Automated descriptions for C. briggsae

Location of project-related files on Textpresso

http://textpresso-dev.caltech.edu/concise_descriptions/

Location of the concise description files for C. elegans:

• For viewing the latest dump:

http://tazendra.caltech.edu/~postgres/cgi-bin/data/concise_dump_new.ace

• Script: /home/postgres/work/citace_upload/concise/dump_concise.pl
• File location: /home/postgres/public_html/cgi-bin/data/concise_dump_new.ace

Semantic categories in a Concise Description for C. briggsae

1. Orthology/Similarity to C. elegans and human
2. Processes
3. Molecular Function
4. Sub-cellular localization (Cell component)

Source files for homology data

1. Orthologs file:

2. Best BlastP hits file: ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/c_briggsae/PRJNA1073/c_briggsae.PRJNA10731.WS245.best_blastp_hits.txt.gz

• Contact: Michael Paulini

Source file for Process, Molecular function and Sub-cellular localization (cell component)data

• gene association file for C. brigssae: ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/ONTOLOGY/gene_association.WS245.wb.c_briggsae

• Process:
  • All rows with column 15 (assigned by) with 'WB' are WormBase annotations, those with 'UniProtKB' or 'InterPro' are from those databases
  • Need data from these rows:
    • where column 9: has value 'P' (Process),
    • column 2 (DB_Object ID): the associated genes, i.e WBGene ID,
    • column 3 (DB_Object symbol), i.e, Cbr-bli-4
    • column 5: GOID, eg, GO:0000346
    • column 6: DB:Reference (Reference), eg.PMID:12062106
    • column 7: Evidence code, i.e, IEA
    • column 8: With, eg. INTERPRO:IPR000209

• Molecular Function:
  • Need data from these rows:
    • where column 9 has value 'F' (Molecular Function)
    • column 2, associated genes, has U
    • column 3: DB_Object symbol, eg, wht-7,
    • column 5: GOID, eg, GO:0000346
    • column 6: DB:Reference (Reference), eg.PMID:12062106, GO_REF:0000002
    • column 7: Evidence code, eg, IMP
    • column 8: 'With (or) From' eg., INTERPRO:IPR002293,