Download - From OBO to OWL and back again – a tutorial
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From OBO to OWL and back again – a tutorialDavid Osumi-Sutherland, Virtual Fly Brain/FlyBaseChris Mungall – GO/LBL
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+I use OBO, why should I care about OWL? OWL 2 is a W3C standard with a large and growing ecosystem of
developers. Using OWL ontologies in Protégé 4 you can use fast reasoners
to: Query your ontology
This could be the basis for sophisticated queries on your website
Quickly find mistakes Automate classification
Non-lossy round tripping from OBO to OWL and back is now easy continue developing in OBO while taking advantage of OWL and
Protégé for reasoning This may be a first step to developing in OWL/Protégé
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+Take home messages An ontology is a classification There are lots of useful ways to classify stuff Maintaining multiple classification schemes by
hand is hard So automate what you can
Everybody makes mistakes So get the computer to find errors for you
Re-use other people’s work where possible import class hierarchies and relations use common patterns
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+What is an ontology ?
A set of defined, inter-related terms to use in annotation/metadata/knowledge bases.
A classification
A query-able store of (scientific) knowledge that uses logical inference.
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+What is an ontology ?
A set of defined, inter-related terms to use in annotation/metadata/knowledge bases.
A classification
A query-able store of (scientific) knowledge that uses logical inference.
depends on
depends on
depends on
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+What (use) is an ontology?
A set of defined, inter-related terms to use in annotation.
Relations between terms allow annotations to be grouped in scientifically meaningful ways
requires an ontology to be an accurate and scientifically meaningful classification and store of scientific knowledge.
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+What is an ontology ? A classification
appendage
antenna fore
wing
wing
hindwing
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+OBO-OWL cheat sheet: classification OBO format :
name: antenna is_a: appendage
OWL Manchester Syntax antenna SubClassOf appendage
insect leg S appendage
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+What is an ontology ?
A classification There are lots of scientifically useful ways to
classify a bit of anatomy. its parts and their arrangement its relation to other structures
what is it: part of; connected to; adjacent to, overlapping? its shape its function its developmental origins its species or clade its evolutionary history?
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• It is difficult to keep track of multiple classification chains to: • ensure completeness;• avoid redundancy;• avoid introducing error
due to inheritance of classification criteria from a distant ancestor
Manually maintaining an ontology with multiple
classification schemes is hard
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+OBO-OWL cheat sheet: classification OWL Manchester Syntax
antenna SubClassOf appendage
OBO format : name: antenna is_a: appendage
Protégé
OBO-Edit:
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+class – class relationships are quantified Class:Class relationships are many to many
Does the relation apply to all or just some of the class ? we specify this with quantifiers:
∀: for all, all, only, every ∃: there exists, some
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+Relations – OBO vs OWL
OBO: relation
OWL: object property
part_of
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+relationships specify necessary conditions for class membership Being part of an insect
thorax is a necessary condition of being in the class ‘insect leg’ OBO (quantifiers hidden)
name: insect leg relationship: part_of
thorax OWL (MS):
‘insect leg’ SubClassOf part_of some thorax
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+Relationship record necessary conditions for class membership
part_of ∃insect leg S insect
thorax
insect leg
part_of some ‘insect thorax’
insect
wing
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+Relationships store knowledge in query-able form DL query: part_of some ‘insect thorax’insect leg
insect wing
insect hindwing
insect forewing
insect leg
part_of some ‘insect thorax’
forewing
wing
hindwing
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+OBO-OWL cheat sheet: necessary conditions for class membership
OWL Manchester Syntax antenna SubClassOf
part_of some head
OBO format : name: antenna relationship: part_of
head
Protégé
OBO-Edit:
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+Directionality and quantifiers
True: all ‘insect wing’ part_of some ‘insect thorax’
False: all ‘insect thorax’ has_part some ‘insect wing’
True: all ‘claw’ connected_to some ‘tarsal segment’
False: all ‘tarsal segment’ connected_to some claw
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• It is difficult to keep track of multiple classification chains to: • ensure completeness;• avoid redundancy;• avoid introducing error
due to inheritance of classification criteria from a distant ancestor
Manually maintaining an ontology with multiple
classification schemes is hard
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sense organcapable_of some detection of smell
olfactory sense organ
English: Any sense organ that functions in the detection of smell is an olfactory sense organ
OWL Manchester Syntax antennal sense organ EquivalentTo ‘sense organ’ that part_of some antenna
OBO format : name: antennal sense organ intersection_of: sense organ intersection_of: part_of antenna
The knowledge an ontology contains can be used to automate classification
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sense organcapable_of some detection of smell
olfactory sense organ
nose
sense organ
nose
capable_of some detection of smell
olfactory sense organ
nose
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+OBO-OWL cheat sheet:necessary and sufficient conditions for class membership OWL Manchester Syntax
antennal sense organ EquivalentTo ‘sense organ’ that part_of some antenna
(that / and are interchangable in MS)
OBO format : name: antennal sense organ intersection_of: sense organ intersection_of: part_of
antenna
Protégé
OBO-Edit:
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ERROR MESSAGES ARE YOUR FRIENDS! – They tell you you’ve screwed up before you get embarrassing emails complaining that you’ve screwed up
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+Some classes don’t overlap
X
✗
Y
X Y
OWL DisjointWith OBO: disjoint_from
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+Some classes don’t overlap
musclelumen
of gut
anatomical space
anatomical structure
lumen of gut
muscle
✗
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+Some relations only apply between particular classes.
anatomical structure
biological processcapable_of DR
capable_of ∃ YX S
X Yanatomical
structure biological process
R Drange domain
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biological process
anatomical
structurecapable_of DR
capable_of ∃Sdetectio
n of smell
‘nose
detection of
smell‘
anatomical structure detectio
n of smell
‘
biological process
✗nosenose
✗
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+Some relations entail others
part_of some ‘insect thorax’
insect
wing
overlaps some ‘insect thorax’
insect
wing
part_of
overlaps
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+Some relations chains entail relations
regulates some X
Y
regulates
regulates
part_of
part_of some Z
Y
regulates some X
Z
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regulates ∃Sregulation of mitosis
‘mitosis
part_of∃S
mitotic cell
cycle
regulates regulatespart_of
regulates ∃Sregulation of mitosis
‘mitosis