GO Database Schema and GOOSE

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

Obsolete terms and their replacements

options

• overload term2term table
• create a new table specific to consider/replaced_by tags
• create a new generic term metadata table

Multi-Species and Multi-Organism interactions

See:

• http://www.geneontology.org/GO.annotation.shtml#manySpp

See also the 'taxon column:

• http://www.geneontology.org/GO.format.annotation.shtml#def

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

Cross-products

'Dynamic' cross-products in annotations: the Properties field

See Annotation_Cross_products

This table has been added to the database:

 --- @@ association_property
 --- (column 16 in the gene-association file) 
 CREATE TABLE association_property (
   	id  	serial PRIMARY KEY,
   --
   	association_id	integer not null,
   	foreign key (association_id) references association(id),
   --
       --- @@ association_property.relationship_type_id
       --- eg part_of
   	relationship_type_id	        integer not null,
   	foreign key (relationship_type_id) references term(id),
   --
       --- @@ association_property.term_id
       --- eg CL:0000017
   	term_id	        integer not null,
   	foreign key (term_id) references term(id)
 );