ability to choose from the phylogenies in the database
even with the possibility of constructing a consensus tree
ability to move branches around
choose a subset (pruned phylogeny)
map character changes onto the phylogeny
choose a feature of interest, e.g. by entity
issues of visualizing many characters on a branch
link to genes
e.g. show genes with elevated expression
need to be careful about showing statistics - may be misused or of
generating hypotheses for user (they should think for themselves)
BLAST-like similarity search for how a trait (or trait change) maps
across a tree
for example, a user has discovered elevated expression of a gene in
certain branches of the tree; are there phenotypes that are similar
to this distribution?
Questions that this might be used for
Evolvability
Constraints
Parallel evolution
Phenotype correlation (Todd Vision): Report-out
Whiteboard examples
matrix showing numerical summaries
find cloud of similar annotations
traits vs traits, traits vs genes, genes vs genes
cells would be number of branches on which the two traits change in
common (traits vs traits), or number of mutants they have in common
(traits vs traits, and traits vs genes), or number of traits in
common (genes vs genes)
problem of whether to use entity alone, entity and attribute
(character), or EQ (character state)
problem of opening a can of worms by offering too detailed of an
analysis, especially if it involves ancestral state reconstruction
using phylogenies
e.g., is limblessless associated with elongation
tree view
highlight terminal taxa or phylogenies for bringing up a matrix for
body-plan view
highlight different areas and ask for traits affecting all of those
highlight different areas and then map the corresponding and
correlated traits onto a tree
Semantics: Report-out
most queries aren’t complex, and often simply want to have a list
(e.g., genes, phenotypes)
for this, complex semantics may not be needed
shallower ontologies, or higher-level (more general) terms may
largely suffice
searching or analyzing phenotypes by similarity would require more
rigorous or deep semantics
too fine grained ontologies may be problematic for annotation
allelic links:
emerging dataset of genetic mutations that are experimentally proven
to have caused evolutionary change (D. Stern); experiments that
allow strong hypotheses for polarity of gene change
directionality of allelic changes may be important
may need an evolves-from (develops-from?) relationship
restrict some queries to where information (e.g. gene expression) is
available for >50% of the taxa
Visualizations: phylogenies, body maps, time series, geography
Discussion
Data interrelationships
Other data types or dimensions we haven’t looked at
