Ccc.cgi documentation

Updating the Form for New Groups

• Actions
  • Subroutine : sub process
    • This subroutine lists the different actions that curators can take and the expected behavior while using the form:
      • Login - Accessed from the front page. Curator selects name from list on front page, clicks login, and is taken to Search Page. A curator must be selected from the list in order to continue.
      • List Component-GO Term - Accessed from the front page. Clicking on this link takes curators to a page that lists the index of Textpresso Cellular Component Terms to GO Cellular Component (CC) Terms. This index is organized alphabetically and based solely on curation.
      • Search - Accessed from search page. Clicking on this link will take curators to a page that lists search results based on curator specifications.
      • Submit - Accessed from curation page. Clicking on Submit will send annotations to Protein2GO and return a status message at the top of the curation page.
      • autocompleteJQ - Allows for autocompleting on GO term names when searching from the Search page or selecting new GO terms during curation.

• Adding New Curators
  • Subroutine : subpopulateCurators
    • Need to map each new curator to their MOD (as represented in all of the accompanying directories where their files are stored)
    • Also need to map each curator to their Protein2GO login email (for testing purposes, users can use kimberly's login)

• Adding New Link Outs to Gene/Gene Product Pages

• Autcomplete
  • sub autocompleteJQ
    • This subroutine covers the autocomplete action when searching or entering a new GO term for curation.
    • The list of GO terms accessible by autocomplete depends on whether the user is searching for a GO term or entering a new GO term for curation. The reason for this is that the GO Term search is restricted to only those GO terms associated with an annotation (otherwise there is no data to retrieve). The list of GO Terms for the search function is derived from the ccc_component_go_index table. For curation, the list is derived from the GO obo file and associated postgres tables.
    • The list is restricted to Cellular Component terms and does not include obsolete terms.

• Submitting Annotations (Curation)
  • sub submitPage
    • This subroutine has the code for the display of source file sentences, associated metadata, annotation options, and actions for submitting annotations.
    • Annotations made are given a 'valid' value and the current timestamp when made.
    • Curators can choose a sentence classification from the list that will be stored with the sentence metadata.
    • Curators can also add a comment that will be stored with the sentence metadata.
    • New classifications delete old classifications.