In-scope Use Cases for Phase 1 Prototype Development

Use case	Entry Point	comments/ideas
1. Reconcile a gene tree and species tree chosen from tree databases or submitted in some standard form.	Gene family name or tree + taxon tree or list (tree derived from taxon list using phylomatic-like tool)
2. Show all gene and genome duplications in a gene family tree.	fasta file, list of genes or exemplar gene for a gene family	showing genome duplications is not included in initial requirements
3. Find all gene trees showing a duplication event at a specific point on a species tree.	reference point (node) in species tree.
12. Show sampled gene copy number for all taxa gene family identifier	Show total gene # and then gene family copy number for selected families, against species tree
4. Find points on a species tree where a set of genes (e.g. all genes within a pathway or GO category) originated and/or diversified.	gene sequence(s), gene name(s) pathway, GO annotation

Note: #4 is out of Phase 1 scope but still has a status 1 (indicating high priority).

Below is the start of discussion regarding the details of use cases for the TR prototype

This discussion originally started from a comment by Jim Leebens-Mack on the Meeting page for December 21, 2009.

(corresponds to [Use Case #1])

Researcher initiates term search of gene family database (alternatively, researcher may initiate search with BLAST query)
- return a list of gene families containing genes with term in annotation
Researcher requests the estimated gene tree for a gene family included in the term search results
- return gene tree with links to alignment
Researcher wants to see duplication events and speciation events on the returned gene tree
- show reconciled tree in ATV or fat tree format.
Researcher wants to highlight those duplications in the gene tree which have been associated with whole genome duplications
- Show distinct marker (e.g. star) on gene tree for duplication events associated with polyploidization (this feature may not be in the initial release).

(corresponds to [Use Case #3])

Researcher requests species tree
- return species tree graphic (e.g. Phytozome tree)
Researcher requests a list of all gene families with exhibiting duplication events just above a specific node on the species tree (e.g. last common ancestor of all rosids).
- return list
Researcher requests subset of gene families in the return list with genes mapping to one, two, or all three triplicated syntenic blocks in Vitis genome.
- return list (again, this feature may not be in the initial release)
Researcher clicks on a gene family and requests view of genomic context for all gene family members in the Vitis genome
- Link out to gbrowse view?.

(corresponds to [Use Case #4])

Researcher runs BLAST search with query sequence.
- return hit list with gene family IDs for each hit.
Researcher requests gene family tree
- return gene tree as above
Researcher asks for species tree view with duplication events mapped on to species tree.
- return species tree with duplications indicated as hash markers or increased line thickness...
- If initial query was a GO category or metabolic pathway, this view would simply show duplication events summed across all gene families with genes in the requested GO category or metabolic pathway.