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Computing with phenotypic diversity using semantic descriptions

Lightning talk for iEvoBio 2013

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Computing with phenotypic diversity using semantic descriptions

  1. 1. Computing with phenotypic diversityusing semantic descriptionsJim Balhoff
  2. 2. Phenotypic data a cytoplasmic terminal death domain essential for proteininteractions with signaling adaptor complexes. The flste370fmutation 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 ofscales, teeth and gill rakers resembling the fls phenotype (A–C). Heterozygous Nkt zebrafish show an intermediate phenotype of scale loss andpatterning 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 1and 2 (arrows, F). Cb1-5, ceratobranchial bones.doi:10.1371/journal.pgen.1000206.g002Table 1. Quantitative effect of fls on scale number and shapeand the effect of background modifiers in Danio rerio strainson flsdt3Tpl.Zebrafish Model of Human Ectodermal Dysplasia
  3. 3. Many terms“lacrymal bone...flat’’ Mayden 1989“lacrimal...small, flat”Grande and Poyato-Ariza1999“lacrimal...triangular’’ Royero 1999“first infraorbital (lachrimal)shape...flattened”Kailola 2004“fourth infraorbital...anterior andposterior parallel”Zanata and Vari 2005
  4. 4. Many conceptsparamereYoder et al. 2010
  5. 5. PhenoscapeTAO:ethmoidcartilage“ethmoid plate form”Entity“rounded”CharacterPATO:roundQualityStateEQ phenotype}
  6. 6. Phenoscape• Knowledgebase:• EQ annotation of ~11,000 character states,~50 previously published morphologicalphylogenetic studies
  7. 7. PhenoscapeMutation of brpf1 gene inDanio:Ictalurus punctatus:Laue et al (2008)
  8. 8. Semantic descriptionsspecimens &taxonomyDarwinCore (Darwin-SW)descriptivedataComparative Data AnalysisOntology (CDAO)phenotypes &anatomyUberon, Phenotype and TraitOntology (PATO)
  9. 9. States to organismsOTU“red”“mesosomacolor”matrixcellinverse(has_State) ∘belongs_to_TU ∘denotes → denotes
  10. 10. States to phenotypes“red”“mesosomacolor”Entity: HAO:mesosomaQuality: PATO:redhas_part some(mesosoma andbearer_of some red)Phenotype1denotes onlyPhenotype1
  11. 11. Organisms to phenotypesOTU IAO:denotesIAO:denotes only[organisms exhibitingphenotype; EQ classdescription][organism]characterstatetype[organism] type[organisms exhibitingphenotype]
  12. 12. _:otu_1111cdao:TU_:coding_2222"Szepligetella levipetiolata"cdao:CharacterStateDatum_:char_3333cdao:Character_:state_4444cdao:CharacterStateDomain"sigmoid""notaulus shape"iao:denotes"Szepligetella levipetiolata"_:determ_6666dwc:Identificationurn:catalog:NCSU:NCSU:34852dsw:Specimenhao:female_organismrdf:typehao:notauluspato:sigmoidhas_part some (phenotype_4444rdfs:subClassOfand bearer_of some )rdfs:labelrdf:typerdfs:labeliao:denotesrdfs:labelrdf:typerdf:typecdao:has_Statecdao:belongs_To_Charactercdao:belongs_To_TUrdf:typeowl:allValuesFromrdf:typerdf:typerdf:typedsw:toTaxondsw:hasIdentificationrdf:typerdfs:labelrdf:type_:organism_5555dsw:idBasedOndsw:IndividualOrganism rdf:typeOWL instancesOWL classes
  13. 13. Semantic descriptions• Mullins et al. 2012. A revision of Evaniscus (Hymenoptera,Evaniidae) using ontology-based semantic phenotypeannotation. ZooKeys• Balhoff et al. 2013. A semantic model for speciesdescription applied to the ensign wasps (Hymenoptera:Evaniidae) of New Caledonia. Systematic Biology(describes semantics)• Taxonomic descriptions available as RDF in Dryad••• Phenoscape is working to provide KB data in RDF
  14. 14. Conclusion• Standardize association of character data withphenotype models and referenced organisms• Common model for Phenoscape annotationsand wasp taxonomic descriptions• Character state annotations can denote classesdescribing any semantic model (not only EQ)• Specimen identifiers and a standard model forcollections data in RDF are needed (Darwin-SW, BCO)
  15. 15. Acknowledgments• Phenoscape project:• Hilmar Lapp, Chris Mungall• Deans Lab: Andy Deans, Matt Yoder, IstvánMíko, Trish Mullins• National Science Foundation