More cmap schema

[Ken Youens-Clark]

On Jul 18, 2004, at 7:06 PM, Miskell, Craig wrote:

> I just poked a bit more, and discovered that the cmap_species data has 
> 6
> columns, but my schema only has 5.  Schema:
>
> CREATE TABLE cmap_species (
>   species_id number(11) DEFAULT '0' NOT NULL,
>   accession_id varchar2(20) DEFAULT '' NOT NULL,
>   common_name varchar2(64) DEFAULT '' NOT NULL,
>   full_name varchar2(64) DEFAULT '' NOT NULL,
>   display_order number(11) DEFAULT '1' NOT NULL,
>   CONSTRAINT pk_cmap_species PRIMARY KEY (species_id)
> );
>
> Data:
> 1       rice    Rice    Oryza sativa    1       4530
> 6       wheat   Wheat   Triticum aestivum       3       4565
> 2       barley  Barley  Hordeum vulgare 3       4513
> 3       oat     Oat     Avena sp.       3       50455
> 4       maize   Maize   Zea mays        4       4577
> 5       sorghum Sorghum Sorghum bicolor 4       4558
> 11      wildrice        Wild rice       Zizania palustris       2
> 103762
> 12      rye     Rye     Secale cereale  3
>
> I'm definitely using cmap 0.11, which the gramene installation docs
> indicate is correct for rel 13.0.  It looks like I've missed something
> critical - any suggestions?

That last bit of data is a deprecated column called "ncbi_taxon_id."  
Here is the CREATE statement for that version of the table:

CREATE TABLE cmap_species (
   species_id number(11) DEFAULT '0' NOT NULL,
   accession_id varchar2(20) DEFAULT '' NOT NULL,
   common_name varchar2(64) DEFAULT '' NOT NULL,
   full_name varchar2(64) DEFAULT '' NOT NULL,
   display_order number(11) DEFAULT '1' NOT NULL,
   ncbi_taxon_id number(11) DEFAULT NULL,
   CONSTRAINT pk_cmap_species PRIMARY KEY (species_id)
);

CREATE INDEX acc_id_species_id on cmap_species (accession_id, 
species_id);

This field was removed after adding a generic attribute system to CMap 
(where you can attach any key/value pair of data to any object in the 
database).

ky