Talk:Bio GMOD GenericGenePage

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Revision as of 08:06, 17 January 2009 by JimHu (Talk | contribs)

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Stuff Jim made up while implementing this for EcoliWiki after the Jan 2009 GMOD meeting

In the absence of a schema to check against, I developed this by example from Josh's Flybase example. In the process, I made some arbitary decisions that may be incompatible with what people want for the spec. Please suggest changes!

  • We noticed that the examples did not provide strand information, which makes sense, because UniProt doesn't care about strand. We added a strand attribute with values + and -, following GFF3
  • EcoliWiki represents an E. coli K-12 "pangenome", for which we currently have two strains (more coming soon). For this reason, we have multiple entries for mapLocation elements.
  • For the GO terms:
    • following the FlyBase example, I only showed GO term and evidence code. The list is a nonredundant list of GO term:Evidence code pairs; in many cases there may be multiple annotations using the same pairs, but based on different publications.
    • The GO list omits IEA annotations.
    • The evidence code includes the code for the evidence code type (IDA, IMP, etc). Flybase omits this.
  • The parameters are passed to PHP without using cgi parameters or mod_rewrite, by using the PHP global $_SERVER["PATH_INFO"].
    • gene_symbol in the example is only one way to get this return. You can also use different URLs for locus tags.

--JimHu 08:06, 17 January 2009 (UTC)