Difference between revisions of "WBGene information and status pipeline"
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# /home/acedb/cron/populate_gin_locus.pl | # /home/acedb/cron/populate_gin_locus.pl | ||
# /home/acedb/cron/populate_gin.pl | # /home/acedb/cron/populate_gin.pl | ||
− | '''New Scripts:''' | + | ='''New Scripts:'''= |
Revision as of 17:01, 20 September 2013
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 | Use - Protein2GO data conversion | Comment |
---|---|---|---|---|---|---|---|---|---|---|
WBGene identifier | gin_wbgene | Yes | Yes | Yes | Yes | Yes | ||||
CGC_name | gin_locus | Yes | Yes | Yes | Yes | No | ||||
Other_name | gin_synonyms | No | Yes | Yes | No | Yes | Yes | No | ||
Sequence_name | gin_sequence (double check this) | Yes | Yes | Yes | Yes | No | ||||
Public_name | gin_wbgene | Yes (but only when no CGC_name or Sequence_name) | 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 | ||
Molecular_name | gin_molname | No | Yes | No | Yes | Yes | No | Maybe | ||
Status | gin_dead | Yes | Yes | Yes | Yes | Yes | Yes | |||
Merged_into | gin_history, gin_dead (confirm) | No | Yes | Yes | No | Historical_gene tag? | ||||
Split_into | gin_history | No | Yes | Yes | No | Historical_gene tag? | ||||
Corresponding_transcript | gin_sequence | No | Yes | No | Yes | Confirm | ||||
Corresponding_CDS | gin_sequence | No | Yes | No | Yes | Confirm | ||||
Corresponding_protein | gin_protein, gin_seqprotein (Need to check about this.) | No | Yes | No | Yes | Confirm | Yes, but we'll need isoform data in WB | |||
Species | 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 | 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:
- /home/acedb/cron/populate_gin_locus.pl
- /home/acedb/cron/populate_gin.pl