Infectious Disease Ontology


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  • Infectious Disease Ontology

    1. 1. Infectious Disease Ontology (IDO) Lindsay Cowell and Barry Smith NCBO Council Call, October 9, 2007
    2. 2. IDO Training / Ontology-Building Workshop Cold Spring Harbor Laboratory September 19 – 20, 2007 Supported by the Burroughs Wellcome Fund
    3. 3. We have data, e.g.: <ul><li>TBDB: Tuberculosis Database, including Microarray data </li></ul><ul><li>VFDB: Virulence Factor DB </li></ul><ul><li>TropNetEurop Dengue Case Data </li></ul><ul><li>ISD: Influenza Sequence Database at LANL </li></ul><ul><li>MPD/MRD/CPP: Protein Data of PIR Resource Center for Biodefense Proteomics Research </li></ul><ul><li>PathPort: Pathogen Portal Project </li></ul>
    4. 4. Purpose of Infectious Disease Ontology (IDO) <ul><li>Retrieval and integration of infectious disease relevant data </li></ul><ul><ul><li>Sequence and protein data for pathogens </li></ul></ul><ul><ul><li>Case report data for patients </li></ul></ul><ul><ul><li>Clinical trial data for drugs, vaccines </li></ul></ul><ul><ul><li>Epidemiological Data for surveillance, prevention </li></ul></ul><ul><ul><li>... </li></ul></ul><ul><li>Goal: to make data deriving from different sources comparable and computable </li></ul>
    5. 5. We need common controlled vocabularies to describe ID data <ul><li>What content is needed to adequately cover the infectious domain? </li></ul><ul><ul><li>Host-related terms (e.g. carrier, susceptibility) </li></ul></ul><ul><ul><li>Pathogen-related terms (e.g. virulence) </li></ul></ul><ul><ul><li>Terms for the biology of disease pathogenesis (e.g. evasion of host defense) </li></ul></ul><ul><ul><li>Population-level terms (e.g. epidemic, endemic) </li></ul></ul><ul><li>Not yet addressed: </li></ul><ul><ul><li>Treatment </li></ul></ul><ul><ul><li>Prevention ... </li></ul></ul>
    6. 6. The GO Biological Process Strategy <ul><li>Collect terms for all (canonical) biological processes in all organisms </li></ul><ul><li>Will this strategy work when we need to collect terms for disease-specific processes involving pluralities of organisms at different scales? </li></ul>
    7. 7. The CARO Strategy <ul><li>Model organism researchers seek results valuable for the understanding of human disease. </li></ul><ul><li>This requires the ability to make reliable cross-species comparisons, </li></ul><ul><li>For this anatomy is crucial. </li></ul><ul><li>But different MOD communities have developed their anatomy ontologies in uncoordinated fashion. </li></ul>
    8. 8. Different anatomy ontologies have different axes of classification Structural: tissue, organ, cell Functional: cardiovascular system, nervous system Spatial: head, trunk, limb Stage: developmental staging series + various mixtures of these
    9. 9. CARO – Common Anatomy Reference Ontology <ul><li>for the first time provides guidelines for model organism researchers who wish to achieve comparability of annotations </li></ul><ul><li>for the first time provides guidelines for those new to ontology work </li></ul><ul><li>See Haendel et al., “CARO: The Common Anatomy Reference Ontology”, in: Burger (ed.), Anatomy Ontologies for Bioinformatics: Springer, in press. </li></ul>
    10. 10. CARO-conformant ontologies already in development: <ul><ul><li>Fish Multi-Species Anatomy Ontology (NSF funding) </li></ul></ul><ul><ul><li>Ixodidae and Argasidae (Tick) Anatomy Ontology </li></ul></ul><ul><ul><li>Mosquito Anatomy Ontology (MAO) </li></ul></ul><ul><ul><li>Spider Anatomy Ontology </li></ul></ul><ul><ul><li>Xenopus Anatomy Ontology (XAO) </li></ul></ul><ul><ul><li>undergoing reform : Drosophila and Zebrafish Anatomy Ontologies </li></ul></ul>
    11. 11. IDO Strategy <ul><li>Reference ontology (template) with terms relevant to any infectious disease </li></ul><ul><li>Built on OBO Foundry principles and incorporating cross-products from other Foundry ontologies </li></ul><ul><li>Disease- and organism-specific ontologies built as refinements on the CARO model </li></ul><ul><ul><li>types of host, types of vector, types of pathogen, types of disease </li></ul></ul>
    12. 12. Plasmodium species causing Malaria: <ul><li>Plasmodium falciparum </li></ul><ul><li>Plasmodium vivax </li></ul><ul><li>Plasmodium ovale </li></ul><ul><li>Plasmodium malariae </li></ul>
    13. 13. Malaria Vectors <ul><li>of 422 species of Anopheles worldwide, about 40 are significant vectors for malaria in humans </li></ul><ul><li>IDO Malaria ontology will contain those terms which apply to all types of malarial plasmodium infection </li></ul>
    14. 14. Life cycle of Plasmodium in humans and mosquitoes Host Place Stage both skin of person biting person liver pre-erythrocytic schizogonous cycle (asexual) person blood stream erythrocyte schizogonous cycle (asexual) person blood stream gametocyte formation both skin biting mosquito gut gamete formation mosquito gut fertilisation mosquito gut ookinete formation mosquito exterior of midgut Sporogony both skin of person biting
    15. 15. IDO will take its structure from here RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy / placeholder) Anatomical Entity (FMA, CARO) Organ Function (placeholder) Phenotypic Quality (PATO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Process (GO)
    16. 16. Independent Continuants in IDO (and its disease-specific extensions) <ul><li>Anatomical locations that are sites of infection will be imported from the FMA: e.g. lung, kidney </li></ul><ul><li>Proteins that serve as virulence factors (e.g. Eap in S.a.) and those that participation in an immune response (e.g. complement proteins, immunoglobulin) will be imported from PRO </li></ul><ul><li>Cells that participate in an immune response (e.g. those of hematopoetic lineage) and those which are utilized or damaged by the pathogen (e.g. epithelial cells) will be imported from the CL. </li></ul><ul><li>Species that are pathogenic in a given host such as humans will be imported from the NCBI taxonomy of organisms (e.g. Mycobacterium tuberculosis, HIV) </li></ul>
    17. 17. Occurrents in IDO (Processes) <ul><li>Imported from GO BP when possible </li></ul><ul><li>Processes not in GO that belong in GO will be submitted as term requests </li></ul><ul><li>Processes at the population level will be entered directly into IDO (e.g. emergence, epidemiological spread of disease) </li></ul>
    18. 18. Processes
    19. 19. Dependent Continuants in IDO <ul><li>Qualities (for submission to PATO) </li></ul><ul><li>Roles (something is a pathogen only relative to some host) </li></ul>
    20. 20. Qualities
    21. 21. Roles
    22. 22. Examples of Definitions Symbiont : a role whose bearer has a relationship with another bearer in which both bearers are biotics belonging to different species and the fitness of at least one bearer is highly dependent on the other Commensal : a role whose bearer has role symbiont and whose fitness increases as a result of this role Factor : a role played by a portion of physical substance in a biological process Adhesion factor (adhesin) : a role whose bearer has role factor and whose bearer is utilized by a biotic to establish adherence to a surface in a host
    23. 23. Future Work <ul><li>Vaccines </li></ul><ul><li>Plant pathogens </li></ul><ul><li>Parasites </li></ul><ul><li>Relations to Disease Ontology </li></ul>
    24. 24. Gemina (Lynn Schriml)
    25. 25. Gemina Ontologies <ul><li>= OBO Disease Ontology </li></ul>
    26. 26. Getting Involved <ul><li>Wiki </li></ul><ul><ul><li> Infectious_Disease_Ontology </li></ul></ul><ul><li>Email list </li></ul><ul><ul><li>[email_address] </li></ul></ul><ul><ul><li> </li></ul></ul><ul><li>Infectious Disease Ontology Consortium </li></ul>
    27. 27. Disease-specific IDO test projects <ul><li>IMBB/VectorBase – Vector borne diseases ( A. gambiae, A. aegypti, I. scapularis, C. pipiens, P. humanus ) </li></ul><ul><ul><li>Christos Louis </li></ul></ul><ul><li>Colorado State University – Dengue Fever </li></ul><ul><ul><li>Saul Lozano-Fuentes </li></ul></ul><ul><li>Duke – Tuberculosis </li></ul><ul><ul><li>Carol Dukes-Hamilton </li></ul></ul><ul><li>Cleveland Clinic – Infective Endocarditis </li></ul><ul><ul><li>Sivaram Arabandi </li></ul></ul><ul><li>MITRE, Mount Sinai – Influenza </li></ul><ul><ul><li>Joanne Luciano, Stuart Sealfon </li></ul></ul><ul><li>University of Michigan – Brucilosis </li></ul><ul><ul><li>Yongqun He </li></ul></ul>