RG: Software (Retired): Difference between revisions
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** #target_genes -> int | ** #target_genes -> int | ||
** species -> list of Species | ** 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 | * Species | ||
Line 23: | Line 26: | ||
** etc... | ** etc... | ||
* | * GeneProduct | ||
** symbol ->string | ** symbol ->string | ||
** species -> Species | ** species -> Species | ||
** full_name ->string | ** full_name ->string | ||
** etc... | ** etc... | ||
* Evidence | |||
* Target | * Target | ||
** | |||
** etc (and similar to GP)... | |||
* Ortholog | * Ortholog | ||
** status -> bool | |||
** date_complete -> data || undef | |||
** references_used -> list of string | |||
** references_outstanding -> list of string | |||
** etc (and similar to GP)... | |||
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. | 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. |
Revision as of 23:04, 7 March 2008
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
- homologs -> list of Ortholog
- !homologs -> list of Ortholog
- #homologs -> int
- #!homologs -> int
- #comprehensive -> int
- common_name -> string
- ncbi_taxa_id -> int
- etc...
- GeneProduct
- symbol ->string
- species -> Species
- full_name ->string
- etc...
- Evidence
- Target
- etc (and similar to GP)...
- Ortholog
- status -> bool
- date_complete -> data || undef
- references_used -> list of string
- references_outstanding -> list of string
- etc (and similar to GP)...
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.
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:
foo bar bibble babble
- An ortholog parser that converts a tab-delimited file to a list of Ortholog. The files format looks like:
foo bar bibble babble
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.