Difference between revisions of "Common Gene Page"
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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
Contents
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.