[Gmod-help] FlyBase Chado mapping tables

[Josh Goodman]

Hi Dave,

I don't think that this structure will work for what I'm trying to do.  Let me elaborate a bit more. 
  What we have is a mapping table that lays out field by field where data for that field can be 
found in Chado.  For example, say a user wants to be able to locate where the Symbol field in our 
gene report (http://flybase.org/reports/FBgn0013765.html) comes from in Chado.  This doc explicitly 
states what the SQL used to extract that information needs to be.  There isn't a one to one 
correspondence between the mapping tables and Chado modules because a gene report pulls data from 
multiple modules.

I put up a rough draft of the FlyBase Chado page (http://gmod.org/wiki/index.php/FlyBase_Chado) 
along with a rough approximation of what the field mapping docs will look like 
(http://gmod.org/wiki/index.php/FlyBase_Gene_Report).  What I would like to keep doing is setup a 
new page for each FlyBase data class that has a mapping table.  I tried putting them all into one 
page but I started to get warning messages about editing large pages from wikimedia.

I asked the Harvard dev folks about additional Chado module documentation required in addition to 
what is already provided on the GMOD pages for and they didn't seem to think that they had anything 
to add.  Unless they change their mind, or unless someone convinces them otherwise, I don't think 
the FlyBase module specific pages will be required.

What do you think?

Josh

Dave Clements wrote:
> Hi Josh,
> 
> It's great to hear that this is going on and thanks for thinking of us.
> 
> I have a suggested plan.  Please let me know what you think of it.
> 
> New Pages:
> 
>     * "FlyBase Chado" Introductory page that describes what the rest of
>       the FlyBase chado doc, and use of Chado at flybase.
>     * "FlyBase Chado - Audit Module" Doc on audit module tables.
>     * "FlyBase Chado - Companalysis Module" Doc on comp analysis modules
>     * etc.
> 
> 
> New Page Content:
> 
>     * In the newly generated pages, it would be nice to have separate
>       sections for each table.  This generates HTML anchors which other
>       pages can then point to.
>     * Fomat any wiki tables with class="wikitable" to make it look
>       reasonable.  Or, come up with a flybase/chado specific CSS class,
>       send it to me, and I'll add it to MediaWiki:Common.css.
>     * For every module include a link to the equivalent generic module
>       page.  For example, on "FlyBase Chado - Audit Module" include a
>       link to "Chado Audit Module".
>     * For every table include a link to the equivalent generic table
>       doc.  Let's assume that the section names will retain the same
>       format, e.g., "Table: analysis"
>     * Put a "[[Category:Chado FlyBase]]" tag on each page.  We'll make
>       that a subcategory of both Chado and FlyBase.
> 
> 
> Existing Page Content:
> 
>     * The next time we regenerate the chado module documentation we'll
>       modify each module page to include a link to the equivalent
>       FlyBase module page.  We'll also modify each table description to
>       include a link to the equivalent FlyBase table section.
> 
> Please let me know what you think.
> 
> Again, thanks for doing this,
> 
> Dave C
> 
> 
> 
> On Tue, Jun 3, 2008 at 3:39 PM, Josh Goodman <jogoodma at indiana.edu 
> <mailto:jogoodma at indiana.edu>> wrote:
> 
> 
>     Hello again,
> 
>     FlyBase is currently in the midst of a doc-a-thon this week to get
>     as much of our long overdue documentation written as possible.  One
>     of the things that is being documented is how a field in a FlyBase
>     report corresponds to Chado.  What we basically have is a simple 2
>     column table with the field name in one column and the SQL used to
>     extract that field in the other.  What I'm working on is building an
>     automated workflow that will take this internal doc and turn it into
>     a GMOD wiki compatible file that can be uploaded for public viewing
>     on a regular basis.  Which leads me to my question, do you have any
>     ideas or preferences for where this information should live on the
>     GMOD site?
> 
>     Cheers,
>     Josh
> 
>