Revision as of 15:20, 6 October 2016

gpi File

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

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

and also on the content of files submitted here:

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

Header content:

!gpi-version: 1.2

!Project_name: WormBase

!!WB_release: WS256

!Contact Email: help@wormbase.org

!Date: 20161006

column	name	required?	cardinality	GAF column	Example for WormBase (Gene OR Transcript OR Protein)	Tag in AceDB model
01	DB	required	1	1	WB	n/a
02	DB_Object_ID	required	1	2/17	WBGene00006605 OR C15F1.3a OR WP:CE23546	Gene OR Transcript OR Protein ID
03	DB_Object_Symbol	required	1	3	tra-2 OR tra-2 OR TRA-2	Public_name in ?Gene model or capitalized version of Public_name in ?Gene model
04	DB_Object_Name	optional	0 or 1	10	n/a	n/a
05	DB_Object_Synonym(s)	optional	0 or greater	11	Other_name in ?Gene model or capitalized version of Other_name in ?Gene model
06	DB_Object_Type	required	1	12	gene	n/a	n/a	gene
07	Taxon	required	1	13	taxon:6239	n/a	n/a	taxon:6239
08	Parent_Object_ID	optional	0 or 1	-	WB:WBGene00000035	WBGene ID from Column 1 of TM output prefaced with 'WB:'	n/a	n/a
09	DB_Xref(s)	optional	0 or greater	-	-	UniProtKB:P38433	n/a	for all, if value exists, add unique values from xrefs.txt as follows: Column 7 of xrefs.txt prefaced with 'CCD:' and Column 8 of xrefs.txt prefaced with "UniProtKB:"; if no values, then skip	n/a
10	Gene_Product_Properties	optional	0 or greater	-	See Note 4 below	n/a	n/a	n/a	n/a

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

The input file is a comma-separated text file converted from an Excel spreadsheet sent to us by MGI.

The file is called: mgi_gpi_input.txt (the file has the carriage return symbols - need to remove?)

and is located on mangolassi here: /home/acedb/kimberly/ccc/ccc_gpi/mgi/input_files

There are duplicate entries in the mgi_gpi_input file that we will need to remove before we create the gpi file.

column	name	required?	cardinality	GAF column	Example for MGI	Column in mgi_gpi_input	Value if not in mgi_gpi_input (i.e. fixed value)
01	DB_Object_ID	required	1	2/17	1861229	Column 1, stripped of 'MGI:' prefix	n/a
02	DB_Object_Symbol	required	1	3	Adam21	Column 2, no changes	n/a
03	DB_Object_Name	optional	0 or 1	10	a disintegrin and metallopeptidase domain 21	Column 4, no changes	n/a
04	DB_Object_Synonym(s)	optional	0 or greater	11	n/a	n/a	n/a
05	DB_Object_Type	required	1	12	n/a	n/a	gene
06	Taxon	required	1	13	n/a	n/a	taxon:10090
07	Parent_Object_ID	optional	0 or 1	-	MGI:1861229	Column 1, no changes	n/a
08	DB_Xref(s)	optional	0 or greater	-	UniProtKB:Q9JI76	Column 3, add 'UniProtKB:' as prefix (note there are some entries with no value in Column 3)	n/a
09	Gene_Product_Properties	optional	0 or greater	-	n/a	n/a	n/a

@@ Line 55: / Line 55: @@
 | 04 || DB_Object_Name || optional || 0 or 1 || 10 || n/a || n/a
 |-
-| 05 || DB_Object_Synonym(s) || optional || 0 or greater || 11 || If CGC_name exists, then Sequence_name, Column 3 of TM output, AND Other_name, Column 4 of TM output; If no CGC_name, but Sequence_name, then Other_name, Column 4 of TM output || For all, also check Column 4 of xrefs.txt, if entry contains a number AND lower case letter after the first '.', strip number after second '.' if the latter exists, and add all resulting unique values (if no number AND lower case letter after the first '.', then we can skip this column in the xrefs file); for all, also check Column 5 of xrefs.txt, if value exists, add unique values prefaced with 'WP:'; if no values, then skip || n/a
+| 05 || DB_Object_Synonym(s) || optional || 0 or greater || 11 || Other_name in ?Gene model or capitalized version of Other_name in ?Gene model
 |-
 | 06 || DB_Object_Type || required || 1 || 12 || gene || n/a || n/a || gene