Difference between revisions of "Specifications for WB gpi file"

Revision as of 18:57, 20 March 2013

These specifications are based on the documentation on the GO wiki:

We will need to create a new file with each WormBase release using the xrefs file generated for C. elegans that is available on the ftp site:

The file is named according to the release, e.g., c_elegans.WS236.xrefs.txt.gz

Output will be sorted according to ascending WBGene ID.

column	name	required?	cardinality	GAF column	Example for UniProt	Example for WormBase	Column in xrefs file	Value if not in xrefs file
01	DB_Object_ID	required	1	2/17	Q4VCS5-1	WBGene00000035	2	n/a
02	DB_Object_Symbol	required	1	3	AMOT	ace-1	3, if no value in 3, then 1
03	DB_Object_Name	optional	0 or 1	10	Angiomotin	n/a	n/a
04	DB_Object_Synonym(s)	optional	0 or greater	11	KIAA1071\|AMOT	ACE1	Other_name in ?Gene model
05	DB_Object_Type	required	1	12	protein	gene	n/a	gene
06	Taxon	required	1	13	taxon:9606	taxon:6239	n/a	taxon:6239
07	Parent_Object_ID	optional	0 or 1	-	UniProtKB:Q4VCS5	WB:WBGene00000035	Gene ID in ?Gene model prefaced with WB:
08	DB_Xref(s)	optional	0 or greater	-	-	UniProtKB:P38433
09	Gene_Product_Properties	optional	0 or greater	-	See Note 4 below

@@ Line 27: / Line 27: @@
 | 01 || DB_Object_ID || required || 1 || 2/17 || Q4VCS5-1 || WBGene00000035 || 2 || n/a
 |-
-| 02 || DB_Object_Symbol || required || 1 || 3 || AMOT || ace-1 ||
+| 02 || DB_Object_Symbol || required || 1 || 3 || AMOT || ace-1 || 3, if no value in 3, then 1
 |-
 | 03 || DB_Object_Name || optional || 0 or 1 || 10 || Angiomotin || n/a || n/a