Lightning talk for iEvoBio 2013

1. Computing with phenotypic diversity
using semantic descriptions
Jim Balhoff

2. Phenotypic data
http://www.linnean-online.org/
and a cytoplasmic terminal death domain essential for protein
interactions with signaling adaptor complexes. The flste370f
mutation is an A to T transversion at a splice acceptor site,
Figure 2. The dominant gene Nkt is phenotypically similar, however complements fls mutants. Nkt homozygotes show complete loss of
scales, teeth and gill rakers resembling the fls phenotype (A–C). Heterozygous Nkt zebrafish show an intermediate phenotype of scale loss and
patterning defect (arrows) while no effect on fin development is seen (D). Heterozygous Nkt also show a dominant effect on the number of teeth
(arrows, E) and gill rakers (F), showing deficiencies along the posterior branchial arches and formation of rudimentary rakers along ceratobranchial 1
and 2 (arrows, F). Cb1-5, ceratobranchial bones.
doi:10.1371/journal.pgen.1000206.g002
Table 1. Quantitative effect of fls on scale number and shape
and the effect of background modifiers in Danio rerio strains
on flsdt3Tpl
.
Zebrafish Model of Human Ectodermal Dysplasia

3. Many terms
“lacrymal bone...flat’’ Mayden 1989
“lacrimal...small, flat”
Grande and Poyato-Ariza
1999
“lacrimal...triangular’’ Royero 1999
“first infraorbital (lachrimal)
shape...flattened”
Kailola 2004
“fourth infraorbital...anterior and
posterior margins...in parallel”
Zanata and Vari 2005

4. Many concepts
paramere
Yoder et al. 2010
http://dx.doi.org/10.1371/journal.pone.0015991

5. Phenoscape
TAO:ethmoid
cartilage
“ethmoid plate form”
Entity
“rounded”
Character
PATO:round
Quality
State
EQ phenotype
}

6. Phenoscape
• Knowledgebase: http://kb.phenoscape.org/
• EQ annotation of ~11,000 character states,
~50 previously published morphological
phylogenetic studies

7. Phenoscape
Mutation of brpf1 gene in
Danio:
Ictalurus punctatus:
Laue et al (2008)

8. Semantic descriptions
specimens &
taxonomy
DarwinCore (Darwin-SW)
descriptive
data
Comparative Data Analysis
Ontology (CDAO)
phenotypes &
anatomy
Uberon, Phenotype and Trait
Ontology (PATO)

9. States to organisms
OTU
“red”
“mesosoma
color”
matrix
cell
inverse(has_State) ∘belongs_to_TU ∘denotes → denotes

10. States to phenotypes
“red”
“mesosoma
color”Entity: HAO:mesosoma
Quality: PATO:red
has_part some
(mesosoma and
bearer_of some red)
Phenotype1
denotes only
Phenotype1

11. Organisms to phenotypes
OTU IAO:denotes
IAO:denotes only
[organisms exhibiting
phenotype; EQ class
description]
[organism]
character
state
type
[organism] type
[organisms exhibiting
phenotype]

12. _:otu_1111
cdao:TU
_:coding_2222
"Szepligetella levipetiolata"
cdao:CharacterState
Datum
_:char_3333
cdao:Character
_:state_4444
cdao:CharacterState
Domain
"sigmoid""notaulus shape"
iao:denotes only
phenotype_4444
urn:lsid:ubio.org:
namebank:
6018767
dwc:Taxon
"Szepligetella levipetiolata"
_:determ_6666
dwc:Identification
urn:catalog:NCSU:
NCSU:34852
dsw:Specimen
hao:female_organism
rdf:type
hao:notaulus
pato:sigmoid
has_part some (
phenotype_4444
rdfs:subClassOf
and bearer_of some )
rdfs:label
rdf:type
rdfs:label
iao:denotes
rdfs:label
rdf:type
rdf:type
cdao:has_State
cdao:belongs_To_Character
cdao:belongs_To_TU
rdf:type
owl:allValuesFrom
rdf:type
rdf:type
rdf:type
dsw:toTaxon
dsw:hasIdentification
rdf:type
rdfs:label
rdf:type
_:organism_5555
dsw:idBasedOn
dsw:IndividualOrganism rdf:type
OWL instancesOWL classes

13. Semantic descriptions
• Mullins et al. 2012. A revision of Evaniscus (Hymenoptera,
Evaniidae) using ontology-based semantic phenotype
annotation. ZooKeys
• Balhoff et al. 2013. A semantic model for species
description applied to the ensign wasps (Hymenoptera:
Evaniidae) of New Caledonia. Systematic Biology
(describes semantics)
• Taxonomic descriptions available as RDF in Dryad
• http://dx.doi.org/10.5061/dryad.2gd84
• http://dx.doi.org/10.5061/dryad.2jd88
• Phenoscape is working to provide KB data in RDF

14. Conclusion
• Standardize association of character data with
phenotype models and referenced organisms
• Common model for Phenoscape annotations
and wasp taxonomic descriptions
• Character state annotations can denote classes
describing any semantic model (not only EQ)
• Specimen identifiers and a standard model for
collections data in RDF are needed (Darwin-
SW, BCO)

15. Acknowledgments
• Phenoscape project: http://phenoscape.org/
wiki/Contributors#Project_team
• Hilmar Lapp, Chris Mungall
• Deans Lab: Andy Deans, Matt Yoder, István
Míko, Trish Mullins
• National Science Foundation