Micropub Pipeline

From WormBaseWiki
Jump to navigationJump to search
  • Authors submit Micropublication
  • Editor submits Micropublication to reviewers
  • Reviewer's response and eventual Author's corrections

once the Micropublication is accepted Authors should:

  • submit final high resolution images -possibly jpg format to editors
  • submit final version of the manuscript to editors

Editors will:

DOI request

  • Request a DOI at EZID

EZID 2017.png

Update Micropublication

  • Add date in Header
  • Add Reviewer
  • Add Received date, Accepted Date, WB Release, Online publishing date
  • Add citation


  • Reviewed by: Veena Prahlad
  • Received 12/12/2016, Accepted 01/27/2017. Available starting WormBase release WS259, Published Online 02/08/2017.
  • Copyright: © 2017. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
  • Citation: Hiebert, T; Chicas-Cruz, A; McCormick, K. (2017): Basal pharyngeal pumping elevated in C. elegans mod-5 mutants. WormBase. Dataset. https://doi.org/10.17912/W2H59W

Hyperlinking step

  • hyperlink entities in the submission (possible to use GSA mark up scripts?)

Track Micropub

  • Update the Micropublication tracking excel sheet here:


Generate new WBPaperID

  • Generate a new WBPaper via the Paper Editor here:


  • To fill out the form:
    • Enter new paper
    • Enter non PMID paper
    • Number automatically inferred
    • status valid
    • species choose
    • identifier -> add DOI. format example: doi10.17912/W2159J
    • contained in ignore
    • erratum in ignore
    • title -> put in title. e.g.: Basal pharyngeal pumping elevated in C. elegans mod-5 mutants
    • author put in manually -free text. Format: Last name space initial(s). Enter one author at a time (if need to edit a box will pop up at the bottom)
    • affiliation leave blank
    • journal -> Micropublication: biology
    • abstract In our case all description, does not deal with special characters
    • publisher -> generally filled in for books
    • editor -> generally filled in for books
    • pages blank
    • volume blank
    • year yyyy
    • month mm
    • day dd
    • type -> micropublication
    • fulltext_url -> micropub journal url e.g.: http://www.micropublicationbiology.org/hiebert-2017--mod-5mutants.html
    • remark -> If any
    • gene (batch) automatically populated we will put in manually for now the genes under study
    • gene (evi) only when gene names are not approved/non standard
    • curation_flags put author_person
    • curation_done something part of cecilia curation
    • internal_comment an internal remark
    • primary_data put in primary (beware that this should be a drop down but it does not behave as such until you put in a value, which should be <primary>)

Generate new WBPictureID

  • Create WBPaperID folder
  • Put in the high resolution jpg file
  • Generate new WBPictureID in Picture OA