Micropub Pipeline
From WormBaseWiki
Revision as of 18:12, 6 September 2018 by Draciti (talk | contribs) (→Automatically import bibliographic info from Data Cite to WormBase paper editor)
- 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:
Contents
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
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:
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>)
Automatically import bibliographic info from Data Cite to WormBase paper editor
PaperIDs are generated through the ticketer: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_paper_ticket.cgi The DOI will be put in by a micropub editor via the ticketer as well.
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)
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? |
Identifier | DOI | Generated through the ticketer |
Title | Title | <titles>
<title>Application of the red-shifted channelrhodopsin Chrimson for the Caenorhabditis elegans cGAL bipartite system</title> </titles> |
Author | Author names | <creators>
<creator> <creatorName>Cao, Mengyi </creatorName> </creator> <creator> <creatorName>Chai, Cynthia </creatorName> </creator> </creators> |
Journal | Micropublication: biology | Generated through the ticketer |
Abstract | Abstract text | <descriptions>
<description descriptionType="Abstract">Channelrhodopsins are light-gated ion channels that serve as photoreceptors in photosynthetic microbes and have been applied as crucial optogenetic tools in genetic.. </description> </descriptions> |
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? |
Day | NA | DataCite does not store Month and Day, is it ok to put just the year? |
Type | micropublication | NA |
Fulltext_url | URL | URL on top of the page, above Metadata, e.g. https://www.micropublication.org/Cao_2018_Chrimson.html |
gene | ok to skip genes for automatic import or how do you extract for papers? | NA |
curation_flags | Author-person | NA |
primary_data | Primary | NA |
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