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 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 3146 total relations 9 unique relations 23 obsolete terms 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) 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)

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)

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)

“Remedies” extension to IDOMAL Artemisia Chinchona

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)

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, classes) Decided to develop two scripts to deal with the issues faced 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, classes) Decided to develop two scripts to deal with the issues faced Freely available at

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 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

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)

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)

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

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”? 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”?

Malaria transmission vs pathogen transmission Malaria transmission vs pathogen transmission

IDOMAL 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, 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, biological process –multi-organism process –process of host –process of host population –process of pathogen –process of vector –process of vector population biological process –multi-organism process –process of host –process of host population –process of pathogen –process of vector –process of vector population

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”. 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”.

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) ? 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) ?

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) 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)

IDOMAL: THE END