Integrating phenotype ontologies across multiple speciesCaltech 2009<br />Chris Mungall<br />
Conservation of phenotypes<br />
How do we compare phenotypes across species?<br />Multiple project or species specific phenotype ontologies<br />MP: mouse...
Anatomical and structural entities in OBO<br />
MP<br />MP<br /><ul><li>is_a hierarchy
hand-crafted</li></li></ul><li>PATO EQ Descriptions<br />PATO:<br />ontology of qualities<br />EQ Descriptions<br />An exp...
Examples<br />
Relational Qualities<br />Have a bearer<br /> - have an additional dependency on some type of entity<br />
EQ expressions can be written in obo format<br />Why?<br />	Formal semantics<br />	Edit within OBO-Edit as genus-different...
EQ expressions can be written in obo format<br />Why?<br />	Formal semantics<br />	Edit within OBO-Edit as genus-different...
EQ expressions can be written in obo format<br />
EQ vs dedicated phenotype ontology<br />Some groups pre-compose phenotype descriptions<br />terms generated in advance by ...
Methodologies<br />
Unifying descriptions<br />Equivalence Mappings<br />	between<br />	term<br />	EQ expression<br />
Methods<br />Use obol to generate first pass and updates<br />parses term name<br />assumes semi-controlled syntax<br />Ma...
Results<br />
Advantages<br />Reuse PATO across ontologies<br />Make sure we’re saying the same thing<br />We can use the OBO-Edit reaso...
Reasoning<br />
Reasoner Results: HP/MP<br />
Comparing across species<br />Requirements:<br />Phenotype ontology mappings<br />Mappings between anatomy ontologies<br /...
Mapping AOs to Uberon<br />
Phenoblast: Quantifying similarity<br />SimJ: 0.42<br />MaxIC: 13.4<br />SimJ: 0.17<br />MaxIC: 6.2<br />SimJ: 0.32<br />M...
Recovering<br />pathway<br />members<br />by phenotypic<br />similarity<br />
Conclusions<br />Sharing ontologies is good<br />PATO / EQs can be used to help build ontologies as well as in annotation<...
Upcoming SlideShare
Loading in …5
×

Integrating phenotype ontologies across multiple species

1,127
-1

Published on

Published in: Technology
1 Comment
0 Likes
Statistics
Notes
  • Be the first to like this

No Downloads
Views
Total Views
1,127
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
26
Comments
1
Likes
0
Embeds 0
No embeds

No notes for slide

Integrating phenotype ontologies across multiple species

  1. 1. Integrating phenotype ontologies across multiple speciesCaltech 2009<br />Chris Mungall<br />
  2. 2. Conservation of phenotypes<br />
  3. 3. How do we compare phenotypes across species?<br />Multiple project or species specific phenotype ontologies<br />MP: mouse<br />HP: human<br />WP: worm<br />TO: plant<br />APO: fungi<br />Data is not comparable<br />How do we know they are built according to the same principles?<br />
  4. 4. Anatomical and structural entities in OBO<br />
  5. 5. MP<br />MP<br /><ul><li>is_a hierarchy
  6. 6. hand-crafted</li></li></ul><li>PATO EQ Descriptions<br />PATO:<br />ontology of qualities<br />EQ Descriptions<br />An expression consisting of:<br />a PATO ID (Q)<br />A bearer entity (E)<br />Optional additional tags<br />
  7. 7. Examples<br />
  8. 8. Relational Qualities<br />Have a bearer<br /> - have an additional dependency on some type of entity<br />
  9. 9. EQ expressions can be written in obo format<br />Why?<br /> Formal semantics<br /> Edit within OBO-Edit as genus-differentia definitions<br /> Use the OBO-Edit reasoner<br />Can also be translated to OWL<br />
  10. 10. EQ expressions can be written in obo format<br />Why?<br /> Formal semantics<br /> Edit within OBO-Edit as genus-differentia definitions<br /> Use the OBO-Edit reasoner<br />Can also be translated to OWL<br />
  11. 11. EQ expressions can be written in obo format<br />
  12. 12. EQ vs dedicated phenotype ontology<br />Some groups pre-compose phenotype descriptions<br />terms generated in advance by ontology editor<br />ontology editors adds defs etc<br />dedicated phenotype ontology<br />often species-specific<br />Other groups post-compose phenotype descriptions<br />descriptions composed as needed by annotators<br />no dedicated phenotype ontology <br />
  13. 13. Methodologies<br />
  14. 14. Unifying descriptions<br />Equivalence Mappings<br /> between<br /> term<br /> EQ expression<br />
  15. 15. Methods<br />Use obol to generate first pass and updates<br />parses term name<br />assumes semi-controlled syntax<br />Manually edit obo xp file<br />
  16. 16. Results<br />
  17. 17. Advantages<br />Reuse PATO across ontologies<br />Make sure we’re saying the same thing<br />We can use the OBO-Edit reasoner to compute the is_a hierarchy<br />We can enhance queries within species.<br />E.g. find all genes that have a phenotype affecting sperm (CL:0000019 / WBbt:0006798)<br />We can compare across species<br />
  18. 18. Reasoning<br />
  19. 19. Reasoner Results: HP/MP<br />
  20. 20. Comparing across species<br />Requirements:<br />Phenotype ontology mappings<br />Mappings between anatomy ontologies<br />Uberon<br />Multi-species anatomy ontology<br />No assumption of homology<br />Analogy is useful to; e.g. eyes<br />Scope: metazoans<br />Applicability outside vertebrates controversial<br />Better to focus on cells (CL)<br />
  21. 21. Mapping AOs to Uberon<br />
  22. 22. Phenoblast: Quantifying similarity<br />SimJ: 0.42<br />MaxIC: 13.4<br />SimJ: 0.17<br />MaxIC: 6.2<br />SimJ: 0.32<br />MaxIC: 12.1<br />
  23. 23. Recovering<br />pathway<br />members<br />by phenotypic<br />similarity<br />
  24. 24. Conclusions<br />Sharing ontologies is good<br />PATO / EQs can be used to help build ontologies as well as in annotation<br />Find mistakes<br />Automatically build DAG (reasoning)<br />Mapping a phenotype ontology to EQs gives you the best of both worlds<br />Control over the terms used in annotation<br />Comparing data across species<br />Where anatomical similarities permit..<br />
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×