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Towards an ontology of vector- borne diseases: MalIDO, the first step.

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Presentation on theme: "Towards an ontology of vector- borne diseases: MalIDO, the first step."— Presentation transcript:

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2 Towards an ontology of vector- borne diseases: MalIDO, the first step.

3 Vector-borne diseases Diseases transmitted to humans or other animals through the bite of an arthropod, usually an insect. In contrast to most* other infectious diseases it involves three organisms. Vector-borne diseases Diseases transmitted to humans or other animals through the bite of an arthropod, usually an insect. In contrast to most* other infectious diseases it involves three organisms.

4 Insects and disease in the world (2001) DiseaseDeathsDALYs Malaria ("official" figures)1,12442,280 (estimated)2,700100,000 African trypanosomiasis501,598 Chagas' disease13649 Leishmaniasis Lymphatic filariasis05,644 Dengue fever, DHF, DHF-ss21653 AIDS2,30089,800 Numbers in Thousands; DALY: Disability-Adjusted Life Years DiseaseDeathsDALYs Malaria ("official" figures)1,12442,280 (estimated)2,700100,000 African trypanosomiasis501,598 Chagas' disease13649 Leishmaniasis Lymphatic filariasis05,644 Dengue fever, DHF, DHF-ss21653 AIDS2,30089,800 Numbers in Thousands; DALY: Disability-Adjusted Life Years

5 Insect- and arthropod-transmitted diseases: a partial list Malaria; African trypanosomiasis (sleeping disease); American trypanosomiasis (Chagas’ disease); Leishmaniasis; Lymphatic filariasis (several forms); Dengue fever, DHF, DHF-SS; Yellow fever; Myiasis; Onchocerciasis; Tungiasis; Bubonic plague; Relapsing fever; various Encephalitides; Typhus; Lyme disease; Japanese river fever; Urticaria; Loiasis; Dysenterrhoea; various Dermatitides; and several more...

6 Vector-borne diseases: Pathogens Vector-borne diseases: Pathogens (Arbo)Viruses (e.g. Dengue, Yellow fever, misc. encephalitides, etc.) Rickettsiae (e.g. Rocky Mountain spotted fever) Bacteria (e.g. Bubonic plague, Lyme disease) Protozoa (e.g. Malaria, Leishmaniasis, sleeping disease, Chagas' disease) Worms (e.g. Lymphatic filariasis, Onchocerciasis) Insects (Myiasis) (Arbo)Viruses (e.g. Dengue, Yellow fever, misc. encephalitides, etc.) Rickettsiae (e.g. Rocky Mountain spotted fever) Bacteria (e.g. Bubonic plague, Lyme disease) Protozoa (e.g. Malaria, Leishmaniasis, sleeping disease, Chagas' disease) Worms (e.g. Lymphatic filariasis, Onchocerciasis) Insects (Myiasis)

7 Vector-borne diseases: Vectors Vector-borne diseases: Vectors Mosquitoes (e.g. Malaria, Lymphatic filariasis, misc. encephalitides, Yellow fever, Dengue fever) Sandflies (e.g. Leishmaniasis) Ticks (e.g. Lyme disease, misc. encephalitides) Blackflies (Onchocerciasis) Tsetse (African trypanosomiasis) Kissing bugs (American trypanosomiasis) Fleas (Bubonic plague) and a few more… Mosquitoes (e.g. Malaria, Lymphatic filariasis, misc. encephalitides, Yellow fever, Dengue fever) Sandflies (e.g. Leishmaniasis) Ticks (e.g. Lyme disease, misc. encephalitides) Blackflies (Onchocerciasis) Tsetse (African trypanosomiasis) Kissing bugs (American trypanosomiasis) Fleas (Bubonic plague) and a few more…

8 Vector-borne diseases: Problems in disease control Vector-borne diseases: Problems in disease control Three organisms involved: Host (patient), vector, pathogen. Complicated epidemiology through vectors. Three organisms involved: Host (patient), vector, pathogen. Complicated epidemiology through vectors.

9 Malaria Dengue Lymphatic filariasis American & African Trypanosomiasis Trypanosomiasis Vector-borne diseases: Endemic countries Vector-borne diseases: Endemic countries

10 Vector-borne diseases: Endemic countries Vector-borne diseases: Endemic countries

11 Vector-borne diseases: Endemic areas: tropics! Vector-borne diseases: Endemic areas: tropics!

12 Vector-borne diseases: Endemic areas: tropics! Vector-borne diseases: Endemic areas: tropics!

13 Vector-borne diseases: Endemic areas: tropics! Vector-borne diseases: Endemic areas: tropics!

14 Vector-borne diseases: Problems in disease control Vector-borne diseases: Problems in disease control Three organisms involved: Host (patient), vector, pathogen. Complicated epidemiology through vectors. Mostly in the tropics. Important factors: Poverty, geography, insecticide resistance. Three organisms involved: Host (patient), vector, pathogen. Complicated epidemiology through vectors. Mostly in the tropics. Important factors: Poverty, geography, insecticide resistance.

15 Vector-borne diseases: Problems in disease control Vector-borne diseases: Problems in disease control Three organisms involved: Host (patient), vector, pathogen. Complicated epidemiology through vectors. Mostly in the tropics. Important factors: Poverty, geography, insecticide and drug resistance. Lack of vaccines with exception of Yellow fever. Three organisms involved: Host (patient), vector, pathogen. Complicated epidemiology through vectors. Mostly in the tropics. Important factors: Poverty, geography, insecticide and drug resistance. Lack of vaccines with exception of Yellow fever.

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17 Only build an ontology if: You have a body of data to annotate. You can think of good use cases. You have community buy-in or can build that buy-in. You commit to not wasting time on trivia. You convince funders to pay for it. You can take criticism. You commit to being Open Source and encourage community feedback. [...] you can make annotated data available You are pragmatic about technical issues. You can commit to using the Relations Ontology. You can commit to (re)-use community tools. You are or are deemed to be “a person overly obsessed with minor details.” You have a body of data to annotate. You can think of good use cases. You have community buy-in or can build that buy-in. You commit to not wasting time on trivia. You convince funders to pay for it. You can take criticism. You commit to being Open Source and encourage community feedback. [...] you can make annotated data available You are pragmatic about technical issues. You can commit to using the Relations Ontology. You can commit to (re)-use community tools. You are or are deemed to be “a person overly obsessed with minor details.” From M. Ashburner (2007) IDO Workshop

18 Only build an ontology if: You have a body of data to annotate. You can think of good use cases. You have community buy-in or can build that buy-in. You commit to not wasting time on trivia. You convince funders to pay for it. You can take criticism. You commit to being Open Source and encourage community feedback. [...] you can make annotated data available You are pragmatic about technical issues. You can commit to using the Relations Ontology. You can commit to (re)-use community tools. You are or are deemed to be “a person overly obsessed with minor details.” You have a body of data to annotate. You can think of good use cases. You have community buy-in or can build that buy-in. You commit to not wasting time on trivia. You convince funders to pay for it. You can take criticism. You commit to being Open Source and encourage community feedback. [...] you can make annotated data available You are pragmatic about technical issues. You can commit to using the Relations Ontology. You can commit to (re)-use community tools. You are or are deemed to be “a person overly obsessed with minor details.” From M. Ashburner (2007) IDO Workshop

19 Only build an ontology if: You have a body of data to annotate. You can think of good use cases. You have community buy-in or can build that buy-in. You commit to not wasting time on trivia. You convince funders to pay for it. You can take criticism. You commit to being Open Source and encourage community feedback. [...] you can make annotated data available You are pragmatic about technical issues. You can commit to using the Relations Ontology. You can commit to (re)-use community tools. You are or are deemed to be “a person overly obsessed with minor details.” You have a body of data to annotate. You can think of good use cases. You have community buy-in or can build that buy-in. You commit to not wasting time on trivia. You convince funders to pay for it. You can take criticism. You commit to being Open Source and encourage community feedback. [...] you can make annotated data available You are pragmatic about technical issues. You can commit to using the Relations Ontology. You can commit to (re)-use community tools. You are or are deemed to be “a person overly obsessed with minor details.” From M. Ashburner (2007) IDO Workshop WHO/Afro, EU/DGXII, IVCC (Gates), MTC (Gates), PMI, etc.

20 Ontologies at the IMBB Assignment of GO terms to An. gambiae gene models (VectorBase). - Finished and passed over to ENSEMBL. Construction of an ontology for the anatomy of mosquitoes. - Finished & upgraded to CARO-compliancy, available through OBO (TGMA). Construction of an ontology for the anatomy of ticks. - Finished, CARO- compliant, available through OBO (TADS), in collaboration with D. Sonenshine. Construction of an ontology addressing insecticide resistance. - Finished, available through OBO (MIRO). Construction of an ontology covering mosquito-specific physiological processes. - In progress. Construction of an ontology covering mosquito-specific physiological processes. - In progress. Construction of an ontology covering tick-specific phusiological processes. Construction of an ontology covering tick-specific phusiological processes. - In progress, in collaboration with D. Sonenshine. Assignment of GO terms to An. gambiae gene models (VectorBase). - Finished and passed over to ENSEMBL. Construction of an ontology for the anatomy of mosquitoes. - Finished & upgraded to CARO-compliancy, available through OBO (TGMA). Construction of an ontology for the anatomy of ticks. - Finished, CARO- compliant, available through OBO (TADS), in collaboration with D. Sonenshine. Construction of an ontology addressing insecticide resistance. - Finished, available through OBO (MIRO). Construction of an ontology covering mosquito-specific physiological processes. - In progress. Construction of an ontology covering mosquito-specific physiological processes. - In progress. Construction of an ontology covering tick-specific phusiological processes. Construction of an ontology covering tick-specific phusiological processes. - In progress, in collaboration with D. Sonenshine.

21 Vector-borne diseases: Building an ontology Vector-borne diseases: Building an ontology Use IDO as a "template”.

22 Vector-borne diseases: Building an ontology Vector-borne diseases: Building an ontology Use IDO as a "template”. Single ontology for all, or different ones? If different ones, based on vector, or pathogen, or disease? If based on disease, how specific (e.g. one or four for malaria, what about filariasis)? If based on vector, what balance to keep? Use IDO as a "template”. Single ontology for all, or different ones? If different ones, based on vector, or pathogen, or disease? If based on disease, how specific (e.g. one or four for malaria, what about filariasis)? If based on vector, what balance to keep?

23 Vector-borne diseases: Building MalIDO Vector-borne diseases: Building MalIDO Start with malaria and continue from there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's progress. Include information on vectors as well, in addition to pathogens and diseases. Link MalIDO to existing ontologies. Use MalIDO as a “template” for other vector-borne diseases. Start with malaria and continue from there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's progress. Include information on vectors as well, in addition to pathogens and diseases. Link MalIDO to existing ontologies. Use MalIDO as a “template” for other vector-borne diseases.

24 Vector-borne diseases: Building MalIDO Vector-borne diseases: Building MalIDO Start with malaria and continue from there. Start with malaria and continue from there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's progress. Refine/edit MalIDO based on IDO's progress. Include information on vectors as well, in addition to pathogens and diseases. Include information on vectors as well, in addition to pathogens and diseases. Link MalIDO to existing ontologies. Link MalIDO to existing ontologies. Use MalIDO as a “template” for other vector-borne diseases. Use MalIDO as a “template” for other vector-borne diseases. Start with malaria and continue from there. Start with malaria and continue from there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's progress. Refine/edit MalIDO based on IDO's progress. Include information on vectors as well, in addition to pathogens and diseases. Include information on vectors as well, in addition to pathogens and diseases. Link MalIDO to existing ontologies. Link MalIDO to existing ontologies. Use MalIDO as a “template” for other vector-borne diseases. Use MalIDO as a “template” for other vector-borne diseases.

25 Vector-borne diseases: Building MalIDO Vector-borne diseases: Building MalIDO Start with malaria and continue from there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's progress. Include information on vectors as well, in addition to pathogens and diseases. Link MalIDO to existing ontologies. Use MalIDO as a “template” for other vector-borne diseases. Start with malaria and continue from there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's progress. Include information on vectors as well, in addition to pathogens and diseases. Link MalIDO to existing ontologies. Use MalIDO as a “template” for other vector-borne diseases.

26 MalIDO: Extended Info (12 September 2008) MalIDO: Extended Info (12 September 2008) Total terms = 1469 process has 1179 descendants role has 103 descendants quality has 131 descendants object has 454 descendants developmental stage has 25 descendants object aggregate has 11 descendants terms with 0 parents: 6 (<1%) terms with 1 parents: 1364 (92%) terms with 2 parents: 85 (6%) terms with >2 parents: 1413 (<1%)  63% of terms have definitions (930 of 1469) Total terms = 1469 process has 1179 descendants role has 103 descendants quality has 131 descendants object has 454 descendants developmental stage has 25 descendants object aggregate has 11 descendants terms with 0 parents: 6 (<1%) terms with 1 parents: 1364 (92%) terms with 2 parents: 85 (6%) terms with >2 parents: 1413 (<1%)  63% of terms have definitions (930 of 1469)

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28 Insect- and arthropod-transmitted diseases: a partial list Malaria; African trypanosomiasis (sleeping disease); American trypanosomiasis (Chagas’ disease); Leishmaniasis; Lymphatic filariasis (several forms); Dengue fever, DHF, DHF-SS; Yellow fever; Myiasis; Onchocerciasis; Tungiasis; Bubonic plague; Relapsing fever; various Encephalitides; Typhus; Lyme disease; Japanese river fever; Urticaria; Loiasis; Dysenterrhoea; various Dermatitides; and several more...

29 Pantelis Topalis John Vontas Manolis Dialynas ??? IMBB-FORTH

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