RG: Software (Retired)

Reference Genome Software

Software for use with the Reference Genome project.

Status Tracker

There is a very early alpha of the status tracker here. Mostly a placeholder. The tool's front end is written with GWT and the backend will be with the new OBD API. All data passed between the two will have to be serializable.

API and Objects

• Meta: a general object for general queries.
  • #target_genes -> int
  • species -> list of Species
  • get_gene_products(with_constraint?) -> list of GeneProduct
  • get_targets(with_constraint?) -> list of Target
  • get_orthologs(with_constraint?) -> list of Ortholog

• Species: as GO, but with extras
  • homologs -> list of Ortholog
  • !homologs -> list of Ortholog
  • #homologs -> int
  • #!homologs -> int
  • #comprehensive -> int
  • common_name -> string
  • ncbi_taxa_id -> int
  • etc...

• Evidence: as GO
  • etc...

• Target: an object representing a target for the MODs
  • symbol
  • id
  • etc (and similar to GP)...

• Ortholog: an object representing a curated gene product
  • status -> bool
  • date_complete -> data || undef
  • references_used -> list of string
  • references_outstanding -> list of string
  • etc (and similar to GP)...

• GeneProduct: as GO
  • symbol ->string
  • species -> Species
  • full_name ->string
  • etc...

• Paralog?

• Xenolog?

• Report: a set of functions to apply to groups of the above for page generation, automatic sanity checking would be nice.
  • ???

The Target and Ortholog objects may be a subclass of a YTD superclass. This superclass will need to be able to read and write to the database and be able to maintain temporary values in case of validation/sanity issues (or similar functionality). Maybe also a subclass of GeneProduct.

Also, we're going to have to spend a bit of time making sure the the login/authentication is done properly--the last thing that we'll want is bots coming in and clicking on things.

Parsers

Two parsers will also be necessary for the tool.

• A target parser that converts a tab-delimited file to a list of Target. The files format looks like:

mod-id ???

• An ortholog parser that converts a tab-delimited file to a list of Ortholog. The files format looks like:

gene-symbol gene-id reference-p date-complete #-ref-used outstanding-refs

Summary and Graph Views

An alpha of the summary and graph views can currently be found here. This uses parts of a newer AmiGO framework written in perl.

This viewer has only been tested in Safari 3.x, FireFox 2.x, and Opera 9.x.

• Hovering over a node brings up details.
• The graph can be clicked and dragged.
• The mouse wheel zooms in and out.
• The zoom may also be controlled by ctrl-a and ctrl-z (if the browser does not use these for other functions).
• Checking a species causes them to highlight.