Difference between revisions of "Specifications for WB gpi file"
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http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format#Final_format_.2809_Jan_2013.29_2 | http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format#Final_format_.2809_Jan_2013.29_2 | ||
| − | We will need to create a new file with each WormBase release. | + | 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: |
| + | |||
| + | ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS236/species/c_elegans/ | ||
| + | |||
| + | The file is named according to the release, e.g., c_elegans.WS236.xrefs.txt.gz | ||
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| − | | 01 || DB_Object_ID || required || 1 || 2/17 || Q4VCS5-1 || WBGene00000035 || | + | | 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 || |
|- | |- | ||
| 03 || DB_Object_Name || optional || 0 or 1 || 10 || Angiomotin || n/a || n/a | | 03 || DB_Object_Name || optional || 0 or 1 || 10 || Angiomotin || n/a || n/a | ||
Revision as of 18:52, 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:
ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS236/species/c_elegans/
The file is named according to the release, e.g., c_elegans.WS236.xrefs.txt.gz
| 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 | ||
| 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 |
