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Publication module

Paul Kiddle edited this page Sep 20, 2018 · 1 revision


The publication module can be used to automatically draft scholar manuscripts to be submitted for publication to peer-reviewed and open access Journals. When you enter data into Scratchpads we correctly structure them and annotate them according to internationally accepted Biodiversity data exchange standards. This enables us to easily generate manuscripts without you having to worry about how to format the manuscript and its components (references, tables, figures, specimens catalogs, taxon descriptions etc) according to the publisher's requirements.

This documentation page will guide you through the process of compiling a manuscript based on the data already in your Scratchpad and submitting it for review to the publisher.


Enabling the tool

Before you can use the tool you will have to enable it

  1. From the Admin menu go to Structure > Tools
  2. Under Publication enable the Taxonomic paper (Pensoft Writing Tool)
  3. Click Save

Drafting a manuscript for Biodiversity Data Journal

Taxonomic paper

  1. From the Admin menu go to Content

  2. Under Publication click add next to Taxonomic paper (Pensoft Writing Tool)

  3. Title

    Provide the title of your manuscript

  4. Authors

    Select people from your Scratchpad site that should be named as authors of the manuscript. One of the authors should be the Submitting author. For the people you include as authors of the manuscript you can assign access levels. People can either edit & comment or only comment on the manuscript

    If an author name is not already present in your Scratchpad as a person you will have to add him/her first. For more information go to the how to add and edit users page

    Affiliations and other relevant data for the authors are automatically drawn from their profile pages

  5. Abstract & Keywords

    Provide the text that will be the abstract of your manuscript. You can italisise words using the corresponding I button in text editor

    Keywords can be either single words or short phrases and should be separated with commas (,)

  6. Contributors

    Optionally you can provide names as contributors o the manuscript. Contributors, as authors, should already exist in your Scratchpad as users/people. Contributors can be granted access (editing & commenting or commenting) to the manuscript

  7. Introduction

    Write the introduction to your manuscript. On how to embed citations to reference, tables or figures please see the coresponding section below

  8. Material & Methods

    Text entered here will be titled as Materials & Methods. On how to embed citations to reference, tables or figures please see the coresponding section below

    To import a table with selected specimen records click on the Create a specimen table button in the text editor toolbar

    1. In the overlay window you can search for specimens based on the taxonomic name

    2. To select the specimen records you wish to include click on the tick box on the left of a specimen

    3. You can select which columns you wish to include in the manuscript table by selecting them

    4. When ready scroll down the window and click Import

  9. Data resources

    Provide a description of the data resources used (if external)

  10. Treatments

    Select the taxa you wish to include in the manuscript (new taxa or redescription or taxa)

    Select the fields you want to include from the Taxon description content type. Typically this would include the field Diagnostic description along with other fields from this content type. Please note that you cannot provide extra data through this interface, if you wish to change something in the included information you will have to do so from the corresponding Taxon description content type for this taxon

    In many cases you would like to “protect” the new taxon name from being exposed to the public before publication. To do so we suggest you use a “placeholder” name in the taxonomy for this specific name (e.g. Humulus sp.). You can define the final name in this section

    Provide the Genus, specific epithet and infraspecific epithets as well as the name authority

    Select a Holotype and optionally paratypes from your Scratchpads specimen records

  11. Discussion

    This text will be titled as the discussion of the manuscript

  12. Supplementary files

    You can attach supplementary files (e.g. MS Excel or pdf files)

    To add a new file click Select media, browse and upload your file(s)

  13. Acknowledgments

    This text will be titled as Acknowledgements in the manuscript

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