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Computing with phenotypic diversity using semantic descriptions

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Computing with phenotypic diversity
using semantic descriptions
Jim Balhoff

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Phenotypic data
http://www.linnean-online.org/
and a cytoplasmic terminal death domain essential for protein
interactions ...

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Many terms
“lacrymal bone...flat’’ Mayden 1989
“lacrimal...small, flat”
Grande and Poyato-Ariza
1999
“lacrimal...triangular’...

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Computing with phenotypic diversity using semantic descriptions

  1. 1. Computing with phenotypic diversity using semantic descriptions Jim Balhoff
  2. 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. 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. 4. Many concepts paramere Yoder et al. 2010 http://dx.doi.org/10.1371/journal.pone.0015991
  5. 5. Phenoscape TAO:ethmoid cartilage “ethmoid plate form” Entity “rounded” Character PATO:round Quality State EQ phenotype }
  6. 6. Phenoscape • Knowledgebase: http://kb.phenoscape.org/ • EQ annotation of ~11,000 character states, ~50 previously published morphological phylogenetic studies
  7. 7. Phenoscape Mutation of brpf1 gene in Danio: Ictalurus punctatus: Laue et al (2008)
  8. 8. Semantic descriptions specimens & taxonomy DarwinCore (Darwin-SW) descriptive data Comparative Data Analysis Ontology (CDAO) phenotypes & anatomy Uberon, Phenotype and Trait Ontology (PATO)
  9. 9. States to organisms OTU “red” “mesosoma color” matrix cell inverse(has_State) ∘belongs_to_TU ∘denotes → denotes
  10. 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. 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. 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. 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. 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. 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

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