Transcript idomal - Buffalo Ontology Site

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)
IDOMAL current (June 2012)
•
•
•
•
•
•2548 unique terms (active)
•2513 definitions
•3289 total relations
•9 unique relations
•23 obsolete terms
2390 unique terms (active)
2377 definitions
3146 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)
IDOMAL current (June 2012)
•
•
•
•
•
•2548 unique terms (active)
•2513 definitions
•3289 total relations
•9 unique relations
•23 obsolete terms
2390 unique terms (active)
2377 definitions
3146 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)
IDOMAL current (June 2012)
•
•
•
•
•
•2548 unique terms (active)
•2513 definitions
•3289 total relations
•9 unique relations
•23 obsolete terms
2390 unique terms (active)
2377 definitions
3146 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)
Chinchona
Artemisia
“Remedies” extension to IDOMAL
IDOMAL
statistics
IDOMAL published (10/01/07)
IDOMAL current (12/01/26)
•
•
•
•
•
•2548 unique terms (active)
•2513 definitions
•3289 total relations
•9 unique relations
•23 obsolete terms
2390 unique terms (active)
2377 definitions
3146 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, 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 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
IDOMAL
statistics
IDOMAL published (10/01/07)
IDOMAL current (12/01/26)
•
•
•
•
•
•2548 unique terms (active)
•2513 definitions
•3289 total relations
•9 unique relations
•23 obsolete terms
2390 unique terms (active)
2377 definitions
3146 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)
IDOMAL current (12/01/26)
•
•
•
•
•
•2548 unique terms (active)
•2513 definitions
•3289 total relations
•9 unique relations
•23 obsolete terms
2390 unique terms (active)
2377 definitions
3146 total relations
9 unique relations
23 obsolete terms
NEW: Drug resistance; remedies
and medicinal plants; transmission.
How about, finally,
integrating IDOMAL into
IDO?
OWLized & BFO2-ized (in
progress)
Imported/merged terms from other
ontologies (e.g. OPL, OGMS)
Complexity of IDO vs. IDOMAL
“simple” infection vs. vector-borne disease
IDO
host
pathogen
IDOMAL
host
pathogen
vector
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”?
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,
• 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”.
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) ?
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)
IDOMAL:
THE END