CMAP schema

[Miskell, Craig]

> -----Original Message-----
> From: Ken Youens-Clark [mailto:kclark at cshl.org] 
> Sent: Tuesday, 20 July 2004 3:37 a.m.

> On Jul 18, 2004, at 7:01 PM, Miskell, Craig wrote:
> 
> > However, marker_sorghum *does* appear to be used 
> (marker_view.cgi), and
> > try as I might, I can't find any hint of a schema anywhere 
> on the web.
> > It's definitely not in the cmap sql.  Can someone help me 
> out here, or
> > tell me that I don't actually need it?
> 
> Craig,
> 
> Sorry for your troubles setting up Gramene.  It can be quite a chore 
> given all the pieces and how they fit together.  You are correct that 
> the "CMAP_*" tables listed  above are not used and should not 
> have been 
> included (they look to be some sort of working tables that didn't get 
> deleted).  The "MARKER_SORGHUM" table is used by that version of 
> "marker_view.cgi" script, and here is the CREATE statement for it:
> 
> CREATE TABLE marker_sorghum
> (     marker_id                       NUMBER   (11)                   
> DEFAULT '0'  NOT NULL
>    , name                            VARCHAR2 (30)                   
> DEFAULT ''
>    , map_name                        VARCHAR2 (30)                   
> DEFAULT ''
>    , start_position                  NUMBER   (12,2)                 
> DEFAULT '0'
>    , bin1                            VARCHAR2 (30)                   
> DEFAULT ''
>    , bin2                            VARCHAR2 (30)                   
> DEFAULT ''
>    , restriction_enzyme              VARCHAR2 (30)                   
> DEFAULT ''   , short_name                      VARCHAR2 (30)  
>           
>         DEFAULT ''
>    , ssr_type_and_size               VARCHAR2 (30)                   
> DEFAULT ''   , species                         VARCHAR2 (30)  
>           
>         DEFAULT ''
>    , loci_detected_by_probe          NUMBER   (11)                   
> DEFAULT '0'
>    , dominant_type                   VARCHAR2 (30)                   
> DEFAULT ''
>    , locus_for_multi_locus_probes    VARCHAR2 (30)                   
> DEFAULT ''
>    , locus_name                      VARCHAR2 (50)                   
> DEFAULT ''
>    , duplicate_genetic_probe         VARCHAR2 (30)                   
> DEFAULT ''
>    , void_notes                      VARCHAR2 (30)                   
> DEFAULT ''
>    , sequence_source                 VARCHAR2 (90)                   
> DEFAULT ''
>    , genbank_acc                     VARCHAR2 (30)                   
> DEFAULT ''
>    , additional_genbank_acc          VARCHAR2 (30)                   
> DEFAULT ''
>    , overgo1                         VARCHAR2 (30)                   
> DEFAULT ''
>    , overgo2                         VARCHAR2 (30)                   
> DEFAULT ''
> );
> 
> All the "MARKER_*" tables in the latest release have been 
> removed from 
> the CMap schema as they are not part of the CMap application -- they 
> were simply put into the CMap schema for Gramene as they were 
> somewhat 
> related.  They've since been placed into their own space to reduce 
> confusion about what to release.
Thanks for this, and your other reply about cmap_species.  The data
import is proceeding well now.

BTW, I've had a few other problems along the way that I was able to
solve on my own (e.g. constraint naming conflicts, triggers needing to
be added to importTsvData.pl).  I figure I should share the fixes - is
this mailing list the right place, or is there someone who handles that
sort of thing specifically?

Thanks,
Craig
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