GO Database Schema and GOOSE: Difference between revisions
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(New page: Documentation on the GO Database can be found here: * http://www.geneontology.org/GO.database.shtml This page is for notice of plans to modify or extend the database == Multi-Species and...) |
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--- association_species_qualifier.species_id should be that of the other organism in the interaction. | --- association_species_qualifier.species_id should be that of the other organism in the interaction. | ||
CREATE TABLE association_qualifier ( | CREATE TABLE association_qualifier ( | ||
id serial PRIMARY KEY, | |||
-- | |||
association_id integer not null, | |||
foreign key (association_id) references association(id), | |||
-- | |||
--- @@ association_species_qualifer.species_id | |||
--- The species of the interacting organism (eg host) | --- The species of the interacting organism (eg host) | ||
--- Example: in cytolysis of cells of another organism (GO:0051715) | --- Example: in cytolysis of cells of another organism (GO:0051715) | ||
--- this would be the species playing the 'other organism' role | --- this would be the species playing the 'other organism' role | ||
species_id integer, | |||
foreign key (species_id) references species(id) | |||
); | ); | ||
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* Sohel/Mary - can you post proposal for dealing with homology in the database | * Sohel/Mary - can you post proposal for dealing with homology in the database | ||
== Cross-products == |
Revision as of 14:12, 21 June 2007
Documentation on the GO Database can be found here:
This page is for notice of plans to modify or extend the database
Multi-Species and Multi-Organism interactions
See:
See also the 'taxon column:
We need to record the second taxon in the schema. This is a current spot for this in gene_product, but it is wrong. It needs to go in as an attribute of association. The load xsl will then need changed to reflect this
Here is the proposed new table:
--- @@ association_species_qualifier --- (see http://www.geneontology.org/GO.annotation.shtml#manySpp) --- (column 13 in gene_association file, ONLY WHEN card>1, this is the next entry) --- to be used only in conjunction with terms that have the term 'interaction between organisms' as an ancestor. --- gene_product.species_id is for the organism type encoding the gene or gene product, --- association_species_qualifier.species_id should be that of the other organism in the interaction. CREATE TABLE association_qualifier ( id serial PRIMARY KEY, -- association_id integer not null, foreign key (association_id) references association(id), -- --- @@ association_species_qualifer.species_id --- The species of the interacting organism (eg host) --- Example: in cytolysis of cells of another organism (GO:0051715) --- this would be the species playing the 'other organism' role species_id integer, foreign key (species_id) references species(id) );
Reference Genomes
- Sohel/Mary - can you post proposal for dealing with homology in the database