IDOMAL: an update. IDOMAL statistics IDOMAL published (October 2010) 2390 unique terms (active) 2377...

IDOMAL:IDOMAL:an updatean update

IDOMAL statisticsIDOMAL 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“Remedies” extension to IDOMAL

ArtemisiaArtemisia

ChinchonaChinchona


IDOMAL published (10/01/07)


IDOMAL current (12/01/26)





OBO <-> OWL ConversionOBO <-> 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

• 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/

OBO2OWL & OWL2OBO scriptsOBO2OWL & 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







OWLized & BFO2-ized (in OWLized & BFO2-ized (in progress)progress)





How about, finally, How about, finally, integrating IDOMAL integrating IDOMAL into IDO?into IDO?




OWLized & BFO2-ized (in OWLized & BFO2-ized (in progress)progress)


Complexity of IDO vs. IDOMALComplexity of IDO vs. IDOMAL

I D O

host pathogen

IDOMALIDOMAL

host host

pathogenpathogen

vectorvector

““simplesimple”” infection vs. vector-borne disease infection vs. vector-borne disease

Malaria typesMalaria 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

IDOMALIDOMAL

• 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

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 unitsVB_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) ?

AcknowledgementsAcknowledgements

• 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:IDOMAL:THE ENDTHE END

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IDOMAL: an update. IDOMAL statistics IDOMAL published (October 2010) 2390 unique terms (active) 2377...

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