Needs Analysis Workshop/Report-out Day1
From phenoscape
Evo Group report-out
- need to improve ontologies, e.g. for describing behavior
- need to improve tools for analyzing images
- covariance of entities, attributes
- broader queries of entities within particular constraints, such as structures
- need capacity to store media (e.g., images, movies)
- need environmental, ecological, and geographical data
Devo Group report-out
- identifying homologies among distantly related taxa
- for example, do fishes have digits? E.g., if genes have similar effects on fins as on digit development.
- patterns of covariation
- for example, cusps on mammalian teeth
- could be used to identify "character modules" that are well-connected
- connections within modules should be more stable than between
- for a branch hypothesized to be under positive selection (from e.g. a molecular analysis), identify candidate phenotypes that could have been selected for
- map synapomorphies onto a phylogeny
- identify phenotypes with highest rate of change on that lineage
- needs phylogeny that is selectable and manipulable
- use the database to point out holes in the knowledge
Discussion
- enrichment analysis: given a list of genes, which phenotype terms are overrepresented among them
- capturing representing variation seems to be a general problem and challenge, but critically needed
- variation in regulatory (or morphogenic) gene expression and corresponding phenotypic changes (Hox gene expression example)
- polyphenism: variability of phenotype that can distinguish species but is also dependent on environmental factors or variable levels of gene expression
- do we need to capture frequencies for polymorphisms to represent variability
- there are morphological differences even between inbred strains, for example for JAX mouse strains in cranial morphology
- integrating with genomic resources:
- linking out to genome databases seems mandatory
- alerting features
- for example, saving queries as RSS feeds
