Merging Papers

From WormBaseWiki
Jump to: navigation, search

Paper Pipeline

Merging papers:

In paper merges there is a paper that will acquire a merge (and get an Acquires_merge tag in the .ace file) and a paper that is being merged into another (will get a Merged_into tag in the .ace file).

Which paper to merge into which, in some cases, actually matters. If authors or other users are familiar with a paper with one ID, then probably best to keep the familiar ID.

New Protocol

Tested by merging 32994 into 32993.

1. Determine which paper will be merged into another paper and enter the WBPaper ID of the paper that will acquire the merge into the number box on the paper editor.

2. Scroll to the bottom of the page and enter the WBPaper ID of the paper to be merged in the box to the right of Merge WBPaper. To the right of this box it will show the ID of the paper that is acquiring the merge. Click on Merge.

Make Merge a box to click on. - works like rest of editor -- changed to work differently from rest of editor, has button now -- J 2010 04 08

3. The resulting page will show the data for each paper, with the data from the paper acquiring the merge in the boxes with a white background and the data from the paper being merged in the boxes with a red background.

List WBPaper ID next to each - on the left hand side. Will help to keep things straight. -- done (but don't like it) -- J 2010 04 08

Have a check box to the left of each red box that is on for replace or merge by default, but could be turned off by a curator if, for some reason, a piece of data should not be replaced or merged. - do deleting in other form

4. For each piece of data attached to a paper, the editor will indicate whether that data will be replaced by data from the paper being merged or will be appended to the data for the paper acquiring the merge.

5. The order of the data in the editor:

a. Status: valid or invalid. Action: Replace

b. pubmed_final: final. Action: Replace

c. Identifiers: PMID, WBPaper IDs, Medline IDs. Action: Merge

WBPaper ID of paper to be merged appeared automatically in the white box. Should be listed in the red box?

Show everything in white or red box, so it's clear to the curator exactly what is happening.

d. Title: text. Action: Replace

e. Authors: Author IDs, Person IDs, Verification Status, Evidence. Action: Alert Cecilia that Authors need to be merged.

f. Journal: text. Action: Replace

g. Abstract: text. Action: Replace

h. Pages: text. Action: Replace

i. Volume: text. Action: Replace

j. Year: text. Action: Replace

k. Month: text. Action: Replace

l. Day: text. Action: Replace

m. Type: number. Action: Merge Show the text translation of the number, as curators probably don't know what type corresponds to which number. -- done J 2010 04 08

n. Gene: WBGene IDs. Action: Merge Show the locus names, too. If curators are looking at the papers, they won't want to have to check every WBGene ID in WB. -- done J 2010 04 08

o. Primary_data: text. Action: Replace.

6. When finished checking all data values to be merged or replaced, click on the Merge button.

7. In the resulting window, curators will see any remaining information from the paper that was merged. If some information remains...

Old Protocol

To perform the merge in the paper editor:

  1. Enter the ID of the paper to be merged in the paper editor.
  2. Make this paper's ID invalid by deselecting the valid box to the right of the ID and selecting the update box to the right of that.
  3. Also, add the ID of the paper to which this paper is being merged in the form of WBPapernnnnnnnn, select the valid button and the update button and enter the data into postgres b by clicking on the Update Info! button.

For the paper that is acquiring the merge, do essentially the same thing:

  1. Enter its ID in the paper editor and then add the invalid paper's ID, in the form WBPapernnnnnnnn, to the list of identifiers for the paper that is acquiring the merge.
  2. Select the valid and update button and click on Update Info!.

If information, such as authors, title, abstract, needs to be transferred from one paper to another, this has to be done manually:

  1. Cut and paste the information from one entry into another, make the information invalid in the old paper entry and valid in the new paper entry.
  2. Don't forget to check the update box for each entry you change and click on Update Info! when you're done.

There is a link to the .ace file on the page that is returned after you click on Update Info!, so you can check the .ace file to see that everything looks okay.

--Kimberly

Papers to be Checked for Merging

WBPaper00035423 and WBPaper00035448