Using the Paper Editor

From WormBaseWiki
Jump to: navigation, search

Accessing the Editor

The paper editor is accessible either from the curation index page (click on the second link, paper_editor.cgi): http://tazendra.caltech.edu/~azurebrd/cgi-bin/index.cgi

or directly at: http://tazendra.caltech.edu/~postgres/cgi-bin/paper_editor.cgi

If you don't have the password to access these forms on tazendra, you can get it from Juancarlos.

Might be helpful to reorganize the index page, to put all of the paper-related forms together. We could keep the link to the old editor, but make a note on the index page that this is the old editor.

Signing In

Before performing any actions with the paper editor, select your name from the drop-down list of curators at the top of the page.

Entering New Papers

There are several different ways to add papers to postgres and hence, Textpresso and WormBase, but in general, there are two types of papers: those indexed by PubMed and those not indexed by PubMed. The former constitute the majority of published articles that we have in our paper collection, while the latter includes articles and books not currently indexed by PubMed as well as meeting abstracts and Worm Breeder's Gazette articles. Below is an explanation of how to enter papers from each of these different sources.

  • From the front page of the editor, scroll down to the bottom of the page and click on the link Enter New Papers.
  • This will bring you to a page that is divided into three parts:
    • Top section - for entering papers with a PMID that were not picked up by the 'elegans' keyword search.
    • Middle section - for entering papers that do not have a PMID.
    • Bottom section - this is the largest section and contains information about the papers that were returned from the daily 'elegans' keyword search. Information about the paper includes: PMID, Author(s), Title, Abstract (if available), Paper Type, and Journal. At the far right side of the page is the Flags box for recording the actions taken for each paper.

Paper Editor Top Section - Entering PubMed Papers Not Picked up by Daily 'elegans' Keyword Search

The top section of the paper editor is used to enter papers that are indexed by PubMed (i.e., have a PMID) but would not normally be picked up by the daily 'elegans' keyword search.

  • To enter a paper of this type, copy and past the paper's corresponding PMID into the box in the middle of the page. Multiple PMIDs should be entered one per line.
  • If the paper being entered is used solely as evidence for curation, e.g. a concise description or topic, and does NOT otherwise contain information about C. elegans, check the non_nematode (formerly functional_annotation) flag box. The 'non_nematode' flag alerts paper and author curators so they don't have to download the corresponding PDF or curate author-person connections for those papers. In the past, papers used to help write concise descriptions about conserved, but information-poor C. elegans genes constituted the bulk of papers flagged as 'functional annotation'. Fewer and fewer of these types of papers are now being added to the database.
  • Select primary, not_primary, or not_designated from the drop-down menu below the non_nematode check box. The primary flag indicates that the paper has primary research data; the not_primary flag indicates that the paper does not contain primary research data (e.g., Review, Editorial, Comment, etc.); the not_designated tag is used only for meeting abstracts and Worm Breeder's Gazette articles that do report primary research findings, but are not typically curated.
  • If the paper is priority for author-person curation, select priority. If not, select not_priority. In general, papers given priority for author-person curation are those papers that either report primary research findings or are reviews or other such articles largely focused on C. elegans research. Reviews that contain only a small section on C. elegans and are written by people outside of the field are not highest priority for author-person curation and are designated 'not priority'.
  • Once all of the flags have been chosen, click on 'Enter PMIDs'.
  • The resulting page will show the WBPaper IDs assigned to the newly created paper(s).

Paper Editor Middle Section - Entering Papers not Indexed by PubMed

We occasionally enter papers from journals that are not currently indexed by PubMed. These papers are often brought to our attention by authors when they are asked to verify their papers that do exist in WormBase. To enter these papers:

  • Click on the button that say 'Enter non-PMID paper'.
  • After a few seconds, this will take you to a blank editor page where a new WBPaper ID has been assigned.
  • For each paper, enter (at least) the following information.
  • Note that to enter information you'll need to click within the second column (from the left) of the form in order to get a box where you can enter text.

Publication Information

  • An identifier, such as a DOI or ISBN - enter the identifier in lower case (e.g. doi) and then follow that with the identifier, no space in between the two
  • Title
  • Authors, one per line
  • Journal
  • Abstract
  • Pages
  • Volume
  • Year (select from drop-down list)
  • Month (if applicable, select from drop-down list)
  • Day (if applicable, select from drop-down list)
  • Type (select from drop-down list)

Genes and Curation Flags

  • Genes studied in the paper (if known, can be entered as batch or as gene (evi), if needed)
  • Curation flags
    • Select author-person if this paper will be priority for author-person curation
    • Select non_nematode if this paper is for gene function or topic curation but has no experimental nematode data
  • Next to the primary_data, type in either:
    • primary
    • not_primary
    • not_designated (for meeting abstracts and Worm Breeder's Gazette articles only)

Note that Textpresso does contain the information about primary, not_primary; retrieved by:

/data2/data-processing/download/celegans/scripts/scripts_to_fetch_data_from_postgres/primary.com

Paper Editor Bottom Section - Approving PubMed-Indexed Papers from Daily 'elegans' Keyword Search

Entering Meeting Abstracts

Entering Worm Breeder's Gazette Articles

Performing Searches

  • The front page of the paper editor can be used to perform searches based on the values of data in the postgres paper tables.
  • General points:
    • Depending upon the type of data being searched, the searches can be performed by either entering text into each of the boxes or selecting a value from a drop-down menu. For example, paper identifiers use a search box, while paper type uses a drop down list.
    • The number search is used for entering a WBPaper ID and the value in the box can be erased by clicking on the 'x' to the right of the box.
    • Substring searches can be used to enter only part of the value, e.g. 24957743 or 57743 instead of pmid24957743.
    • Searches may be performed as case-insensitive searches by clicking on the appropriate box.
    • You may enter search terms into multiple boxes. Search results are presented as a list according to how many matches were found for one or more search criteria.



Back to Paper Pipeline