1 / 19

IDOMAL:

The latest IDOMAL statistics (June 2012) show a growth to 2,548 unique active terms, 2,513 definitions, and 3,289 total relations, maintaining 9 unique relations and 23 obsolete terms. New additions include important areas such as drug resistance, remedies, medicinal plants, and transmission processes. Ongoing development focuses on enhancing interoperability between different ontologies using OWL and OBO formats, addressing memory issues with the implementation of Perl scripts for conversion. This detailed update is crucial for advancing biomedical ontology management.

maxime
Télécharger la présentation

IDOMAL:

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related