Difference between revisions of "Specifications for WB gpi file"

Revision as of 18:49, 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.

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	Column in xrefs file
02	DB_Object_Symbol	required	1	3	AMOT	ace-1	CGC_name in ?Gene model; if no CGC_name, then Sequence_name in ?Gene_model
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 15: / Line 15: @@
 ! Example for UniProt
 ! Example for WormBase
-! Tag in AceDB model
+! Column in xrefs file
-! Value for file if not an AceDB tag
+! Value if not in xrefs file
 |-
-| 01 || DB_Object_ID || required || 1 || 2/17 || Q4VCS5-1 || WBGene00000035 ||Gene ID in ?Gene model
+| 01 || DB_Object_ID || required || 1 || 2/17 || Q4VCS5-1 || WBGene00000035 ||Column in xrefs file
 |-
 | 02 || DB_Object_Symbol || required || 1 || 3 || AMOT || ace-1 || CGC_name in ?Gene model; if no CGC_name, then Sequence_name in ?Gene_model