Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
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
×
Upcoming SlideShare
Phenotype-based Matching Using PhenoDB Terms in BHCMG PhenoDB to Maximize Whole Exome/Genome Sequencing Data Interpretation - Nara Sobreira
Next
Download to read offline and view in fullscreen.

0

Share

Download to read offline

Integrating phenotype ontologies across multiple species

Download to read offline

Related Books

Free with a 30 day trial from Scribd

See all
  • Be the first to like this

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 />

Views

Total views

1,398

On Slideshare

0

From embeds

0

Number of embeds

4

Actions

Downloads

27

Shares

0

Comments

0

Likes

0

×