Gene - GO Curation Status

Specifications for Gene - GO Curation Status Form

• Specifications for a weekly script to generate a webpage that lists which C. elegans protein-coding genes do not have one or more aspects (BP, MF, CC) of GO curation.

Input Files

• http://snapshot.geneontology.org/annotations/wb.gpad.gz
• ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.PRJNA13758.current_development.gene_product_info.gpi.gz

Output

• A web page that lists genes that do not have annotation for one or more aspects of GO.
• The page will be sectioned according to BP, MF, and CC.
• There would be links at the top of the page to each section (since the page could be long).
• Each section will have two, sortable columns (default sorting would be alphabetically by gene name):
  • The value in gin_locus, or gin_sequence, and the WBGene id
    • mmcm-1 (WBGene00014202)
    • the gene name and id would together link to the corresponding page in WB (https://wormbase.org/species/c_elegans/gene/WBGene00014202)
  • The number of references in postgres that are Type:Journal_article and list that gene in pap_gene
    • 7
    • the number in the reference column would link to a page listing the matching papers that are, in turn, linked to their page in the paper editor
    • this is the same as the results of performing a gene search in the paper editor: SELECT joinkey, pap_gene FROM pap_gene WHERE pap_gene = '00014200'

Script Details

• The script would look at all of the C. elegans genes annotated for a given aspect in the snapshot gpad file and compare that to the list of protein-coding genes in the gpi file.
• Genes that don't have an annotation for either BP, MF, or CC but are in the gpi file would be listed in the section of the page for that aspect.
  • We'll treat each aspect independently, i.e. a gene may have an no BP but an MF, but it would still be listed in the BP section.
  • Since aspect is not captured in the gpad file, we'll need to use the relations listed in column 3 of the gpad
    • BP relations:
      • involved_in
      • acts_upstream_of*
      • acts_upstream_of_or_within*
    • MF relations:
      • enables
      • contributes_to
    • CC relations:
      • part_of
      • colocalizes_with
• For now, we are only interested in protein-coding genes, so in the gpi file we only want to look at genes that have an entry beginning with 'UniProtKB:' in column 8

Future Proofing

• The gpad/gpi file format is likely going to change a bit sometime in the coming year, so we will need to make some modifications to the script.
• There may also be some changes to the CC relations, but that would be reflected in the overall changes to the file.
• It might be nice to include a link-out to a pre-canned TPC search (especially if we could do an aspect-specific search).