Towards an ontology of

vector-borne diseases:

MalIDO, the first step.

Towards an ontology of

vector-borne diseases:

MalIDO, the first step.

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.

Insects and disease in the world (2001)Insects and disease in the world (2001)

Disease Deaths DALYs

Malaria ("official" figures) 1,124 42,280 (estimated) 2,700 100,000

African trypanosomiasis 50 1,598

Chagas' disease 13 649

Leishmaniasis 59 2357

Lymphatic filariasis 0 5,644

Dengue fever, DHF, DHF-ss 21 653

AIDS 2,300 89,800

Numbers in Thousands; DALY: Disability-Adjusted Life Years

Disease Deaths DALYs

Malaria ("official" figures) 1,124 42,280 (estimated) 2,700 100,000

African trypanosomiasis 50 1,598

Chagas' disease 13 649

Leishmaniasis 59 2357

Lymphatic filariasis 0 5,644

Dengue fever, DHF, DHF-ss 21 653

AIDS 2,300 89,800

Numbers in Thousands; DALY: Disability-Adjusted Life Years

Insect- and arthropod-transmitted diseases: a partial

list

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...

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...

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)

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…

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.

MalariaMalariaDengueDengueLymphatic filariasisLymphatic filariasis

American & AfricanAmerican & AfricanTrypanosomiasisTrypanosomiasis

American & AfricanAmerican & AfricanTrypanosomiasisTrypanosomiasis

Vector-borne diseases:Endemic countries

Vector-borne diseases:Endemic countries

Vector-borne diseases:Endemic countries

Vector-borne diseases:Endemic countries

Vector-borne diseases:Endemic areas: tropics!

Vector-borne diseases:Endemic areas: tropics!

Vector-borne diseases:Endemic areas: tropics!

Vector-borne diseases:Endemic areas: tropics!

Vector-borne diseases:Endemic areas: tropics!

Vector-borne diseases:Endemic areas: tropics!

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.

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.

Only build an ontology if: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

Only build an ontology if: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

Only build an ontology if: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.

Ontologies at the IMBBOntologies 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 Construction of an ontology covering mosquito-specific physiological

processes. - In progress.processes. - In progress. Construction of an ontology covering tick-specific phusiological Construction of an ontology covering tick-specific phusiological processes. processes.

- In progress, in collaboration with D. Sonenshine.- 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 Construction of an ontology covering mosquito-specific physiological

processes. - In progress.processes. - In progress. Construction of an ontology covering tick-specific phusiological Construction of an ontology covering tick-specific phusiological processes. processes.

- In progress, in collaboration with D. Sonenshine.- In progress, in collaboration with D. Sonenshine.

Vector-borne diseases:Building an ontology

Vector-borne diseases:Building an ontology

Use IDO as a "template”. Use IDO as a "template”.

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?

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.

Vector-borne diseases:Building MalIDO

Vector-borne diseases:Building MalIDO

Start with malaria and continue from Start with malaria and continue from

there.there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's Refine/edit MalIDO based on IDO's

progress.progress. Include information on vectors as well, in Include information on vectors as well, in

addition to pathogens and addition to pathogens and

diseases.diseases. Link MalIDO to existing ontologies.Link MalIDO to existing ontologies. Use MalIDO as a “template” for other Use MalIDO as a “template” for other

vector-borne diseases.vector-borne diseases.

Start with malaria and continue from Start with malaria and continue from

there.there. Use upper levels of IDO as much as possible. Refine/edit MalIDO based on IDO's Refine/edit MalIDO based on IDO's

progress.progress. Include information on vectors as well, in Include information on vectors as well, in

addition to pathogens and addition to pathogens and

diseases.diseases. Link MalIDO to existing ontologies.Link MalIDO to existing ontologies. Use MalIDO as a “template” for other Use MalIDO as a “template” for other

vector-borne diseases.vector-borne diseases.

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.

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)

Insect- and arthropod-transmitted diseases: a partial

list

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...

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...

Pantelis Topalis

John Vontas

Manolis Dialynas

???

IMBB-FORTH