OBO-Edit tutorial
David Osumi-Sutherland
FlyBase / Virtual Fly Brain / OBO-Edit
Working Group (OEWG)
Resources
• Slides and test tutorial can be downloaded
from the bottom of the Tutorial wiki page:
– http://www.bioontology.org/wiki/index.php/OBOEdit
• The latest version of OE2 (beta release), is
here:
– http://oboedit.org/2.1betarelease/
Your backgrounds
• Who here has never used an ontology editing
tool?
• Who here is an OBO-Edit user?
– If you are, have you used Cross-Products?
• Who here is a Protégé user?
• Protégé 3
• Protégé 4
– With reasoner?
• For those of you who speak OWL(ish), I'll try to provide translations to
OWL Manchester syntax.
OBO 101
•
An ontology contains terms (e.g. hand) and
relationships (e.g. hand has_part finger)
•
Terms refer to types (classes).
•
Types are classifications of things
(instances) in the real world, based on
some set of criteria.
– My left hand is an instance of the type hand
•
The criteria for membership of a class
(type) is recorded using textual definitions,
relationships, or some combinations of the
two
– name: hand
– def: “An anatomical structure that has four
fingers and a thumb and is attached to the
end of an arm.” [reference: DOS]
– relationship: hand has_part finger
– relationship: hand has_part thumb
– relationship: part_of arm
Image from Gray’s Anatomy (copyright
expired)
OBO basics- instance/type distinction
• If OBO terms refer to types, why worry about
instances?
– instances are central to defining OBO type-level
relations
• OBO <-> OWL:
– OWL class = OBO type
– OWL individual = OBO instance
OBO relations
• Instance level relations (by convention written in bold)
– 'my left little finger' part_of 'my left hand'
• Note – quantifiers – all, some – are not needed.
• Type level relations (by convention, written in italic).
– Type level relations are defined using instance level relations + quantifiers.
• In OBO, the quantifiers (all, some) are buried in the definition of the
type-level relation.
– e.g.- X part_of Y is defined as:
» for all x,t if Xxt then there is some xy such that Yyt and x
part_of y at t
• OBO <-> OWL:
– OBO instance level relation = OWL property
– In OWL, quantifiers are used explicitly in ontology construction when relating
classes
• OBO: finger part_of hand can be written in OWL using the OBO instance
level relation with added quantifiers: all finger part_of some hand *
– OBO is_a = OWL SubClassOf
*Ignoring the time component of the OBO definitions, as this cannot be expressed in OWL
Quantifiers
• It is critical to be aware of the direction of quantifiers when using OBO
relations:
True: All breasts are part of some human
False: All humans have breasts
True: All vertebrate motor neurons release neurotransmitter acetylcholine
False: All neurons that release acetylcholine are vertebrate motor neurons.
Be especially careful in cases where the instance level relation is symmetric:
True: All lion’s mane connected_to some lion’s neck
False: All lion’s neck connected_to some lion’s mane
Relationships and definitions
• You should think of the relationships a term
has as a formalised part of their definition.
• A regular relationship in OBO (SubClassOf in
OWL) specifies necessary conditions for
membership of a class.
– e.g. finger part_of hand (all finger part_of some
hand) states that a necessary condition of being in
the class finger is to be part of some hand.
Transitivity
• If a relation is transitive:
– A rel B rel C rel D therefore A rel D
• U1 neuron is_a U neuron is_a motor neuron
– therefore U1 neuron is_a motor neuron
• ellipsoid body part_of central complex part_of adult
brain
– therefore ellipsoid body part_of adult brain
Transitivity and redundancy
• ellipsoid body part_of central complex part_of
adult brain
– therefore ellipsoid body part_of adult brain
• therefore asserting the relationship "ellipsoid body
part_of adult brain" in your ontology would be
redundant.
Some simple reasoning
• U neuron part_of larval antennal segment
– (All U neuron part_of some larval antennal segment)
• U1 neuron is_a U neuron
• therefore U1 neuron part_of larval antennal
segment
– (All U neuron part_of some larval antennal segment;
U1 neuron SubClassOf U neuron therefore…)
• So, adding 'U1 neuron' part_of 'larval antennal
segment’ would be redundant.
Demo – OBO basics
Basic OBO-Edit2 editing setup
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- 2 x Ontology Tree Editor (OTE)
- One parent editor
- One text editor
- One search panel
- One reasoner manager
- One graph viewer (Note - currently only
works with Link Pile Reasoner on)
Browsing
Browsing - Trees
The ontology tree editor is a good way to browse down the
ontology graph, but not all parents visible in one view
Click to
expand or
contract
branch
help
Preferences
save a picture
Quick Filtering
Browsing - parents
The parent editor provides a quick way to check all parental
relationships – usually these are not all these are visible in a single
tree view
help
Preferences
save a picture
help
Preferences
save a picture
Graph viewer setup
For an uncluttered view:
Browsing - graphs
A good way to view and browse ancestral relationships, graphs of ancestors via
transitive relations answer questions
e.g.- what is X? What is X part of? What does X develop from?
Note – currently requires link pile reasoner to be turned on.
Browsing – The Text Editor
Basic Searching - single leg
Basic searching – multi-leg
AND/OR
Add new leg
nesting (parentheses)
Remove leg
All searches can also be filters or
renders
Rendering options
Editing
Drag and drop editing in the ontology
tree editor (OTE)
• Left clicking a term choose it
• Right clicking displays a menu of editing
options
• Dragging and dropping single or multiple
terms allows terms to be copied, moved or
merged.
Global vs local selection modes
local mode
-selection in other
components doesn’t
affect selection here
global mode
- 2 way auto
sync with other
components
Drag and drop term move
Drag and drop term move
Drag and drop term move
Drag and drop term
merge
Making new terms
• First, make sure your ID generator is set up
correctly:
Edit profile
ID prefix
ID length
start from
end at
Create new child
Committing
Check this box to commit text edits automatically.
Note, committing will not change your ontology file
Deletion, obsoletion, destruction
OTE – right click menu:
… deletes the relationship between the selected term and its immediate
parent in the ontology tree editor. When the selected term has only one
parent, this option switches to:
… changes the status of term to obsolete. The OBO file retains
the ID for future reference and to prevent re-use. To indicate
replacement terms, drag suitable terms to the obsoleted term
=>
Within the context of a single editing session, or a pre-release file, you may
wish instead to destroy the term completely (BUT BE CAREFUL!)
Parent Editor
Delete parent relationship
Does what it says. But be careful it adds is_a
parents by default. For other relations, switch
after adding
Graph Editor
Graph Editor
Hide parent terms
Hide child terms
show parent terms
show child terms
hide term
• Right click provides editing options and
hide-all
• Choosing quick filtering => manageable
view
Making new relationships in the graph
editor – demo only
Time savers
• Cloning
– Right click clone option makes clone of chosen
term – identical in every way except for ID and
‘CLONE OF’ appended to term name
• Create multiple children
– Right click ‘create multiple children’ option. Does
what is says on the box. Pops up interface were a
bunch of new terms can be named at once.
Managing multiple inheritance
Disjunction
• X disjoint_from Y
– Nothing that is an instance of X is also an instance of Y.
• e.g. anatomical structure disjoint_from biological process
– Nothing exists that is an instance of both of these types.
– Extremely useful for error checking
– also speeds up some reasoners
• OBO <-> OWL
– 0BO disjoint_from ≅ OWL DisjointWith
Using the reasoner to check for
disjoint violations - demo
• In the test ontology, make one of the children of
biological process an is_a child of sensillum.
• Now run the link pile reasoner
• Undo
• Making disjoints - demo
– by hand
– automatically making all children disjoint (use
sparingly!)
Ways to classify neurons
• sensory
– Sensory modality
– Sense organ
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•
motor
interneuron
– local
– relay
• neurotransmitter
– serotonergic,
– dopaminergic…
• Location
– cell body
– fasciculation pattern (e.g.- labial nerve)
– innervation pattern (antennal lobe glomerulus DL1)
all siblings in the same color are (probably) disjoint_from each other.
Multiple inheritance needed
• Name: ORN ab1a
• Def: A cholinergic olfactory neuron whose
dendrite innervates an ab1 basiconic sensillum on
the 3rd segment of the antenna. Like other
antennal olfactory neurons, it sends an axon
through the antennal nerve that innervates a
single antennal lobe glomerulus DL1
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olfactory neuron
cholinergic neuron
antennal sensory neuron
DL1 innervating neuron
Multiple inheritance is very hard to manage by
hand
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
Cross Products
• In OBO, cross products, also known as
intersections, provide a way to record
necessary and sufficient definitions.
• necessary and sufficient definitions allow
classification to be automated using reasoners
• OBO <-> OWL
– intersection_of ≅ EquivalentTO
Genus and Differentia
• Anatomy of a cross product:
– name: antennal sensillum
– genus: sensillum
– differentium: (part_of antenna)
• In OBO format
– intersection_of: sensillum
– intersection_of: part_of antenna
• In OWL:
– EquivalentTO: sensillum and part_of some antenna
OBO-Edit reasoners
• OBO-Edit2 currently has 3 reasoners
• In the near future, 2 of these will be retired,
leaving just the ‘rule based reasoner’ (RBR)
• Currently the link pile reasoner is needed for
flagging disjointness violations and for running
the graph viewer. For everything else you
should use the RBR
Cross Product Demo
• Choose the term 'antennal sensillum'
– Check out the text editor cross product tab
• Turn the reasoner off.
– You should see antennal sensillum at the root
• Run the rule-based-reasoner
– check out how the term is integrated nonredundantly into the classification hierarchy.
– view the parent editor
Cross Product Demo
• Using terms from other ontologies
– cholinergic neuron
– olfactory sensillum
Making new cross product terms
• Add a new root class:
Cross Product demo
• Making new cross products
– glutamatergic neuron
– taste sensillum
– chemosensory sensillum
• Re-run the rule-based-reasoner
• Check the sensillum hierarchy
– Explain how olfactory sensillum got its parent
Useful renders for working with crossproducts
• Cross-Product detector:
• Multiple asserted inheritance detector:
• Unclassified term detector:
• Incompletely classified term detector:
Combining Cross-Products with
relationships => hidden assertions
• How can we record the generalization – All neurons with the
function ‘smell’ are cholinergic?
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–
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name: olfactory receptor neuron
intersection_of: neuron
intersection_of: has_function smell
relationship: releases_neurotransmitter acetylcholine
(OWL: EquivalentTo( neuron AND has_function some smell ), SubClassOf(
releases_neurotransmitter some acetylcholine )
• Why is this potentially dangerous?
–
Future editors using ‘has_function smell’ to record the function of a neuron class
may not be aware that they are adding the assertion that the class is cholinergic
• Safeguards:
– if neurons classifed by neurotransmitter are disjoint, the reasoner can flag
contradictions.
– Keep a record of all examples (perhaps as a standardised comment)
– State this assertion in the term definition with a link to a supporting reference.
Hidden assertion demo
Detecting redundancy with the
reasoner
Use the Rule Base Reasoner*
Redundant relationship
*Link pile reasoner over-flags redundancy when cross-product terms are present
If the reasoner is flagging relationships
you don’t think are redundant
• Are you sure your intended meaning for a
relationship is transitive?
– e.g.- develops_from (transitive) is sometimes used
as if it means ‘directly develops from’ (nontransitive)
– In that case – request a new relation.
– If you are interested in how to link relations such as develops_from and
develops_directly_from so that they can be used for reasoning, please ask me
or Chris after the tutorial
Advanced Searching
• OE2 can combine string searching and logical
querying.
• Logical querying requires the reasoner to be
turned on.
Logical queries
** Note – reasoner required **
Find all sensilla that are part of some head:
The first leg of the search finds all subtypes of sensillum. The second leg finds all parts of
the head. The ‘matches all’ radio button ensures the two legs are combined by a
boolean AND.
OWL-DL: sensillum and part_of some head
Logical queries
** Note – reasoner required **
How is sensillum classified?
What does adPN DL1 develop_from ?
Note – this query has no OWL equivalent
Importing foreign ‘helper’ terms
• Formalising definitions is likely to require
terms from other ontologies.
• If you want to reason using the classification
from another ontology, you need to import
the full classification of each term.
• In order to keep up-to-date, you need a
mechanism to re-import the foreign terms you
use.
Creating and maintaining a helper
term filter
1.
2.
Open foreign ontology and run the rule based reasoner
In the search tool, add the following two filter legs for each helper term
First leg finds helper term
2nd leg finds terms that classify
helper term
3
Load / Save
Saving helper terms
Saving helper terms
Check filter terms
Avoid importing foreign ID rules
Make sure “allow
dangling parents” is
NOT checked
Record version of foreign ontology here
Saving helper terms
Load helper term filter
Refreshing helper terms
• The examples I’ve shown here use term
names.
• This make the filter easy to read and edit, but
names often change.
• Therefore more sustainable to use IDs instead.
Instantiating inferred is_a for release
• If your users are not using your ontology with
a reasoner, you made need to pre-reason for
them.
• To do this, you can use the ‘save implied links’
function in the save interface:
Acknowledgements – OBO-Edit
developers
• Current developers
– Amina Abdulla
– Chris Mungall
– Jennifer Deegan
• Former developers
– John Day-Richter
– Nomi Harris
Acknowledgements - OEWG
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Amina Abdulla, Chris Mungall, Karen Eilbeck, Suzanna Lewis, - BBOP, LBNL, Berkeley, CA, USA
Midori A. Harris, Jennifer Deegan, Amelia Ireland, Jane Lomax - GO-EBI, Hinxton, UK
David Hill, Alexander D. Diehl, Harold Drabkin - MGI, The Jackson Laboratory, Bar Harbor, ME, USA
Karen R. Christie - SGD, Department of Genetics, Stanford University, Stanford, CA, USA
Tanya Berardini - TAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, USA
Petra Fey - DictyBase, Northwestern University, Chicago, IL, USA
Carol A. Bastiani, Ranjana Kishore - WormBase, California Institute of Technology, Pasadena, CA, USA
Victoria Petri - RGD, Medical College of Wisconsin, Milwaukee, WI, USA
Colin Batchelor- Royal Society of Chemistry, Cambridge UK
Shuly Avraham - Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Pankaj Jaiswal - Gramene, Department of Plant Breeding, Cornell University, Ithaca, NY, USA
Melissa Haendel - ZFIN, University of Oregon, Eugene, OR, USA
John Osborne - Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL, USA
Acknowledgments
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Michael Ashburner
FlyBase
Virtual Fly Brain
ICBO