Specifications for WB gpi file

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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:


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)

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 CGC_name; if no CGC_name then Sequence_name n/a 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 Other_name; if value in CGC_name, then also Sequence_name; also take Molecular_name values, but first strip WP: prefix and any numbers after second '.' in transcript names to only take unique CE and transcript names (e.g., WP:CE21219 becomes CE21219 and T28F12.2a.1 becomes T28F12.2a) 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 WBGene ID prefaced with WB: n/a n/a
08 DB_Xref(s) optional 0 or greater - - UniProtKB:P38433 n/a 8, prefaced with UniProtKB: Note: there may be several values per given gene ID n/a
09 Gene_Product_Properties optional 0 or greater - See Note 4 below n/a n/a n/a n/a