Difference between revisions of "Adding new Phenotype2GO annotations to postgres"
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**Caveat: unique entries could be the result of new annotations added or old annotations that were removed, therefore the curator will need to check the newGpaEntries file at each build to make sure they know what is being added and if needed, to delete any annotations from postgres that were removed during the WS build | **Caveat: unique entries could be the result of new annotations added or old annotations that were removed, therefore the curator will need to check the newGpaEntries file at each build to make sure they know what is being added and if needed, to delete any annotations from postgres that were removed during the WS build | ||
*Next Steps, 2015-04-09: | *Next Steps, 2015-04-09: | ||
| − | **'''New script:'''Except for the date in Column 14, compare all columns in two phenotype2go.WSnnn.wb GAF files and output a new newGpaEntries file of all unique lines | + | **'''New script:'''Except for the date in Column 14, will compare all columns in two phenotype2go.WSnnn.wb GAF files and output a new newGpaEntries file of all unique lines |
| − | **The GAF files for generating the WS249 upload are on mangolassi here: /home/acedb/kimberly/citace_upload/go/phenotype2go/new_annotation_entries/WS249_upload | + | **The two GAF files for generating the WS249 upload are on mangolassi here: /home/acedb/kimberly/citace_upload/go/phenotype2go/new_annotation_entries/WS249_upload |
**If needed, curator will manually edit the newGpaEntries file (i.e. remove deleted entries) | **If needed, curator will manually edit the newGpaEntries file (i.e. remove deleted entries) | ||
**Final newGpaEntries file will be used for postgres upload using the populate_gop_OA_pheno2go.pl script | **Final newGpaEntries file will be used for postgres upload using the populate_gop_OA_pheno2go.pl script | ||
Revision as of 20:16, 9 April 2015
- All Phenotype2GO annotations are generated anew with each WS build, however, we only need to add the annotations from the most recent build to the OA tables in postgres.
- The original set of annotations added to postgres came from WS247.
- This set of annotations was first compared to the GAF from UniProt to avoid entering redundant annotations from manual curation.
- Once redundant annotations were removed, the unique file of entries, newGpaEntries, was parsed and data added to the GO OA tables using the script here: /home/postgres/work/pgpopulation/go/go_curation/20141106_kevin_godata/populate_gop_OA_pheno2go.pl
- Subsequent annotations will be generated by comparing the live and staging versions of the phenotype2go.wb files found on the ftp site (e.g. ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS247/ONTOLOGY/phenotype2go.WS247.wb and ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS248/ONTOLOGY/phenotype2go.WS248.wb) and then parsing unique entries into postgres
- Caveat: unique entries could be the result of new annotations added or old annotations that were removed, therefore the curator will need to check the newGpaEntries file at each build to make sure they know what is being added and if needed, to delete any annotations from postgres that were removed during the WS build
- Next Steps, 2015-04-09:
- New script:Except for the date in Column 14, will compare all columns in two phenotype2go.WSnnn.wb GAF files and output a new newGpaEntries file of all unique lines
- The two GAF files for generating the WS249 upload are on mangolassi here: /home/acedb/kimberly/citace_upload/go/phenotype2go/new_annotation_entries/WS249_upload
- If needed, curator will manually edit the newGpaEntries file (i.e. remove deleted entries)
- Final newGpaEntries file will be used for postgres upload using the populate_gop_OA_pheno2go.pl script
