human Ureter Hypnozoite Stage I Independent Continuant Infectious Agent Vector Role Insect Intermediate Host Role Intestine L Leishmania Leishmania major Leishmania major Amastigote Leishmania major Amastigote Stage Leishmania major Lifecycle Stage Leishmania major Metacyclic Promastigote Leishmania major Procyclic Promastigote Leishmania major Promastigote Leishmania major Promastigote Stage Lifecycle Stage Liver Lung M Macrogamete Stage Macrogametocyte Stage Macrophage Mammal Material Entity Merozoite Stage Mesenteric Vein Metacyclic Trypomastigote Stage Microgamete Stage Microgametocyte Stage Midgut Miracidium Stage Mollusca Mus musculus O Occurrent Oncomelania Oncomelania Hepatopancreas Oocyst Stage Ookinete Stage P Parasite Lifecycle Stage Parasite Role Parasite Organism Phlebotominae Phlebotominae Midgut Plasmodium Plasmodium falciparum Plasmodium falciparum Erythrocytic Schizont Plasmodium falciparum Erythrocytic Schizont Stage Plasmodium falciparum Exflagellated Microgametocyte Plasmodium falciparum Gametocyte Stage Plasmodium falciparum Hepatic Schizont Plasmodium falciparum Hepatic Schizont Stage Plasmodium falciparum Lifecycle Stage Plasmodium falciparum Macrogamete Plasmodium falciparum Macrogamete Stage Plasmodium falciparum Macrogametocyte Plasmodium falciparum Macrogametocyte Stage Plasmodium falciparum Merozoite Plasmodium falciparum Merozoite Stage Plasmodium falciparum Microgamete Plasmodium falciparum Microgamete Stage Plasmodium falciparum Microgametocyte Plasmodium falciparum Microgametocyte Stage Plasmodium falciparum Oocyst Plasmodium falciparum Oocyst Stage Plasmodium falciparum Ookinete Plasmodium falciparum Ookinete Stage Plasmodium falciparum Ring Trophozoite Plasmodium falciparum Ring Trophozoite Stage Plasmodium falciparum Schizont Stage Plasmodium falciparum Sporozoite Plasmodium falciparum Sporozoite Stage Plasmodium falciparum Trophozoite Plasmodium falciparum Trophozoite Stage Plasmodium falciparum Zygote Plasmodium falciparum Zygote Stage Proboscis Processual Entity Procyclic Trypomastigote Stage Promastigote Stage R Realizable Entity Ring Trophozoite Stage Role S Salivary Gland Schistosoma Schistosoma haematobium Schistosoma haematobium 24 Hour Schistosomulum Schistosoma haematobium 24 Hour Schistosomulum Stage Schistosoma haematobium 3 Day Schistosomulum Schistosoma haematobium 3 Day Schistosomulum Stage Schistosoma haematobium 3 Hour Schistosomulum Schistosoma haematobium 3 Hour Schistosomulum Stage Schistosoma haematobium 3 Week Worm Schistosoma haematobium 3 Week Worm Stage Schistosoma haematobium 6 Day Schistosomulum Schistosoma haematobium 6 Day Schistosomulum Stage Schistosoma haematobium 7 Week Worm Schistosoma haematobium 7 Week Worm Stage Schistosoma haematobium Cercaria Schistosoma haematobium Cercaria Stage Schistosoma haematobium Daughter Sporocyst Schistosoma haematobium Egg Schistosoma haematobium Egg Stage Schistosoma haematobium Lifecycle Stage Schistosoma haematobium Miracidium Schistosoma haematobium Miracidium Stage Schistosoma haematobium Mother Sporocyst Schistosoma haematobium Schistosomulum Schistosoma haematobium Schistosomulum Stage Schistosoma haematobium Sporocyst Schistosoma haematobium Worm Schistosoma haematobium Worm Stage Schistosoma japonicum Schistosoma japonicum 24 Hour Schistosomulum Schistosoma japonicum 24 Hour Schistosomulum Stage Schistosoma japonicum 3 Day Schistosomulum Schistosoma japonicum 3 Day Schistosomulum Stage Schistosoma japonicum 3 Hour Schistosomulum Schistosoma japonicum 3 Hour Schistosomulum Stage Schistosoma japonicum 3 Week Worm Schistosoma japonicum 3 Week Worm Stage Schistosoma japonicum 6 Day Schistosomulum Schistosoma japonicum 6 Day Schistosomulum Stage Schistosoma japonicum 7 Week Worm Schistosoma japonicum 7 Week Worm Stage Schistosoma japonicum Cercaria Schistosoma japonicum Cercaria Stage Schistosoma japonicum Daughter Sporocyst Schistosoma japonicum Egg Schistosoma japonicum Egg Stage Schistosoma japonicum Lifecycle Stage Schistosoma japonicum Miracidium Schistosoma japonicum Miracidium Stage Schistosoma japonicum Mother Sporocyst Schistosoma japonicum Schistosomulum Schistosoma japiconium Schistosomulum Stage Schistosoma japonicum Sporocyst Schistosoma japonicum Worm Schistosoma japonicum Worm Stage Schistosoma mansoni Schostosoma mansoni 24 Hour Schistosomulum Schistosoma mansoni 24 Hour Schistosomulum Stage Schostosoma mansoni 3 Day Schistosomulum Schistosoma mansoni 3 Day Schistosomulum Stage Schostosoma mansoni 3 Hour Schistosomulum Schistosoma mansoni 3 Hour Schistosomulum Stage Schostosoma mansoni 3 Week Worm Schistosoma mansoni 3 Week Worm Stage Schostosoma mansoni 6 Day Schistosomulum Schistosoma mansoni 6 Day Schistosomulum Stage Schostosoma mansoni 7 Week Worm Schistosoma mansoni 7 Week Worm Stage Schostosoma mansoni Cercaria Schistosoma mansoni Cercaria Stage Schistosoma mansoni Daughter Sporocyst Schostosoma mansoni Egg Schistosoma mansoni Egg Stage Schistosoma mansoni Lifecycle Stage Schostosoma mansoni Miracidium Schistosoma mansoni Miracidium Stage Schistosoma mansoni Mother Sporocyst Schostosoma mansoni Schistosomulum Schostosoma mansoni Schistosomulum Stage Schistosoma mansoni Sporocyst Schistosoma mansoni Worm Stage Schistosomulum Stage Schizont Stage Skin Of Body Specifically Dependent Continuant Sporozoite Stage T Triatominae Triatominae Hindgut Triatominae Midgut Trypanosoma Trypanosoma brucei Trypanosoma brucei Bloodstream Trypomastigote Stage Trypanosoma brucei Epimastigote Stage Trypanosoma brucei Lifecycle Stage Trypanosoma brucei Metacyclic Trypomastigote Stage Trypanosoma brucei Procyclic Trypomastigote Trypanosoma brucei Procyclic Trypomastigote Stage Trypanosoma brucei Trypomastigote Stage Trypanosoma cruzi Trypanosoma cruzi Amastigote Stage Trypanosoma cruzi Epimastigote Stage Trypanosoma cruzi Lifecycle Stage Trypanosoma cruzi Metacyclic Trypomastigote Stage Trypanosoma cruzi Trypomastigote Stage Trophozoite Stage Trypomastigote Stage U Urinary Bladder Ureter V Vertebrate W Worm Stage Z Zygote Stage

Organisms in OPL

Here is brief description and life-cycles of the organisms that are covered in OPL. Trypanosoma cruzi T. cruzi Lifecycle The life cycle of Trypanosoma cruzi involves both vertebrate and invertebrate hosts (see figure below). Metacyclic trypomastigotes are deposited on the mammalian (vertebrate host's) skin through the faeces of the triatomine bug vector. They have the capacity to penetrate skin through wounds, such as the bite from the bug, and across the mucosal membranes surrounding the eyes and mouth. Inside the mammalian host, the trypomastigotes penetrate either phagocytic or non-phagocytic cells, in a manner distinct from phagocytosis. Parasites subvert the host cell Ca2+ -regulated lysosomal exocytic pathway, literally ‘hijacking’ lysosomes to enable them to invade effectively (Sibley and Andrews, 2000; Tan and Andrews, 2002). Within the host cell, trypomastigotes are initially held within a membrane bound vacuole. They subsequently enter the host cell cytoplasm directly, transforming into amastigotes (the intracellular replicative forms) (Tan and Andrews, 2002). Around five days post invasion, the amastigotes transform back into C- shaped trypomastigotes, and the host cell ruptures, releasing the parasites into the bloodstream. These bloodstream trypomastigotes can then either infect further cells, or can be taken up by a reduviid bug. Within the insect vector, epimastigotes develop in the alimentary tract, taking 10 – 15 days to replicate and transform into infective stages in the rectum (Kollien and Schaub, 2000). T. cruzi can also be transmitted via contaminated blood and infected organs used in transplant operations, or congenitally from mother to child. Trypanosoma brucei T. brucei Lifecyle Trypanosoma brucei is also transmitted by an insect vector, in this case the tsetse fly, one of the Glossina sp. Blood stream trypomastigotes are ingested by the tsetse from an infected patient during the insect blood meal. In the midgut of the tsetse, the trypanosomes develop into procyclic forms that divide by binary fission. Some of these then migrate to the salivary glands where they differentiate into infectious metacyclic trypomastigotes. These are transmitted into new hosts during further blood feeds (Barrett et al, 2003). Leishmania sp. Leishmania sp. Lifecycle Leishmania species are also transmitted by insect vectors, in this case metacyclic promastigotes are introduced into the skin by the bite of various species of sand fly. These are taken up by macrophages and transform into intracellular amastigotes (reviewed by Handman and Bullen, 2002), remaining in this form for the duration of the life cycle in the mammalian host. Development within the sand fly vector varies from species to species, but is thought to involve 2 distinct growth phases (Gossage et al, 2003).

Feedback/Comments

Please add feedback/comments in Discussion Section on the top of this wiki page.