Specifications for source files

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Specifications for Textpresso for CCC Source Files

  • The source files can be simplified a bit, but will retain the key information we need for curation and search and retrieval functions for the curation form.
  • The format will continue to be a tab-delimited file containing, in order:
  1. SSC (stands for Textpresso Sentence SCore):Numerical Textpresso sentence score value
  2. Paper database code:numerical identifier:Paper section:Sentence ID in Textpresso document:corpus_date_of_search
    1. For WormBase and dictyBase, who are sending annotations to the Protein2GO tool via web services, this identifier needs to be either a PubMed ID or a doi.
    2. If neither a PubMed ID nor a doi exists, then the annotation cannot be sent to Protein2GO
    3. For TAIR, who is not yet using Protein2GO, it can still be the TAIR document ID
  3. Gene product name or synonym as identified by Textpresso search (names below are as seen on Textpresso web sites)
    1. WormBase: protein (C. elegans)
    2. dictyBase: dicty gene
    3. TAIR: gene (arabidopsis)
  4. Textpresso component category match (names below are as seen on Textpresso web sites)
    1. WormBase: CCC cellular component 2011-02-11
    2. dictyBase: CCC TAIR - this is in bold, because we need to confirm this is the right category for dictyBase
  5. Textpresso sentence (marked up version)

Example sentence:

SSC:6<TAB>PMID:12345678:Abstract:17:dicty_20130411<TAB>DPY-27,DPY-30<TAB>chromosome, chromosomes, nuclear<TAB><The marked-up Textpresso sentence that doesn't have any tabs>

Web page on Protein2GO web services

Back to CCC Form 2.0 Specifications