Difference between revisions of "WBGene information and status pipeline"
From WormBaseWiki
Jump to navigationJump to search| Line 31: | Line 31: | ||
| CGC_name | | CGC_name | ||
| gin_locus | | gin_locus | ||
| − | | Yes | + | | Yes (CGC) |
| If it has this tag, gene is considered good (What does 'good' mean?) | | If it has this tag, gene is considered good (What does 'good' mean?) | ||
| Yes (CGC) | | Yes (CGC) | ||
| Line 44: | Line 44: | ||
| Other_name | | Other_name | ||
| gin_synonyms | | gin_synonyms | ||
| − | | | + | | Yes (checking for different CGC name - see lines 132-137 in script) |
| + | | Yes | ||
| + | | Yes (checking for different CGC name) | ||
| Yes | | Yes | ||
| − | |||
| Yes | | Yes | ||
| Yes | | Yes | ||
| − | |||
| | | | ||
| No | | No | ||
| Line 57: | Line 57: | ||
| Sequence_name | | Sequence_name | ||
| gin_seqname | | gin_seqname | ||
| − | | Yes | + | | Yes (Sequence) |
| + | | No | ||
| + | | Yes (Sequence) | ||
| + | | No | ||
| No | | No | ||
| − | |||
| − | |||
| − | |||
| Yes | | Yes | ||
| | | | ||
| Line 70: | Line 70: | ||
| Status | | Status | ||
| gin_dead | | gin_dead | ||
| − | | Yes | + | | Yes (0) |
| only if value is dead and species ~ elegans$ | | only if value is dead and species ~ elegans$ | ||
| − | | Yes | + | | Yes (0) |
| − | | only if value is dead | + | | only if value is dead; populate with Merged_into and Split_into values |
| − | | | + | | No |
| Yes | | Yes | ||
| Yes | | Yes | ||
| Line 85: | Line 85: | ||
| No | | No | ||
| Yes | | Yes | ||
| + | | No | ||
| Yes | | Yes | ||
| No | | No | ||
| | | | ||
| − | + | | Historical_gene tag uses this when dumping files | |
| − | | Historical_gene tag | ||
| | | | ||
| | | | ||
| Line 98: | Line 98: | ||
| No | | No | ||
| Yes | | Yes | ||
| + | | No | ||
| Yes | | Yes | ||
| No | | No | ||
| | | | ||
| | | | ||
| − | |||
| | | | ||
| | | | ||
| Line 111: | Line 111: | ||
| No | | No | ||
| Yes | | Yes | ||
| + | | No | ||
| No | | No | ||
| Yes | | Yes | ||
| − | |||
| | | | ||
| | | | ||
| Line 124: | Line 124: | ||
| No | | No | ||
| Yes | | Yes | ||
| + | | No | ||
| No | | No | ||
| Yes | | Yes | ||
| − | |||
| | | | ||
| | | | ||
| Line 137: | Line 137: | ||
| No | | No | ||
| Yes | | Yes | ||
| + | | No | ||
| No | | No | ||
| Yes | | Yes | ||
| − | |||
| | | | ||
| | | | ||
| Line 151: | Line 151: | ||
| Yes | | Yes | ||
| No | | No | ||
| − | | | + | | No |
| Yes | | Yes | ||
| No | | No | ||
Revision as of 19:11, 17 October 2013
Contents
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) | Yes | 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 | Yes | 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) |
Current Scripts:
- /home/acedb/cron/populate_gin_locus.pl - updates information from nameserver nightly dumps
- /home/acedb/cron/populate_gin.pl - updates information from WS releases
New Scripts:
Some Relevant Postgres Queries:
SELECT * FROM gin_dead WHERE gin_dead ~ 'merged' AND gin_dead ~ 'split';
SELECT * FROM gin_dead WHERE gin_dead ~ 'split';
Back to Caltech documentation
