WBGene information and status pipeline

Table Summarizing Current/Future Postgres Population

AceDB tag	Postgres table	Current - Nameserver nightly dump	Current - WS bimonthly release	Future - Nameserver nightly dump	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	Use - GSA Markup	Comment
WBGene identifier	gin_wbgene	Yes		Yes (First line in each entry)			Yes	Yes		Yes
CGC_name	gin_locus	Yes (CGC)	If it has this tag, gene is considered good (What does 'good' mean?)	Yes (CGC)	No	No	Yes		No
Other_name	gin_synonyms	Yes (checking for different CGC name - see lines 132-137 in script)	Yes	Yes (checking for different CGC name)	Yes	No	Yes		No
Sequence_name	gin_seqname	Yes (Sequence)	No	Yes (Sequence)	No	No	Yes		No
Status	gin_dead	Yes (0)	only if value is dead and species ~ elegans$	Yes (0)	only if value is dead; populate with Merged_into and Split_into values	No	Yes	Yes	Yes
Merged_into	gin_dead	No	Yes	No	Yes	No		Historical_gene tag uses this when dumping files
Split_into	gin_dead	No	Yes	No	Yes	No
Corresponding_transcript	gin_sequence	No	Yes	No	No	Yes
Corresponding_CDS	gin_sequence + gin_seqprot	No	Yes	No	No	Yes
Corresponding_protein	gin_protein, gin_seqprot	No	Yes	No	No	Yes			Yes, but we'll need isoform data in WB
Molecular_name	gin_molname	No	Yes	No	No	Yes	No		Maybe
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			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.
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)	No	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)

Previous (pre-nameserver move) Scripts:

1. /home/acedb/cron/populate_gin_locus.pl - updates information from nameserver nightly dumps
2. /home/acedb/cron/populate_gin.pl - updates information from WS releases

New (post-nameserver moves) Scripts:

1. /home/postgres/work/pgpopulation/obo_oa_ontologies/ws_updates/populate_pg_from_ws.pl

Some Relevant Postgres Queries:

SELECT * FROM gin_dead WHERE gin_dead ~ 'merged' AND gin_dead ~ 'split';

SELECT * FROM gin_dead WHERE gin_dead ~ 'split';

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