Use Case Discussion

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Last updated: Feb 10, 2010Version comment

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.

Reconcile a gene tree and species tree chosen from tree databases.

(corresponds to [Use Case #1])

  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
  2. Researcher requests the estimated gene tree for a gene family included in the term search results
    • return gene tree with links to alignment
  3. Researcher wants to see duplication events and speciation events on the returned gene tree
  4. 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).

Find all gene trees showing a duplication event at a specific point on a species tree.

(corresponds to [Use Case #3])

  1. Researcher requests species tree
  2. 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
  3. 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)
  4. 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?.

Identify points on species tree where genes in a particular gene family, GO category or genes in a a specific metabolic pathway has diversified (example focuses on a gene family).

(corresponds to [Use Case #4])

  1. Researcher runs BLAST search with query sequence.
    • return hit list with gene family IDs for each hit.
  2. Researcher requests gene family tree
    • return gene tree as above
  3. 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.