WBGene information and status pipeline

From WormBaseWiki
Jump to navigationJump to search

Table Summarizing Current/Future Postgres Population

AceDB tag Postgres table Current - Nameserver nightly dump Current - WS bimonthly release Future - Geneace nightly dump Future - WS bimonthly release Use - Paper or meeting abstract gene connection Use - OA data type curation Use - Dumping scripts -- could be wrong, but I don't think any gin_ tables are used in dumping scripts since we store WBGene IDs. except maybe gin_dead if people want those suppressed or to have some kind of error message or to map to Historical_gene or something like that) Use - Protein2GO data conversion Comment
WBGene identifier gin_wbgene Yes Yes Yes Yes Yes
CGC_name gin_locus Yes If it has this tag, gene is considered good Yes Yes Yes No
Other_name gin_synonyms No Yes Yes No Yes Yes No
Sequence_name gin_sequence (double check this -- no, it's gin_seqname) Yes No Yes Yes Yes No
Public_name gin_wbgene Yes (but only when no CGC_name or Sequence_name) If it has this tag, gene is considered good Don't need (Public_name also in Other_name - confirm this is always the case) Not if also in Other_name Not if also in Other_name Not if also in Other_name No I think we can now ignore the Public_name tag as long as there's always an Other_name value as well -- so if there is no Other_name then we'd look at Public_name ? looking at the script, we're not doing anything with this value)
Molecular_name gin_molname No Yes No Yes Yes No Maybe
Status gin_dead Yes only if value is dead Yes Yes Yes Yes Yes
Merged_into gin_history, gin_dead (confirm -- gin_dead, there is no gin_history table) No Yes Yes No Historical_gene tag?
Split_into gin_history (gin_dead, there is no gin_history table) No Yes Yes No Historical_gene tag?
Corresponding_transcript gin_sequence No Yes No Yes Confirm
Corresponding_CDS gin_sequence + gin_seqprot No Yes No Yes Confirm
Corresponding_protein gin_protein, gin_seqprotein (Need to check about this. -- it's gin_seqprot) No Yes No Yes Confirm Yes, but we'll need isoform data in WB
Species used in gin_dead only if value matches ending in elegans This could perhaps be used to populate a future species tag for papers, but this is not an immediate need. Other use cases?
Version_change No Yes, to make sure we don't attach GO annotations to pseudogenes. One use case would be to know when genes change class, e.g. CDS ->Pseudogene. We may not need to actually store this in postgres, though.

Current Scripts:

  1. /home/acedb/cron/populate_gin_locus.pl
  2. /home/acedb/cron/populate_gin.pl


New Scripts: