IDOMAL: an update. IDOMAL statistics IDOMAL published (October 2010) 2390 unique terms (active) 2377...
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Transcript of 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 published (October 2010)
• 2390 unique terms (active)• 2377 definitions• 3146 total relations• 9 unique relations• 23 obsolete terms
IDOMAL statisticsIDOMAL 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 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)
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 statisticsIDOMAL 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 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
IDOMAL statisticsIDOMAL 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 OWLized & BFO2-ized (in progress)progress)
Imported/merged terms from other ontologies (e.g. OPL, OGMS)
IDOMAL statisticsIDOMAL statistics
IDOMAL published (10/01/07)
• 2390 unique terms (active)• 2377 definitions• 3146 total relations• 9 unique relations• 23 obsolete terms
How about, finally, How about, finally, integrating IDOMAL integrating IDOMAL into IDO?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 OWLized & BFO2-ized (in progress)progress)
Imported/merged terms from other ontologies (e.g. OPL, OGMS)
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