Storing Interspecific maps in Chado

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Storing Interspecific maps in Chado

Cannon, Ethalinda K [COM S]
A proposal for storing interspecific genetic maps in Chado:

1. Create an organism record to represent multiple or unknown species, using the "spp." abbreviation. For example, "Arachis spp." represents multiple or unknown Arachis (peanut) species.

2. Use the stock table to represent the interspecific mapping population and parents (which may themselves be interspecific) and link the organism_id field to the "spp." record. Use a new stock_organism table to link the interspecific stock record to two or more species, represented by organism records.

CREATE TABLE stock_organism (
  stock_organism_id serial NOT NULL,
    PRIMARY KEY (feature_stock_id),
  stock_id INT NOT NULL,
    FOREIGN KEY (stock_id) REFERENCES chado.stock (stock_id) ON DELETE CASCADE INITIALLY DEFERRED,
  organism_id INT NOT NULL,
    FOREIGN KEY (feature_id) REFERENCES chado.organism (feature_id) on DELETE CASCADE INITIALLY DEFERRED,
  rank INT NOT NULL DEFAULT 0,
  CONSTRAINT stock_organism_c1 UNIQUE (stock_id, organism_id, type_id, rank)  
);

3. Attach the featuremap to the stock via the featuremap_stock table (included in Chado 1.3)

CREATE TABLE chado.featuremap_stock (
    featuremap_stock_id serial not null,
      primary key (featuremap_stock_id),
    featuremap_id int not null,
      foreign key (featuremap_id) references chado.featuremap (featuremap_id) on delete cascade INITIALLY DEFERRED,
    stock_id int not null,
      foreign key (stock_id) references chado.stock (stock_id)  on delete cascade INITIALLY DEFERRED
);

4. For markers, the species of origin (if known) or the "spp." record id is provided in the feature.organism_id field and the species in which that marker is mapped can be found via
featurepos - featuremap - featuremap_stock - stock.

I am hesitant to propose that this be added to chado 1.3 unless there is sufficient need and others who have to deal with interspecific maps are okay with this approach.

Ethy



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