User Guide for Curators

User Guide for Textpresso for CCC Form

Where to Find the Form

• The form is currently located at:

http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/ccc/ccc.cgi

• Once we've finished initial testing, the form will be transferred over the our production server.

What We Need from Groups Using the Form

• Instructions on what papers to run through the CCC search and how often to search
• Any filtering steps, e.g. filter against current GAF, filter after Support Vector Machine data type classification

• A gpi (gene product information) file as specified by the GOC: gpad and gpi file format specifications. This allows us to map all gene products mentions in a paper to a MOD identifier and to a UniProtKB identifier so we can send annotations via web services to UniProt's Protein2GO tool.

Logging In

• Each curator can login to the form from http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/ccc/ccc.cgi

• Select your first name from the list of curators and click on login

• The login page also has a button that displays the list of Textpresso Cellular Component category terms and their mapping, based on previous curation, to a GO term and GO ID.
• Previously entered GO terms that don't map to any existing GO term are highlighted in red. Note that the Component - GO term index is based on all previous curation data from the old form that didn't restrict how GO terms were entered. The new form uses an autocomplete to add GO terms which should avoid any future errors in GO term entry.

Making Annotations and Searching

• Once a curator has logged in, they will be taken to the curation page with options for searching and loading files and annotations.
• Search options are (in the order they appear on the form):
  • Sentence-curation - this allows you to search sentences files and exclude curated or noncurated sentences as needed
  • Papers to show - this allows you to set a limit on the number of papers that are returned for any given search. The default value is 10.