Difference between revisions of "Specifications for WB gpi file"

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| 04 || DB_Object_Name || optional || 0 or 1 || 10 || n/a || n/a || n/a || n/a
 
| 04 || DB_Object_Name || optional || 0 or 1 || 10 || n/a || n/a || n/a || n/a
 
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| 05 || DB_Object_Synonym(s) || 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) || n/a || 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 searches to include the Other_name entries.
+
| 05 || DB_Object_Synonym(s) || 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) || n/a || 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.
 
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| 06 || DB_Object_Type || required || 1 || 12 || gene OR transcript OR protein || See Comment || n/a || For transcripts, could we use 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.
 
| 06 || DB_Object_Type || required || 1 || 12 || gene OR transcript OR protein || See Comment || n/a || For transcripts, could we use 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.

Revision as of 15:46, 6 October 2016

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

!Project_name: WormBase

!!WB_release: WS256

!Contact Email: help@wormbase.org

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

!Date: 20161006

Field Values

column name required? cardinality GAF column Example for WormBase (Gene OR Transcript OR Protein) Tag in AceDB model Column in UniProtKB Reference Proteome File Comment
01 DB required 1 1 WB n/a 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 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 n/a
04 DB_Object_Name optional 0 or 1 10 n/a n/a 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 ceh-25 OR ceh-25 OR CEH-25 (showing one, but we would include all Other_name entries) n/a 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.
06 DB_Object_Type required 1 12 gene OR transcript OR protein See Comment n/a For transcripts, could we use 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 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

MGI

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

http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format#Final_format_.2809_Jan_2013.29_2

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