Specifications for WB gpi file
These specifications are based on the documentation on the GO wiki:
We will need to create a tab-delimited file with each WormBase release using the information in AceDB and 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
(Unfortunately there is no one AceDB object or file that has all of the information we need.)
Output will be sorted according to ascending WBGene ID and will contain a two-line header:
!gpi-version: 1.1
!namespace: WB
For CCC curation form:
1) For each gene name identified in a Textpresso sentence, we will look in Column 2 and Column 4 of gpi file for an exact match.
2) The form will then display for each match, in the left-most box where gene name information is displayed, the gene name mapped to the parent object id in Column 7 and the UniProtKB: ID in Column 8, e.g. ace-1:WB:WBGene00000035:UniProtKB:P38433. -- We're making these mappings static at the moment we get the sentence from textpresso, dealing with changing mappings between gene names and DBIDs or UniProt IDs is beyond the scope of what we want to deal with. The sentence can get re-textpressoed in the future with a then-current mapping and re-curated (K&J) Always show all sentences from textpresso even if no genes map to a DBID and/nor a UniProt ID, if that means there are no genes at all in the gene select box, or there's curation to a gene not in the list, then add a comment to the sentence in curation, and add it to ptgo directly. (K&J)
3) Note that the xrefs file is not sorted in order of WBGene ID, but the gpi file should be.
4) Where it is stated that a column can have one or greater values, e.g. 'with', DB_Object_Synonym(s), DB_Xref(s), the values should be given as a pipe-separated list.
From Table Maker:
Col 1: Class Gene
Col 2: Status
Col 3: CGC_name
Col 4: Sequence_name
Col 5: Other_name
Col 6: Corresponding_pseudogene
| column | name | required? | cardinality | GAF column | Example for UniProt | Example for WormBase | Tag in AceDB ?Gene model | Column in xrefs file | Value if not in AceDB ?Gene model or xrefs file |
|---|---|---|---|---|---|---|---|---|---|
| 01 | DB_Object_ID | required | 1 | 2/17 | Q4VCS5-1 | WBGene00000035 | WBGene ID | n/a | n/a |
| 02 | DB_Object_Symbol | required | 1 | 3 | AMOT | ace-1 | n/a | CGC_name, if no CGC_name then Sequence_name | n/a |
| 03 | DB_Object_Name | optional | 0 or 1 | 10 | Angiomotin | n/a | n/a | n/a | n/a |
| 04 | DB_Object_Synonym(s) | optional | 0 or greater | 11 | KIAA1071|AMOT | ACE1 | If CGC_name, then Sequence_name AND Other_name; If no CGC_name, but Sequence_name, then Other_name; for all, check Column 4 of xrefs.txt, strip number after second '.' and add resulting unique values; for all check Column 5 of xrefs.txt, add unique values prefaced with 'WP:' | n/a | n/a |
| 05 | DB_Object_Type | required | 1 | 12 | protein | gene | n/a | n/a | gene |
| 06 | Taxon | required | 1 | 13 | taxon:9606 | taxon:6239 | n/a | n/a | taxon:6239 |
| 07 | Parent_Object_ID | optional | 0 or 1 | - | UniProtKB:Q4VCS5 | WB:WBGene00000035 | n/a | WBGene ID prefaced with 'WB:' | n/a |
| 08 | DB_Xref(s) | optional | 0 or greater | - | - | UniProtKB:P38433 | n/a | for each WBGene, add unique values from xrefs.txt as follows: Column 7 prefaced with 'CCD:' and Column 8 prefaced with "UniProtKB:" | n/a |
| 09 | Gene_Product_Properties | optional | 0 or greater | - | See Note 4 below | n/a | n/a | n/a | n/a |
