Specifications for WB gpi file

gpi File

We will need to create a tab-delimited gpi file with each WormBase release.

Specifications Source

These specifications are based, in part, on the documentation on the GOC's go-annotation github repository:

https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-1_2.md

and also on the content of files submitted here:

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/gpad-gpi/submission/

File Name

wb_nematode.gpi.gz (all nematode species in WB)

Header

Header content:

!gpi-version: 1.2

!Date: 2016-10-06

!Project_name: WormBase

!Release: WS256

!Contact_email: help@wormbase.org

!URL: http://www.wormbase.org

Field Values

column	name	required?	cardinality	GAF column	Example for WormBase (Gene OR Transcript OR Protein)	Tag in AceDB model	Comment
01	DB	required	1	1	WB	n/a	n/a
02	DB_Object_ID	required	1	2/17	WBGene00006796 OR F28F12.2a OR WP:CE21219	Gene OR Transcript OR Protein ID	n/a
03	DB_Object_Symbol	required	1	3	unc-62 OR unc-62 OR UNC-62	Public_name in ?Gene model or capitalized version of Public_name in ?Gene model	n/a
04	DB_Object_Name	optional	0 or 1	10	n/a	n/a	n/a
05	DB_Object_Synonym	optional	0 or greater	11	Other_name in ?Gene model or capitalized version of Other_name in ?Gene model	ceh-25 OR ceh-25 OR CEH-25 (showing one, but we would include all Other_name entries)	This is a little different from what we currently put in the GAF, but I think the slightly different purpose of this file (Noctua, GO website searches, text mining) makes it beneficial to include the Other_name entries. When there are multiple entries, they should be pipe-separated.
06	DB_Object_Type	required	1	12	gene OR transcript OR protein	See Comment	For transcript, could we use the value in the Method tag? Do all of the values in this tag correspond to SO terms? It seems the CV of SO terms would be good to use here, if possible.
07	Taxon	required	1	13	taxon:6239	n/a	NCBI taxonomy ID for corresponding species of entity in Column 2.
08	Parent_Object_ID	optional	0 or 1	n/a	WB:WBGene00006796	Gene ID	The WB gene ID will be the parent ID for each transcript and protein entry. For gene entries, this field will be blank.
09	DB_Xref(s)	optional	0 or greater	n/a	UniProtKB:Q9N5D6 (for gene) OR UniProtKB:Q9N5D6-1 (for protein)	For gene and transcript entries, see comment.	WBGene entries will contain a DB_Xref to the UniProtKB Reference Proteome accession, where available. The Reference Proteome accessions are available in this file: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/WORM/goa_worm.gpi.gz. Unfortunately, the goa_worm file does not currently xref to WBGene IDs. Transcript entries will contain a DB_xref to RNAcentral accessions, where available. Protein entries will contain a DB_xref to the UniProtKB accession; this accession will be an isoform accession of a reviewed Swiss-Prot entry or a TrEMBL accession (e.g., Q9N5D6-1 or A0A0K3ASC5).
10	Gene_Product_Properties	optional	0 or greater	n/a	n/a	n/a	Right now, I can't think of anything we'd need to put in this field, but that could change in future iterations.

Example Entries

DB	DB_Object_ID	DB_Object_Symbol	DB_Object_Name	DB_Object_Synonym	DB_Object_Type	Taxon	Parent_Object_ID	DB_Xref(s)	Gene_Product_Properties
WB	WBGene00006796	unc-62		let-318 pipe nob-5 pipe ceh-25 pipe CELE_T28F12.2	gene	taxon:6239		UniProtKB:Q9N5D6
WB	T28F12.2a	unc-62		let-318 pipe nob-5 pipe ceh-25 pipe CELE_T28F12.2	coding_transcript	taxon:6239	WB:WBGene00006796
WB	WP:CE21219	UNC-62		LET-318 pipe NOB-5 pipe CEH-25 pipe CELE_T28F12.2	protein	taxon:6239	WB:WBGene00006796	UniProtKB:Q9N5D6-1
WB	WP:CE50189	UNC-62		LET-318 pipe NOB-5 pipe CEH-25 pipe CELE_T28F12.2	protein	taxon:6239	WB:WBGene00006796	UniProtKB:A0A0K3ASC5
WB	WBGene00000829	ctb-1		CYTB	gene	taxon:6239		UniProtKB:P24890
WB	MTCE.21	ctb-1		CYTB	coding_transcript	taxon:6239	WB:WBGene00000829
WB	WP:CE35348	CTB-1		CYTB	protein	taxon:6239	WB:WBGene00000829
WB	WBGene00002993	lin-4		CELE_F59G1.6	gene	taxon:6239
WB	F59G1.6	lin-4		CELE_F59G1.6	pre_miRNA	taxon:6239	WB:WBGene00002993	RNAcentral:URS00001E2999
WB	F59G1.6a	lin-4		CELE_F59G1.6	miRNA	taxon:6239	WB:WBGene00002993	RNAcentral:URS0000278C03