Micropub Pipeline

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  • 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
    • Type Micropublication: biology instead of Wormbase in the publisher field (as opposed as shown in the screenshot)
    • Go to the EZID site http://ezid.cdlib.org/, log in and fill out the form as in the figure below

EZID 2017 1.png

Update the Micropublication word doc and convert into PDF

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

Example:

  • 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

Until the hyperlinking pipeline is set up for micropubs, hyperlinking can be done manually for the following objects using the appropriate URL constructors

bioentity ID URL constructor
gene WBGeneID http://www.wormbase.org/db/get?name=WBGenDIS;class=Gene
allele WBVarID http://www.wormbase.org/db/get?name=WBVarID;class=Variation
strain Strain name http://www.wormbase.org/db/get?name=Strain;class=Strain
transgene WBTransgeneID http://www.wormbase.org/db/get?name=WBTransgeneID;class=Transgene
person WBPersonID http://www.wormbase.org/db/get?name=WBPersonID;class=Person
Chemical/Drug/Molecule WBMolID http://www.wormbase.org/db/get?name=WBMolID;class=Molecule
Phenotype WBPhenotypeID http://www.wormbase.org/db/get?name=WBPhenotypeID;class=Phenotype
Anatomy WBbtID http://www.wormbase.org/db/get?name=WBbt;class=Anatomy_term

Track Micropub

  • Update the Micropublication tracking excel sheet here:

https://docs.google.com/spreadsheets/d/1rrMlJpCh1badU-J076wE5AMJeqi7ftTmgm2y7o-NrSI/edit#gid=1819244485

Generate new WBPaperID

  • Generate a new WBPaper via the Paper Editor here:

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

  • 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>)

Handling Errata, Corrigenda, Retractions in the Paper Editor

  • Errata
    • In the original publication: add the WPpaper Id (only the ID) in the erratum_in and leave microPublication as type
    • In the erratum: choose Published_Erratum as type
  • Corrigenda
    • In the original publication: add the WPpaper Id (only the ID) in the corrigendum_in and leave microPublication as type
    • In the corrigendum: choose corrigendum as type
  • Retractions:
    • the paper that gets rectaceted gets the ‘Rectracted Publication’ tag
    • the notice of retraction gets the 'Retraction of Publication’ tag

Automatically import bibliographic info from Data Cite to WormBase paper editor

WBPaperIDs are generated through the ticketer: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_paper_ticket.cgi The DOI and the publisher will be put in by a micropub editor via the ticketer as well.

Logic: Look for WBPapers that have microPublication Biology as publisher, have a DOI but don't have 'title'. For those populate the paper editor fields according to the table below (from Datacite XML)

Script here: /home/postgres/work/pgpopulation/pap_papers/20181011_datacite/update_datacite_papers.pl Set up a cron job daily, runs at 8 pm Pacific, notifies Daniela via e-mail.

Url that goes to DataCite: https://api.datacite.org/dois/application/vnd.datacite.datacite+xml/doi# e.g.:

Paper editor field Value in Paper Editor DataCite
Paper WBPaperID Generated through the ticketer
Status Valid Generated through the ticketer
Species Species name Ask kimberly what is the best way, add a species dropdown in the ticketer? We could do this as we do for the paper editor, but need to sort out what the source data should be. --k. For now we will enter species manually
Identifier DOI Generated through the ticketer
Title Title <titles>
       <title>Application of..</title>
   </titles>
Author Author names <creators>
       <creator>
           <creatorName>Cao, Mengyi  </creatorName>
       </creator>
       <creator>
           <creatorName>Chai, Cynthia  </creatorName>
       </creator>
   </creators>

Note that we may want to strip commas from author names in the paper editor. Current micropublications don't have commas in author names, nor do papers from PubMed. Meeting abstracts do. --k

Journal microPublication Biology Generated through the ticketer
Abstract Abstract text <descriptions>
       <description descriptionType="Abstract">Channelrhodopsins are ... 

</description>

   </descriptions>. Juancarlos add a warning if the import throws an error in the paper editor
Year Year <dates>
       <date dateType="Issued">2018</date>
   </dates>
Month NA DataCite does not store Month and Day, is it ok to put just the year? It looks like other micropubs have a month and day. I think this is up to the micropub team to decide. --k leave out for now DR
Day NA DataCite does not store Month and Day, is it ok to put just the year? It looks like other micropubs have a month and day. I think this is up to the micropub team to decide. --k leave out for now DR
Type micropublication NA
Fulltext_url URL URL on top of the page, above Metadata, e.g. https://www.micropublication.org/Cao_2018_Chrimson.html. Will not extract URL, redundant with DOI
gene ok to skip genes for automatic import? how do you currently extract genes for papers? When we import abstracts from PubMed, the script that processes the XML also performs string matching to identify as many genes/protein names as possible. It'd be nice to have some mechanism to do this at the time of paper creation. --k NA
curation_flags Author-person NA
primary_data Primary NA
  • Questions for kimberly
    • How to deal with Species. Can we add a drop down in the ticketer, are there other ways
    • Authors: until now we have entered authors following this syntax: Last name space initial(s). The Datacite xml has Cao, Mengyi. Would that be OK?
    • DataCite does not store Month and Day, is it ok to put just the year?
    • Genes: ok to skip genes for automatic import? how do you currently extract genes for papers?

Generate new WBPictureID

  • Create WBPaperID folder
  • if authors submit through the form the images are stored here: /home2/acedb/public_html/draciti/Micropublication/uploads/
  • Put in the high resolution jpg file
  • Generate new WBPictureID in Picture OA

Add entry on Micropublication: biology site

  • Generate html page for the micropublication- you can duplicate an existing page and change the content
  • Add the correct PDF for the PDF download button