Phenoscape Grant Renewal Workshop/Notes

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Wednesday afternooon

  • Will be extending the taxonomic scope to extant and extinct vertebrates
    • Create an annotation database spanning the taxonomic scope and their anatomy ontologies
    • Three multi-species anatomy ontologies are being developed: teleosts, amphibians, mammalian anatomy
    • Tree mapping: show when an evolutionary phenotype first appeared
  • EQ support in all involved model organism databases
    • Structure of MP is not consistent with anatomy, or with PATO
    • Mapping from MP to EQ syntax is being worked on
    • MGI isn't in a position to use EQ internally, but for example Phenoscape could provide an EQ-view on mouse phenotypes, using the decomposition of MP into anatomy (or entity) and quality term cross-product
    • Full EQ annotation for OMIM is being planned but not yet funded
    • MGI, Xenbase, and ZFIN all have links from their phenotype data to OMIM
  • Development of anatomy
    • Different approaches between MGI and ZFIN:
      • MGI uses complete anatomy at different developmental stages
      • ZFIN uses one anatomy ontology and adds start and end dates to indicate the developmental period during which it appears (adult structures don't have an end date)
      • Xenbase uses the ZFIN approach
    • Candidate genes for evolutionary change could be derived from anatomy-annotated gene expression studies during development
      • genes responsible for or associated with morphological changes during individual development could be candidates for evolutionary change
      • evolutionary phenotype changes could be used to query morphological changes during development
    • Can we enable queries to generate hyptheses based on ontogeny reflecting evolutionary history?
      • Evolutionary developmental data could come from medaka, stickleback
  • Sequence of steps:
    1. Ontology building
      • Adult phenotype annotations for mutants in Xenbase
      • Presently only 3 species for amphibians: Xenopus, Dermophis, Salamandria
      • Development decoupling from anatomy ontology in mouse
      • Expanding mammalian anatomy to include extinct species
      • Anatomy for amniotes (the clade including mouse and dinosaurs), including extinct taxa (such as dinosaurs)
        • Scope of this could be overwhelming
        • Should be strongly driven (or staged) according to the character matrices to be annotated
        • Chicken anatomy could provide a starting point?
        • There is work on bird anatomy that uses a latin naming scheme
        • Work on any smaller-scope anatomy (or multi-species anatomy) ontology will contribute terms that apply more broadly
        • There may not be very many neomorphs between birds and mammals, though there are a few areas such as the digits in birds where the exact homology relationships aren't as clearly agreed upon.
    2. Mammalian phenotype decomposition
      • Need support for QC'ing the results of automated decomposition
      • Alignment of MP with mouse anatomy
    3. Annotation
      • Which published character matrices are there for dinosaurs?
  • Ontology mapping and alignment
    • Need to align teleost and amphibian anatomy to mouse.
    • Mouse and chicken need to be mapped to amniote anatomy. Mouse is a better start because there are genetic data.
  • Reconciling character-derived trees and character definition and use between different matrices and trees that share taxa (Paul)
    • TaxonSearch
    • Formalizing and generating grammar of character coding and character state definition
    • Analyzing character usage (shared, not shared, rejected) between trees that share taxa
    • Conflicting phylogenies for the same set of taxa often turn out to be based on character codings that are not consistent or not compatible

Idea bin

  • Intermine connection (multiple model organisms, AJAX-based widget for displaying protein family tree)