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WS234 .ace dumper scripts

  • transgene.ace ->transgene objects curated through the Transgene OA
  • var_phene.ace ->variation, rearrangements, transgenes, strains annotated with phenotypes curated through the Phenotype OA
  • mol_phene.ace ->molecules associated with phenotypes curated during object-phenotype curation through the Phenotype OA
  • alle_paper.ace ->object-paper connections curated through object-phenotype curation through the Phenotype OA, for viewing on gene pages in page reference section
  • Molecule.ace ->molecule objects curated through the Molecule OA
  • database.ace ->database objects used in molecule curation, this is a manually-generated file. All modifications to the file need to be done manually to this flat file.
  • process.ace
  • process_curation.ace


six .ace files are now dumped on tazendra and picked up by spica on a weekly basis: files are created Wednesday mornings at 4 am and picked up Thursday morning at 8 am.

Four cronjobs on the acedb account on tazendra :
0 4 * * wed /home/acedb/karen/Molecule/
0 4 * * wed /home/acedb/karen/phenote/paper_object/ 
0 4 * * wed cd /home/acedb/karen/transgene/ 
0 4 * * wed cd /home/acedb/work/allele_phenotype/ (creates 2 .ace files - var_phene.ace and mol_phene.ace)

All six .ace files are placed In the directory :
  /home/acedb/public_html/karen/ symlinked to original folders on tazendra :
  alle_paper.ace -> /home/acedb/karen/phenote/paper_object/alle_paper.ace
  Molecule.ace -> /home/acedb/karen/Molecule/Molecule.ace
  mol_phene.ace -> /home/acedb/work/allele_phenotype/mol_phene.ace
  transgene.ace -> /home/acedb/karen/transgene/transgene.ace
  var_phen.ace -> /home/acedb/work/allele_phenotype/var_phen.ace
database.ace -> /home/acedb/karen/Molecule/database.ace (manually generated file)

One cronjob on spica:
0 8 * * thu /home/citace/cronjobs/
    puts 6 files at  /home/citace/Data_for_citace/Data_from_Karen   writes to /home/acedb/karen/Molecule/Molecule.ace  writes to /home/acedb/karen/phenote/paper_object/alle_paper.ace
(transgene)  writes to  /home/postgres/work/citace_upload/transgene/transgene.ace and transgene.ace<date>
(allele_phenotype)  writes to  /home/postgres/work/citace_upload/allele_phenotype/allele_phenotype.ace.<date>, var_phene.ace, mol_phene.ace<date> and mol_phene.ace
alle_paper.ace  is just a symlink to /home/acedb/karen/phenote/paper_object/alle_paper.ace

other scripts

Transgene Curation | |
Updating obo tables in postgres | | AddToVariationObo | (obsolete)
NBP data parsing |

If any other scripts do anything with any of those files above, it's independent of this script that populates the OA obo_ tables, and I don't know what they are. If there's any specific scripts you want to go over, let me know, and we can sit down together and go through it so you can write up on it on a wiki.


GSA project
Molecule Curation
Phenotype Curation (Variation/Strain/Transgene/Rearrangement)
wbprojects (main WB project overview)

Web Displays

Variation Phenotype

First pass

WB Wiki pages

Caltech Documentation
Help desk schedule


Process pages
Metabolic pathways
Regulatory pathways

Old .ace dumper scripts

transgene.ace- /home/postgres/work/citace_upload/transgene/ -runs on cron job, deposits .ace in Data_from_Karen on citace
var_phene.ace- /home/acedb/work/allele_phenotype/ -run manually
variation .ace dump module called by the
alle_paper.ace- /home/acedb/karen/phenote/paper_object/ -run manually
molecule.ace- /home/acedb/karen/Molecule/ -(also /home/acedb/public_html/karen/)run manually