Proposed GPI1.2 format

gp_information files (GPI)

N.B. The first line in the gp_information file should be;

!gpi-version: 1.2

Proposed format (March 2014)

column	name	required?	cardinality	GAF column	Example for UniProt	Example for IntAct	Example for MGI Gene	MGI protein	MGI RNA
01	DB	required	1	1	UniProtKB	IntAct	MGI	PR	ENSEMBL
02	DB_Object_ID	required	1	2/17	Q4VCS5-1	EBI-9008420	MGI:96175	Q9Z172-1	ENSMUST00000127454
03	DB_Object_Symbol	required	1	3	AMOT	HBA1:HBB	Hoxa3	mSumo3/iso:m1	ENSMUST00000127454
04	DB_Object_Name	optional	0 or 1	10	Angiomotin	Hemoglobin HbA complex	homeobox A3	small ubiquitin-related modifier 3 isoform m1 (mouse)
05	DB_Object_Synonym(s)	optional	0 or greater	11	KIAA1071|AMOT	HBA1-HBB complex|HBA1-HBB heterotetramer	Mo-10
06	DB_Object_Type	required	1	12	protein	complex	gene	protein	transcript
07	Taxon	required	1	13	9606	9606	taxon:10090	taxon:10090	taxon:10090
08	Parent_Object_ID	optional	0 or 1		UniProtKB:Q4VCS5			MGI:MGI:1336201	MGI:MGI:1098592
09	DB_Xref(s)	optional	0 or greater		UniProtKB:P38433	PR:000025934	UniProtKB:P02831	UniProtKB:Q9Z172-1
010	Gene_Product_Properties	optional	0 or greater		See Note 4 below

Notes

1. Where it is stated that a column can have one or greater values, e.g. 'with', DB_Object_Synonym(s), DB_Xref(s), the values should be given as a pipe-separated list.

2. The DB_Xrefs column will be useful for mapping of MOD-specific identifiers/symbols/synonyms to UniProt accessions to assist MOD curators moving to Protein2GO in searching for familiar IDs/gene names. In the case of IntAct complexe IDs, it will be useful to include PRO IDs as an xref to enable a look-up function in Protein2GO. In the case where the value in column #2 represents a MOD gene identifier, the Xref should correspond to the UniProtKB identifier for the GCRP.

3. Identifiers in the Parent_Object_ID column must have a prefix to avoid confusion in cases where an ID from a different database to the one specified in the header is included

4. The Gene Product Properties column can be filled with a pipe separated list of "property_name = property_value". There will be a fixed vocabulary for the property names and this list can be extended when necessary. Supported properties will include: 'GO annotation complete', "Phenotype annotation complete' (the value for these two properties would be a date), 'Target set' (e.g. Reference Genome, Kidney etc.), 'Database subset' (e.g. Swiss-Prot, TrEMBL), go_annotation_summary (textual summary of annotations for an entity)