CMAP schema

[Ken Youens-Clark]

On Jul 18, 2004, at 7:01 PM, Miskell, Craig wrote:

> 	I'm installing (well, trying to) gramene (rel 13-0).  It's been
> a mission so far, and I've had to munge the SQL and importTsvData.pl
> several times to get past various errors, but I'm now stuck.  The cmap
> data (ftp://ftp.gramene.org/pub/gramene/gramene_database/cmap1.tgz)
> contains 6 tables (all of which contain actual data) for which I cannot
> find a schema, and which weren't in the cmap.create.oracle sql script
> from cmap:
> CMAP_DISTINCT_FEATURE_MVIEW
> CMAP_FEATURE_ALIAS_MVIEW
> CMAP_FEATURE_MVIEW
> CMAP_FNA_MVIEW
> CMAP_MVIEW_6
> MARKER_SORGHUM
>
> A quick grep through the source would imply that the first 5 MVIEW
> tables are not used by Gramene.  Can someone confirm that?
> 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.

ky