1. Phenoscape Data Jamboree 2
Introduction and Goals: Paula Mabee
Sept. 28, 2008

2. Phenoscape Data Roundup
Introduction and Goals: Paula Mabee
Sept. 28, 2008

3. Ontologies
Data

4. Cowboys & cowgirls:

5. Jamboree goals: Curate data Evaluate web interface prototypes
Project personnel meeting

6. Curation goals:
Work with taxon experts to annotate characters using ontologies
Feedback on curation workflow and interface
How to make more efficient?
How to make more consistent?
Priorities for next 3-6 months of curation in relation to:
Prioritized use cases
Number of available character X taxon matrices
Original taxonomic scope

7. Phenoscape.org
History: Communication between zebrafish model organism community and Cypriniformes Tree of Life group through NESCent workshops ( )
NSF-DBI to Mabee, Vision, and Westerfield (June 1, 2007)
Goal: Create curated, ontology- based evolutionary phenotype database that maps to genetic databases
Generalizable system: Prototype with ostariophysan fishes

8. Shared ontologies & syntax connects models to humans a
Model organism
Human
Ontology
Mutant Gene
Mutant Gene
Mutant or Missing
Protein
Mutant or Missing
Protein
Ontology
Mutant Phenotype
Mutant Phenotype
(disease)

9. Shared ontologies & syntax connects models to other species a
Zebrafish
Multiple fish species
Mutant Gene
Candidate genes
Mutant or Missing
Protein ?
Ontology
Mutant Phenotype
Natural Phenotypes

10. Zebrafish: Mutagenesis produces phenotypes
no tail mutant
Halpern et al. (1993) Cell
Halpern et al. (1993) Cell

11. Phenotypes mapped to genes
sox9ahi1134
edn1
sox9ahi1134; lockjaw
val
she, stu, edn1-MO
Maxilla: size reduction
Dentary: size reduction
Retroarticular: loss
Opercle: size reduction; loss
Ceratohyal: shape change
Branchiostegals: number decrease
Branchiostegals: shape change

12. Evolutionary phenotypes
Mutation, Gene Flow, Selection, Drift
Species A
Morphology
Species B
Morphology
Species C
Morphology

13. Evolutionary phenotypes Genetic bases of morphology unknown
Mutation, Gene Flow, Selection, Drift ?
Species A
Morphology
Species B
Morphology
Species C
Morphology

14. Needs analysis use cases:
Phenoscape designed to meet top-priority questions/needs of the community concerning development and evolution of morphology, e.g.
Find genes underlying morphological characters (Which ones? How many?)
Discover patterns of correlation across genes and morphology
Formulate models of morphological evolution; data mining and discovery
Phenotypic BLAST to discover similar phenotypes and taxa

15. Prototype with Ostariophysan fishes (zebrafish)
Ostariophysi & outgroups
Mayden et al (unpublished)

16. Phenoscape priorities (yr. 1)
Develop ontologies for evolutionary work
Develop curation tools (Phenote -> Phenex)
Refine syntax for evolutionary characters
Curate phenotypes (characters)

17. Phenoscape ontologies
Cloned:
New:
Teleost Anatomy Ontology
(2233 terms; 387 skeletal)
Teleost Taxonomy Ontology
(36,060 terms;
38,000 synonyms)
Taxonomic Rank Ontology
(8->31 terms)
Zebrafish Anatomy Ontology
(2196 terms; 310 skeletal)
Existing:
Phenotype and Trait Ontology
(1,075 terms)
Evidence
Code
Ontology
Spatial Ontology
(106 terms)
19 June 2008

18. Entity-Quality (EQ) syntax
Caudal fin
Reduced (size)
no tail mutant
Anatomy Ontology:
Quality Ontology: AO
PATO

19. Systematic characters can also be described using Entity-Quality (EQ) syntax
State
Character
Entity
Attribute
Value
Caudal fin
size
reduced AO
PATO
Entity
Quality

20. Curate evolutionary phenotypes from free-text
This is not a computable format
These data cannot be easily compared across taxa
These data cannot be linked to developmental genetics
These data cannot be reasoned across

21. Curation needs: Data entry tool: Phenex
List of ranked papers: 76 “A” papers
Manual data entry (non-expert):
Pdf (1/2 scanned)
Taxon list (manual entry)
Character matrix (manual entry)
Free text character description (manual entry)

22. Curation needs: 4. E/Q ontology recoding of characters and states
This workshop

23. Curation of ichthyological data: proposed
Taxon
# Species
# Papers
# Characters
Cypriniformes
(Mayden; Coburn)
3,268 70
1125
Siluriformes
(Lundberg)
2,867 87
1200
Characiformes
(Dahdul)
1,674
124
800
Gymnotiformes
(Arratia)
134 2
200
Gonorynchiformes 37 80 75
Clupeiformes
(Hilton)
364 60
380
TOTAL
8,344
423
3,780
Original NSF grant estimate (2006)

24. Jamboree goal: ~1,530,165 EQ annotations
Taxon
# A
Papers
# species
# Character
Cypriniformes
(Mayden) 3
299
293
Siluriformes
(Lundberg)
733
477
Gonorynchiformes
(Grande) 69
187
Clupeiformes
(Hilton)
114
282
Ostariophysi 1 20 ?
TOTAL 13
1,235
1,239

26. Acknowledgements
NSF for Phenoscape funding (Mabee, Vision, Westerfield) NSF- DBI
National Evolutionary Synthesis Center NSF EF
NIH HG (to Monte Westerfield)
Phenoscape project: Hilmar Lapp, Wasila Dahdul, Peter Midford, Jim Balhoff,
ZFIN: Monte Westerfield, Melissa Haendel
Cypriniformes Tree of Life (NSF ), colleagues and students (Mayden, Miya, Saitoh, He, Coburn, Arratia, Simon, Conway, Grey, Engeman, Bogutskya, Hilton, Aspinwall); Deep Fin RCN
Suzanna Lewis, Chris Mungall (Lawrence Berkeley National labs)
National Center for Biomedical Ontology