Difference between revisions of "Micropub Pipeline"
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**internal_comment an internal remark | **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>) | **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== | ||
+ | |||
+ | {| class="wikitable" | ||
+ | |- | ||
+ | ! Paper editor field | ||
+ | ! ID | ||
+ | ! DataCite | ||
+ | |- | ||
+ | | 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 | ||
+ | |} | ||
+ | |||
==Generate new WBPictureID== | ==Generate new WBPictureID== |
Revision as of 16:41, 6 September 2018
- 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
Paper editor field | ID | DataCite |
---|---|---|
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 |
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