Difference between revisions of "Common Gene Page"

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(Starter for common gene page)
 
m (Daphnia genome database use case : screen shots)
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where the gene reports are structured XML, with a style sheet to display.  For example,
 
where the gene reports are structured XML, with a style sheet to display.  For example,
 
see this gene page, http://wfleabase.org/lucegene/lookup?id=NCBI_GNO_292134
 
see this gene page, http://wfleabase.org/lucegene/lookup?id=NCBI_GNO_292134
(view the page source to see structured gene page XML)
+
(view the page source to see structured gene page XML).  Or see these screen shots [[Media:Daphnia-genepage.png | daphnia gene page]] and [[Media:Daphnia-genepage-xml.png | gene page xml]].
  
 
There is a simple perl tool to turn annotated GFF data into this gene page XML,
 
There is a simple perl tool to turn annotated GFF data into this gene page XML,

Revision as of 19:18, 6 June 2008

Common Gene Page Rationale

Model organism/genome databases (MODs) produce gene pages of similar gene data, and may benefit from looking at unifying these to common structure, labelling, etc.

A list of common gene page attributes

* Names, symbols/IDs, synonyms
* Map locations
* Sequences
* Reagents
* Gene ontology
* Similar Genes
* Database cross-refs, External links
* Alleles, Transcripts
* Proteins, Structure and Domains
* Expression and Mutant Phenotypes
* Gene Interactions
* Literature references
* Summary Text

Example uses

Early documents and samples

See this folder for some discussion, documents and examples for MOD gene pages from 2004: http://eugenes.org/gmod/gene-report-examples/

More discussion and samples

See this blog entry on a 2005 meeting disccussion, http://blog.gmod.org/common_gene_pages

Daphnia genome database use case

There is an implementation of how this can be used at Daphnia-base, wfleabase.org, where the gene reports are structured XML, with a style sheet to display. For example, see this gene page, http://wfleabase.org/lucegene/lookup?id=NCBI_GNO_292134 (view the page source to see structured gene page XML). Or see these screen shots daphnia gene page and gene page xml.

There is a simple perl tool to turn annotated GFF data into this gene page XML, suitable for search and display, in GMOD genepages in CVS or http://eugenes.org/gmod/gene-report-examples/ for bin/gff2ugpxml.pl

Search and display is then provided by the GMOD LuceGene tool.