Hiding ontologies under the carpet
Frederic Bastian – Bgee team
OntoSIB - August 2013
© 2013 SIB
Big players of Internet never exhibit ontologies
Amazon:
© 2013 SIB
Big players of Internet never exhibit ontologies
Google Knowledge Graph:
© 2013 SIB
Big players of Internet never exhibit ontologies
Google Knowledge Graph:
© 2013 SIB
Big players of Internet never exhibit ontologies
Facebook Open Graph:
© 2013 SIB
Big players of Internet never exhibit ontologies
Facebook Open Graph:
© 2013 SIB
Meanwhile… Bgee is ontology-centric
Expression of mouse Hoxa5
© 2013 SIB
Meanwhile… Bgee is ontology-centric
Expression of mouse Hoxa5
© 2013 SIB
But lists are not usable…
Expression of mouse Hoxa5
© 2013 SIB
Neither are tables
Expression of mouse Hoxa5
© 2013 SIB
Solutions are…
On the analytical side:
- identify the most pertinent biological signal
On the visualization sid...
© 2013 SIB
Solutions are…
On the analytical side:
- identify the most pertinent biological signal
On the visualization sid...
© 2013 SIB
The solution adopted by neXtProt
Revamp the ontologies to make the organization clearer,
and the hierarchy simp...
© 2013 SIB
Bgee needs a different approach
- Bgee includes several species; revamping ontologies
would be too time-consumi...
© 2013 SIB
Solution 1
Summarize information on the fly:
Find by walking the ontology from the root the x most
general terms
© 2013 SIB
Solution 1
1. Start walk from the root
© 2013 SIB
Solution 1
1. Start walk from the root
2. Walk 1st level
2 terms identified
© 2013 SIB
Solution 1
1. Start walk from the root
2. Walk 1st level
3a. Walk 2nd level 1st term
2 terms identified
© 2013 SIB
Solution 1
1. Start walk from the root
2. Walk 1st level
3a. Walk 2nd level 1st term
3b. Walk 2nd level 2nd ter...
© 2013 SIB
Solution 1
1. Start walk from the root
2. Walk 1st level
3a. Walk 2nd level 1st term
3b. Walk 2nd level 2nd ter...
© 2013 SIB
Solution 1
1. Start walk from the root
2. Walk 1st level
3a. Walk 2nd level 1st term
3b. Walk 2nd level 2nd ter...
© 2013 SIB
Solution 1
EMAPA:16060 cavities and their linings
EMAPA:16072 primitive streak
EMAPA:16097 mesenchyme
EMAPA:161...
© 2013 SIB
Solution 1
EMAPA:16060 cavities and their linings
EMAPA:16072 primitive streak
EMAPA:16097 mesenchyme
EMAPA:161...
© 2013 SIB
Solution 2
Find most precise and independent terms:
Walk the ontology from the leaves to the root.
Data found i...
© 2013 SIB
Solution 2
1. Start the walk from the
leaves
© 2013 SIB
Solution 2
1. Start the walk from the
leaves
2. Remove ancestors
© 2013 SIB
Solution 2
Limb example:
EMAPA:17459 footplate
EMAPA:17428 handplate
EMAPA:17713 humerus cartilage condensation...
© 2013 SIB
Solution 3
Display most precise and independent terms, organized by
most general terms
© 2013 SIB
Solution 3
Example: general terms
EMAPA:16405 limb
EMAPA:16748 tail
EMAPA:17213 skeleton
© 2013 SIB
Solution 3
Example: general terms + precise and independent terms
EMAPA:16405 limb
EMAPA:17459 footplate
EMAPA:...
© 2013 SIB
OWLGraphManipulator allows to perform:
• enhanced relation reductions
• class removal and relation propagation
...
© 2013 SIB
Use of OWLGraphManipulator on Uberon:
• From the global version, keep only relevant species.
• Clear relations ...
© 2013 SIB
Development of an ontology to capture confidence in an
annotation, following the Biocuration 2012 meeting.
http...
© 2013 SIB
We annotate homology using Uberon, by providing for each
annotation:
• Uberon ID UBERON:0003126 trachea
• NCBI ...
© 2013 SIB
Conclusion
Some big players on internet make an intensive use of
ontologies (Amazon, Google, Facebook, …)
They ...
© 2013 SIB
Conclusion
In bioinformatics, we have much more information to capture
in ontologies.
But the lack of usability...
Thank You
Marta RosikiewiczSébastien Moretti
Anne Niknejad
Mathieu Seppey
Marc Robinson-Rechavi
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Hiding ontologies under the carpet - OntoSIB 2013

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Hiding ontologies under the carpet - OntoSIB 2013

  1. 1. Hiding ontologies under the carpet Frederic Bastian – Bgee team OntoSIB - August 2013
  2. 2. © 2013 SIB Big players of Internet never exhibit ontologies Amazon:
  3. 3. © 2013 SIB Big players of Internet never exhibit ontologies Google Knowledge Graph:
  4. 4. © 2013 SIB Big players of Internet never exhibit ontologies Google Knowledge Graph:
  5. 5. © 2013 SIB Big players of Internet never exhibit ontologies Facebook Open Graph:
  6. 6. © 2013 SIB Big players of Internet never exhibit ontologies Facebook Open Graph:
  7. 7. © 2013 SIB Meanwhile… Bgee is ontology-centric Expression of mouse Hoxa5
  8. 8. © 2013 SIB Meanwhile… Bgee is ontology-centric Expression of mouse Hoxa5
  9. 9. © 2013 SIB But lists are not usable… Expression of mouse Hoxa5
  10. 10. © 2013 SIB Neither are tables Expression of mouse Hoxa5
  11. 11. © 2013 SIB Solutions are… On the analytical side: - identify the most pertinent biological signal On the visualization side: - display the most pertinent information (e.g., remove redundancy) - guide users to the information they look for
  12. 12. © 2013 SIB Solutions are… On the analytical side: - identify the most pertinent biological signal On the visualization side: - display the most pertinent information (e.g., remove redundancy) - guide users to the information they look for But an ontology-centric display is terrible at guidance and pertinence.
  13. 13. © 2013 SIB The solution adopted by neXtProt Revamp the ontologies to make the organization clearer, and the hierarchy simpler.
  14. 14. © 2013 SIB Bgee needs a different approach - Bgee includes several species; revamping ontologies would be too time-consuming. - Bgee includes in situ hybridizations with great granularity; we don’t want to loose it. - Things are getting even worse with the use of the Uberon ontology. We are now trying the approach of completely hiding the ontologies to the users!
  15. 15. © 2013 SIB Solution 1 Summarize information on the fly: Find by walking the ontology from the root the x most general terms
  16. 16. © 2013 SIB Solution 1 1. Start walk from the root
  17. 17. © 2013 SIB Solution 1 1. Start walk from the root 2. Walk 1st level 2 terms identified
  18. 18. © 2013 SIB Solution 1 1. Start walk from the root 2. Walk 1st level 3a. Walk 2nd level 1st term 2 terms identified
  19. 19. © 2013 SIB Solution 1 1. Start walk from the root 2. Walk 1st level 3a. Walk 2nd level 1st term 3b. Walk 2nd level 2nd term 2 terms identified
  20. 20. © 2013 SIB Solution 1 1. Start walk from the root 2. Walk 1st level 3a. Walk 2nd level 1st term 3b. Walk 2nd level 2nd term 4a. Walk 3rd level 1st term 4 terms identified
  21. 21. © 2013 SIB Solution 1 1. Start walk from the root 2. Walk 1st level 3a. Walk 2nd level 1st term 3b. Walk 2nd level 2nd term 4a. Walk 3rd level 1st term 4b. Walk 3rd level 2nd term 11 terms identified
  22. 22. © 2013 SIB Solution 1 EMAPA:16060 cavities and their linings EMAPA:16072 primitive streak EMAPA:16097 mesenchyme EMAPA:16103 organ system EMAPA:16405 limb EMAPA:16748 tail EMAPA:17213 skeleton EMAPA:17743 vertebral axis muscle system MA:0000003 organ system MA:0002405 postnatal mouse MA:0002433 anatomic region
  23. 23. © 2013 SIB Solution 1 EMAPA:16060 cavities and their linings EMAPA:16072 primitive streak EMAPA:16097 mesenchyme EMAPA:16103 organ system EMAPA:16405 limb EMAPA:16748 tail EMAPA:17213 skeleton EMAPA:17743 vertebral axis muscle system MA:0000003 organ system MA:0002405 postnatal mouse MA:0002433 anatomic region Uberon includes “subsets” that would allow to filter meaningless terms
  24. 24. © 2013 SIB Solution 2 Find most precise and independent terms: Walk the ontology from the leaves to the root. Data found in a term will prevent its ancestors from being display (redundancy), but not its siblings (independency).
  25. 25. © 2013 SIB Solution 2 1. Start the walk from the leaves
  26. 26. © 2013 SIB Solution 2 1. Start the walk from the leaves 2. Remove ancestors
  27. 27. © 2013 SIB Solution 2 Limb example: EMAPA:17459 footplate EMAPA:17428 handplate EMAPA:17713 humerus cartilage condensation EMAPA:16779 hindlimb bud EMAPA:16406 forelimb bud - Visualization tool should allow to easily get information about ancestors of selected terms. - This solution could still lead to an unorganized list of many terms
  28. 28. © 2013 SIB Solution 3 Display most precise and independent terms, organized by most general terms
  29. 29. © 2013 SIB Solution 3 Example: general terms EMAPA:16405 limb EMAPA:16748 tail EMAPA:17213 skeleton
  30. 30. © 2013 SIB Solution 3 Example: general terms + precise and independent terms EMAPA:16405 limb EMAPA:17459 footplate EMAPA:17428 handplate EMAPA:17713 humerus cartilage condensation EMAPA:16779 hindlimb bud EMAPA:16406 forelimb bud EMAPA:16748 tail EMAPA:16752 unsegmented mesenchyme EMAPA:17213 skeleton EMAPA:18344 sternum EMAPA:19387 S1 EMAPA:19388 S2 EMAPA:19364 S3 EMAPA:19365 S4 EMAPA:18010 rib
  31. 31. © 2013 SIB OWLGraphManipulator allows to perform: • enhanced relation reductions • class removal and relation propagation • relation mapping to parent • relation filtering or removal • subgraph filtering or removal • relation removal to subset if non orphan • combination of these methods for generating basic ontologies Used to simplify the Uberon ontology. Owltools enhancement – OWLGraphManipulator
  32. 32. © 2013 SIB Use of OWLGraphManipulator on Uberon: • From the global version, keep only relevant species. • Clear relations to upper_level (obscure) terms • Remove subgraphs of obscure terms, keeping shared classes • keep only is_a, part_of, develops_from, and sub-relations • Simplify graph structure over is_a/part_of Uberon tweaking
  33. 33. © 2013 SIB Development of an ontology to capture confidence in an annotation, following the Biocuration 2012 meeting. http://wiki.isb-sib.ch/biocuration/Confidence_information_draft Quality codes
  34. 34. © 2013 SIB We annotate homology using Uberon, by providing for each annotation: • Uberon ID UBERON:0003126 trachea • NCBI taxon ID 32523 Tetrapoda • HOM ID HOM:0000007 historical homology • Evidence Code ID ECO:0000060 positional similarity evidence • Confidence Code ID CONF:0000003 High confidence • References ISBN:978-0030223693 "Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.591-592 » Homology annotation
  35. 35. © 2013 SIB Conclusion Some big players on internet make an intensive use of ontologies (Amazon, Google, Facebook, …) They invest a lot in usability and user-friendliness. What we can learn from them is: They never, ever, display ontologies as such
  36. 36. © 2013 SIB Conclusion In bioinformatics, we have much more information to capture in ontologies. But the lack of usability prevent biologists to access this knowledge. It is now time to invest more in usability. We hope that our approach will make easier the use of ontologies to analyse gene expression data.
  37. 37. Thank You Marta RosikiewiczSébastien Moretti Anne Niknejad Mathieu Seppey Marc Robinson-Rechavi

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