Worm EvoDevo Case

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Overview

Goals

  1. develop presentation of Kiontke, et al as case study in analysis of characters
  2. develop case study in phenotype-ontology integration with CDAO
  3. analyze bias in Kiontke, et al data

Strategy

  1. background study and preparation
    1. read Kiontke and prior work
    2. read other papers on phenotype ontologies
    3. obtain Kiontke, et al data
    4. adapt Bio::NEXUS to parse data file
    5. adapt Nexplorer to view data
  2. explore mappings of data to ontology terms
    1. identify relevant ontologies (worm onto or more general animal onto)
    2. try an initial mapping with a few characters
    3. get feedback from Kiontke or others
  3. develop integration strategy
    1. decide level of integration with CDAO
    2. import and develop connections
    3. test integration with sample data
  4. develop analysis methodology
    1. specify model, character, tree to be used
    2. code links to HyPhy, PAUP* or other package
    3. run on sample data
  5. carry out analysis

Background

Results

Basic parsing and visualization of data set

The data matrix is a bit complex, with polymorphic characters for various OTUs. The NEXUS file appears to have been generated in MacClade. Parsing with Bio::NEXUS failed. I fixed one error in that the format command (characters block) used double-quotes, which formally are not recognized in the NEXUS standard, instead of single-quotes.

Nevertheless, the file still cannot be parsed in Bio::NEXUS. This deserves further attention, since I do not see any problem with the file. Two features that might cause problems are the charstatelabels command, and the use of both parentheses (indicating polymorphism) and braces (indicating ambiguity) (see Maddison, et al., 1997 p. 603).

Mesquite, however, loads, views and exports the data with no apparent problem, even preserving the polymorphism-vs-ambiguity distinction.

Mappings of data to ontology terms

Identify relevant concepts in applicable ontologies

Foundational Model of Anatomy

for the worm C. elegans, specifically:

Initial mapping with a few characters

CDAO integration strategy

  1. decide level of integration with CDAO
  2. import and develop connections
  3. test integration with sample data

Analysis of character evolution

  1. specify model, character, tree to be used
  2. code links to HyPhy, PAUP* or other package
  3. run on sample data