Detailed Documentation of Form and Scripts

Currently, on mangolassi the ccc.cgi and other scripts and files are here:

azurebrd/public_html/cgi-bin/forms/ccc

• accession
  • This is a file that maps WB WBPaper IDs to PMIDs.
  • For WB, this file is generated each time the search is performed.
• ccc_celegans_2013only
  • I believe these are old test files that can be deleted.
• ccc.cgi
  • This is the code for the curation form.
  • See the User_Guide_for_Curators for documentation of how the form works from a users' perspective.
  • See the ccc.cgi documentation for more specific details about the code.
• ccc.js
  • This is the ccc form javascript code.
  • If we want to change the number of characters needed to begin autocomplete, we can do that here.
• c_elegans.WS234.xrefs.txt and c_elegans.WS236.xrefs.txt
  • These are files generated with each WB build that were used to create the WB gpi file.
• generate_gpi.pl
  • This is the script that will be used to manually generate a new gpi file for WB.
• jquery
  • This directory contains...
• notes
  • This file contains a short bit about mapping WBGene IDs to UniProtKB accessions for the gpi file.
• scripts
  • This directory contains:
    • accession file - This is a mapping file that contains the mappings between WBPaper IDs and PMIDs as well as TAIR doc IDs and PMIDs. Note that we need PMIDs to send annotations to Protein2GO.
    • create_ccc_pgcuration.pl - This perl script creates two postgres tables for a given Textpresso source file:

creates these two tables:

ccc_sentenceclassification
  ccc_mod text,
  ccc_file text,
  ccc_paper text, 
  ccc_section text,
  ccc_sentnum text, 
  ccc_sentenceclassification text,
  ccc_comment text,
  ccc_curator text, 
  ccc_timestamp text,

ccc_sentenceannotation
  ccc_mod text,
  ccc_file text,
  ccc_paper text,
  ccc_section text,
  ccc_sentnum text,
  ccc_geneproduct text,
  ccc_component text,
  ccc_goterm text,
  ccc_evidencecode text,
  ccc_with text,
  ccc_alreadycurated text,
  ccc_comment text,
  ccc_valid text,
  ccc_ptgoid text,
  ccc_curator text,
  ccc_timestamp

• create_ccc_pgindices.pl - This script creates the following two tables for each Textpresso source file:
  • ccc_geneprodindex - this table contains the list of gene products mentioned in the sentence mapped to a MOD ID and a UniProtKB ID.
    • ccc_mod ccc_file ccc_paper ccc_section ccc_sentnum ccc_'table' ccc_timestamp
  • ccc_componentindex - this table lists, for each sentence, the cellular components that matched the Textpresso cellular component category
    • ccc_mod ccc_file ccc_paper ccc_section ccc_sentnum ccc_'table' ccc_timestamp
• gpi files - these files contain gene names, synonyms, and MOD and UniProtKB identifiers. For file format specifications, see:

GO's gpi file format specification

• • dictyBase_07032013.gpi Also change this file name to dicty_gpi for simplicity?
  • TAIR1_gpi
  • worm_gpi This file name needs to be changed from ws238_gpi, but I don't have permission to do this.
• meh - this looks like a test file for ccc_geneprodindex for TAIR.
• old_tables - this is a file that lists the names of the tables used for the previous version of the CCC curation forms.
• out - this looks like another test file for ccc_geneprodindex for TAIR.
• populate_ccc_pg_indices.pg.tair1 and populate_ccc_pg_indices.pg.worm1 - these look like the output files for the populate_ccc_pg_indices.pl for TAIR and WB. Note that for TAIR there are some sentences that were not processed properly.
• populate_ccc_pg_indices.pl - this script populates the two tables: ccc_component index and ccc_geneprodindex
  • Inputs needed:
    • Textpresso source files
    • Mapping file of PMID to MOD Accession for WB and TAIR only (so far). dictyBase docIDs are the same as the PMIDs.
      • This is available from a textpresso-dev URL that needs to be updated with each search run.
    • gpi files - see above. Need to establish where the updated files we be located (i.e., where I can put them) and also update the names of the variables in the script to be more generic. This script maps the gene product names and/or synonyms used to MOD and all UniProtKB IDs.
  • This script takes the raw Textpresso output and generates a human readable version of the sentences, as well as creating mappings of the gene product names or synonyms to IDs and generating a file with paper titles and abstracts for display on the curation form.
• source
  • This directory contains directories for each MOD that has a CCC implementation.
  • In each MOD's directories are the source files from Textpresso searches and the pmid_data file that maps PMIDs to MOD paper identifiers as well as paper titles and abstracts.
• test.html -
• ws234_tablemaker_info - the results of the tablemaker query for gene names and status for creating a gpi file.

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