WBGene information and status pipeline

Table Summarizing Former and Current Postgres Gene Information (gin_ ) Population

AceDB tag	Postgres table	Old (pre-10/2013) - Nameserver nightly dump	Old (pre-10/2013) - WS bimonthly release	Current - Nameserver nightly dump	Current - Geneace nightly dump	Current - 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 - Textpresso and/or GSA Markup	Comment
WBGene identifier	gin_wbgene	Yes		Yes (First line in each entry)			Yes	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		Yes
Other_name	gin_synonyms	Yes (checking for different CGC name - see lines 132-137 in script)	Yes	Yes (checking for different CGC name)	Yes - add to what is already populated from nightly nameserver	No	Yes		No		Yes
Sequence_name	gin_seqname	Yes (Sequence)	No	Yes (Sequence)	No	No	Yes		No		Yes
Status	gin_dead	Yes (0)	only if value is dead and species ~ elegans$	Yes (0)	only if value is dead in the nameserver nightly; populate with Merged_into and Split_into values	No	Yes	Yes	Yes
Suppressed	gin_dead				If Status from nightly geneace = Suppressed, populate gin_dead with Dead Suppressed (if Status in nightly nameserver is 0 (dead)) or populate gin_dead with Suppressed (if Status in nightly nameserver is 1 (live)). Also add Merged_into and/or Split_into if nightly nameserver Status is 0 (dead).
Merged_into	gin_dead	No	Yes	No	Yes - add only when status is dead from nightly nameserver	No		Historical_gene tag uses this when dumping files
Split_into	gin_dead	No	Yes	No	Yes - add only when status is dead from nightly nameserver	No
Corresponding_transcript	gin_sequence	No	Yes	No	No	Yes					Yes
Corresponding_CDS	gin_sequence + gin_seqprot	No	Yes	No	No	Yes					Yes
Corresponding_protein	gin_protein, gin_seqprot	No	Yes	No	No	Yes			Yes, but we'll need isoform data in WB		Yes
Molecular_name	gin_molname	No	Yes	No	No	Yes	No		Maybe		Yes
Species	gin_species	No	No	No	Yes			Yes - added to display of WBGene info in Term information window of OA	May be used to add species information to automated concise description files and also to add taxon IDs to BioGrid interaction file
Pseudogene status	gin_pseudogene	No	No	No	??
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

How this all works (10/2013 - updated 04/2015)

Location of files:

The nightly nameserver and geneace dumps are on the sanger ftp site:

ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/

There are two json dumps (genes and variations) from the respective nameservers, and six .ace dumps (clones, genes, laboratories, rearrangements, strains, and variations) from geneace.

Note that the gene nameserver and geneace are not synchronized. Some changes are evident in the nightly nameserver dump before they are included in the geneace dump.

For updating from nightly gene nameserver and geneace dumps:

/home/postgres/work/pgpopulation/obo_oa_ontologies/geneace/populate_gin_nightly.pl

Called from:

0 20 * * * /home/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl

Went live on tazendra 2013 10 25.

This script is looking at the genes.json and genes.ace.gz files to update WBGene IDs, CGC names, Sequence names, Synonyms (not from Other_name but from a comparison between the CGC name in the json dump and the existing locus and synonym names in postgres) and the Status.

This script is not species-restricted.

Key features of this script:

• Locus and Synonym Names
  • The script queries postgres for a list of locus names and synonyms and puts these into a hash.
  • New synonym entries are appended. This was done so that we wouldn't lose new synonyms because they were picked up in the nameserver dump (from a changed CGC_name value) but not yet included in the nightly geneace dump (the Other_name value).
  • When a gene is killed and merged into another, synonyms are removed from the Dead gene and added to the gin_synonyms table for the live gene into which it was merged.

• Species
  • On 2015-04-02 Michael Paulini added Species information to the genes.ace file dumped nightly from geneace.
  • The script now populates a gin_species table in postgres to record species names, e.g. Caenorhabditis elegans.

• Status
  • Live genes have no entry in the gin_dead table.
  • Dead genes have different entries depending on the information that is available for them:
    • Dead
    • Dead, Merged_into
    • Dead, Merged_into, Split_into
  • Suppressed genes are a special case.
    • They can have Dead Suppressed or Live Suppressed
    • Right now (10/2013), we only have Dead Suppressed

• Sanity Check
  • Since this script wipes out and re-populates postgres data, there is a sanity check so that if the nameserver file contains information on less than 20,000 genes, the script will not run and an email alert is sent. 20,000 is admittedly arbitrary, but hopefully is a reasonable cut-off.

For updating from latest WS release:

See this page for details

There are 2 cronjobs and 3 scripts:

in the acedb account:

cronjob 1 on script 1 (runs daily at 3am PST) : 0 3 * * * /home/acedb/cron/update_ws_tazendra.pl

Also triggers to run 2nd script : /home/acedb/cron/dump_from_ws.sh # dump .ace files from WS to update postgres tables

and write to a timestamp file my $dateOfWsDumpFile = /home3/acedb/cron/dump_from_ws/files/latestDate; echo "$date" >> $dateOfWsDumpFile;

in the postgres account :

cronjob 2 on script 3 (runs daily at 5am PST) : 0 5 * * * /home/postgres/work/pgpopulation/obo_oa_ontologies/ws_updates/populate_pg_from_ws.pl

This script went live on tazendra on 2013 10 21

This script generates files to populate postgres tables for some gin_ tables and obo_ tables for exprcluster when the date in the timestamp file (see above) is more recent than the latest timestamp in gin_molname. In other words, if WS is more recent than the postgres timestamp, the tables are updated (Lines 34 - 55).

For genes (gin_ tables), this script is species-restricted for C. elegans only (we can change this, if needed).

This script populates information that can only be derived from the WS build:

1. Corresponding_transcript
2. Corresponding_CDS
3. Corresponding_protein
4. Molecular_name

If the WS timestamp is more recent than the postgres timestamp, then the subroutine processGeneCds (Line 57) will run.

Values and timestamps are written to a file, then the postgres tables are deleted, values from the files are copied to the postgres tables, and then the files are closed.

For populating gin_protein, the subroutine looks at the CDS objects (WSCDS.ace) and retrieves the Corresponding_protein. To map genes to proteins, CDS and protein are matched (gin_seqprot), genes are matched to CDS (gin_seqprot) and then mapped to protein (gin_protein).

For populating gin_molname (Molecular_name), the subroutine looks at gene objects (WSGene.ace) and adds the value of Molecular_name to gin_molname.

For populating gin_sequence (Corresponding_transcript and Corresponding_CDS) the subroutine looks at gene objects (WSGene.ace) and adds the value to gin_sequence.

We'll know when WS141 comes out (should be mid-to-late December 2013) and cronjob 1 picks it up, if this pipeline works automatically.

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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