Difference between revisions of "Specifications for WB gpi file"
From WormBaseWiki
Jump to navigationJump to search| Line 16: | Line 16: | ||
! Example for WormBase | ! Example for WormBase | ||
! Tag in AceDB model | ! Tag in AceDB model | ||
| + | ! Value for file if not an AceDB tag | ||
|- | |- | ||
| Line 26: | Line 27: | ||
| 04 || DB_Object_Synonym(s) || optional || 0 or greater || 11 || AMOT_HUMAN|KIAA1071|AMOT || ACE1 || Other_name in ?Gene model | | 04 || DB_Object_Synonym(s) || optional || 0 or greater || 11 || AMOT_HUMAN|KIAA1071|AMOT || ACE1 || Other_name in ?Gene model | ||
|- | |- | ||
| − | | 05 || DB_Object_Type || required || 1 || 12 || protein || gene | + | | 05 || DB_Object_Type || required || 1 || 12 || protein || gene || gene |
|- | |- | ||
| − | | 06 || Taxon || required || 1 || 13 || taxon:9606 || taxon:6239 | + | | 06 || Taxon || required || 1 || 13 || taxon:9606 || taxon:6239 ||Taxon:6239 |
|- | |- | ||
| − | | 07 || Parent_Object_ID || optional || 0 or 1 || - || UniProtKB:Q4VCS5 || WB:WBGene00000035 | + | | 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 | + | | 08 || DB_Xref(s) || optional || 0 or greater || - || - || UniProtKB:P38433 || |
|- | |- | ||
| 09 || Gene_Product_Properties || optional || 0 or greater || - || See Note 4 below || | | 09 || Gene_Product_Properties || optional || 0 or greater || - || See Note 4 below || | ||
|- | |- | ||
|} | |} | ||
Revision as of 18:40, 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 | Tag in AceDB model | Value for file if not an AceDB tag |
|---|---|---|---|---|---|---|---|---|
| 01 | DB_Object_ID | required | 1 | 2/17 | Q4VCS5-1 | WBGene00000035 | Gene ID in ?Gene model | |
| 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 | gene | |
| 06 | Taxon | required | 1 | 13 | taxon:9606 | taxon:6239 | 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 |
