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OBO-Edit tutorial
David Osumi-SutherlandFlyBase / 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/OBO
-Edit
• 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 humanFalse: All humans have breasts
True: All vertebrate motor neurons release neurotransmitter acetylcholineFalse: 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 neckFalse: 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
• - 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 - TreesThe 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
Click to expand or contract branch
Preferences
help
save a picture
Quick Filtering
Browsing - parentsThe parent editor provides a quick way to check all parental relationships – usually these are not all these are visible in a single tree view
Preferences
help
save a picture
Preferences
help
save a picture
Graph viewer setup
For an uncluttered view:
Browsing - graphsA good way to view and browse ancestral relationships, graphs of ancestors via transitive relations answer questionse.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
Add new leg
AND/OR
Remove legnesting (parentheses)
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
local mode-selection in other
components doesn’t affect selection here
global mode- 2 way auto
sync with other components
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
… 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:
OTE – right click menu:
… 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 EditorDelete 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 show parent terms
Hide child terms show child termshide 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
• 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– olfactory neuron– cholinergic neuron– antennal sensory neuron– DL1 innervating neuron
It is difficult to keep track of multipleclassification chains to: ensure completeness;avoid redundancy;avoid introducing error due to inheritanceof classification criteria from a distant ancestor
Multiple inheritance is very hard to manage by hand
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 non-
redundantly 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 cross-products
• 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?– 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
Redundant relationship
Use the Rule Base Reasoner*
*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’ (non-transitive)
– 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
OWL-DL: sensillum and 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.
** Note – reasoner required **
Find all sensilla that are part of some head:
Logical queries
How is sensillum classified?
What does adPN DL1 develop_from ?
Note – this query has no OWL equivalent
** Note – reasoner required **
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
Load / Save
First leg finds helper term
2nd leg finds terms that classify helper term
1. Open foreign ontology and run the rule based reasoner2. In the search tool, add the following two filter legs for each helper term
3. Save filter for future maintenance / use as a save filter
Saving helper terms
Saving helper terms
Check filter terms
Make sure “allow dangling parents” is NOT checked
Record version of foreign ontology here Avoid importing foreign ID rules
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:
• Current developers– Amina Abdulla– Chris Mungall– Jennifer Deegan
• Former developers– John Day-Richter– Nomi Harris
Acknowledgements – OBO-Edit developers
Acknowledgements - OEWG
• 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
• Michael Ashburner• FlyBase• Virtual Fly Brain• ICBO