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IDOMAL:

IDOMAL:. an update. IDOMAL statistics. IDOMAL published (October 2010) 2390 unique terms (active) 2377 definitions 3146 total relations 9 unique relations 23 obsolete terms. IDOMAL statistics. IDOMAL published (October 2010) 2390 unique terms (active) 2377 definitions

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IDOMAL:

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  1. IDOMAL: an update

  2. IDOMAL statistics IDOMAL published (October 2010) • 2390 unique terms (active) • 2377 definitions • 3146 total relations • 9 unique relations • 23 obsolete terms

  3. IDOMAL statistics IDOMAL published (October 2010) • 2390 unique terms (active) • 2377 definitions • 3146 total relations • 9 unique relations • 23 obsolete terms IDOMAL current (June 2012) • 2548 unique terms (active) • 2513 definitions • 3289 total relations • 9 unique relations • 23 obsolete terms NEW: Drug resistance; remedies and medicinal plants; transmission. OWLized & BFO2-ized (in progress) Imported/merged terms from other ontologies (e.g. OPL, OGMS)

  4. IDOMAL statistics IDOMAL published (October 2010) • 2390 unique terms (active) • 2377 definitions • 3146 total relations • 9 unique relations • 23 obsolete terms IDOMAL current (June 2012) • 2548 unique terms (active) • 2513 definitions • 3289 total relations • 9 unique relations • 23 obsolete terms NEW: Drug resistance; remedies and medicinal plants; transmission. OWLized & BFO2-ized (in progress) Imported/merged terms from other ontologies (e.g. OPL, OGMS)

  5. IDOMAL statistics IDOMAL published (October 2010) • 2390 unique terms (active) • 2377 definitions • 3146 total relations • 9 unique relations • 23 obsolete terms IDOMAL current (June 2012) • 2548 unique terms (active) • 2513 definitions • 3289 total relations • 9 unique relations • 23 obsolete terms NEW: Drug resistance; remedies and medicinal plants; transmission. OWLized & BFO2-ized (in progress) Imported/merged terms from other ontologies (e.g. OPL, OGMS)

  6. “Remedies” extension to IDOMAL Chinchona Artemisia

  7. IDOMAL statistics IDOMAL published (10/01/07) • 2390 unique terms (active) • 2377 definitions • 3146 total relations • 9 unique relations • 23 obsolete terms IDOMAL current (12/01/26) • 2548 unique terms (active) • 2513 definitions • 3289 total relations • 9 unique relations • 23 obsolete terms NEW: Drug resistance; remedies and medicinal plants; transmission. OWLized & BFO2-ized (in progress) Imported/merged terms from other ontologies (e.g. OPL, OGMS)

  8. OBO <-> OWL Conversion • Exchanging information between different ontological sources is a necessity: • Biomedical ontologies usually written either in OBO or OWL and, often, conversion between these two formats is required • Existing tools show deficiencies: • When converting “arbitrary” OWL files to OBO • Definitions are omitted by existing converters in such files • When the ontologies are relatively large • Converters are memory-intensive • e.g. with Gazetteer (GAZ - 134MB, 518.195 classes) • Decided to develop two scripts to deal with the issues faced Freely available at http://code.google.com/p/obowl/

  9. OBO2OWL & OWL2OBO scripts • Both scripts written in Perl • OWL2OBO • Identifies and successfully converts statements included in “arbitrary” OWL files. • Common mappings are also considered and identified • Tags from IAO ontology and OboInOwl mapping • OBO2OWL • Identifies and successfully converts OBO tags to OWL statements • The user may choose either to generate statements that rely on IAO & oboInOwl mappings or not • They both scale for large ontologies • By using the Perl::Tie function, which does not load file contents into main memory • Less memory-intensive than the existing tools • Tested with a variety of ontologies with positive results

  10. IDOMAL statistics IDOMAL published (10/01/07) • 2390 unique terms (active) • 2377 definitions • 3146 total relations • 9 unique relations • 23 obsolete terms IDOMAL current (12/01/26) • 2548 unique terms (active) • 2513 definitions • 3289 total relations • 9 unique relations • 23 obsolete terms NEW: Drug resistance; remedies and medicinal plants; transmission. OWLized & BFO2-ized (in progress) Imported/merged terms from other ontologies (e.g. OPL, OGMS)

  11. IDOMAL statistics IDOMAL published (10/01/07) • 2390 unique terms (active) • 2377 definitions • 3146 total relations • 9 unique relations • 23 obsolete terms How about, finally, integrating IDOMAL into IDO? IDOMAL current (12/01/26) • 2548 unique terms (active) • 2513 definitions • 3289 total relations • 9 unique relations • 23 obsolete terms NEW: Drug resistance; remedies and medicinal plants; transmission. OWLized & BFO2-ized (in progress) Imported/merged terms from other ontologies (e.g. OPL, OGMS)

  12. Complexity of IDO vs. IDOMAL “simple” infection vs. vector-borne disease I D O host pathogen IDOMAL host pathogen vector

  13. Malaria types • Four pathogens, different manifestations, different epidemiology, different short and long term prognosis, similar (if not same) therapy. In addition, P.f. malaria can take diverse roads: “uncomplicated”, severe, cerebral (Not stages, neither chronic vs acute). • Are these different diseases? (four ontologies that overlap by >99%). • Primary aim of the ontology: satisfy “users” or be “correct”?

  14. Malaria transmission vs pathogen transmission

  15. IDOMAL • biological process • multi-organism process • process of host • process of host population • process of pathogen • process of vector • process of vector population • quality • quality of host • quality of host population • quality of vector • quality of vector population • quality of parasite • quality of the environment, e.g. temp, hum, wind,

  16. Resistance versus Refractoriness • In IDO “protective resistance”is “disposition”while “susceptibility”is “quality”. • “Insecticide resistance” and “drug resistance” are “phenotypes”. Most OBO ontologies handle phenotypes as “quality”. In IDOMAL “Insecticide resistance” is “quality of vector” while “drug resistance” is quality of pathogen. • “Refractoriness”is “disposition”.

  17. VB_cv and units • Publication descriptor can be moved over IDO’s “data items”? • Units could be treated the same way or, perhaps, • Would have to be passed into UO (Units of measurements ontology) ?

  18. Acknowledgements • The people who did the work: • Emmanuel Dialynas, Vicky Dritsou, Elvira Mitraka, Pantelis Topalis • The projects that provided us with the dough: • VectorBase (NIAID), Synergasia (GSRT), EVIMalR and Transmalariabloc (EU-DG XII)

  19. IDOMAL: THE END

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