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Integrated Workflow for Publications and Datasets: Manuscript Preparation

This guide outlines the different stages involved in the Integrated Workflow for research publications and datasets.

Open Access Publishing (OA)

At this stage
  • You will prepare your publication for submission and peer-review

  • In the process of choosing where to submit your manuscript you may want to check the list of eligible titles for the various Read & Publish deals that Strathcyde has signed with publishers like Springer Nature, Wiley, SAGE, Cambridge, Taylor & Francis or Oxford University Press. Having a manuscript with a Strathclyde submitting corresponding author accepted in any of this titles will entitle the authors to Gold Open Access at no additional cost. Please check with the Open Access Team at for more information.

  • You may also use tools like Think. Check. Submit. to identify trusted journals and publishers for your research. Consider publishing in an Open Access journal to maximise the impact of your research. The Directory of Open Access Journals lists over 16,000 journals, over 11,000 of which do not charge a publishing fee (APC). You can use the Open Journal Matcher tool to identify the best-matching Open Access journals based on your draft abstract.

  • At this stage you may wish to check with the Open Access Team if your submission to a fully Open Access journal (such as any title published by MDPI, Frontiers or PLoS besides journals like Scientific Reports, Optics Express or Nature Comms) qualifies for Open Access funding for the mandatory APC fee from the library. The criteria for Open Access funding eligibility are summarised in our "Funding Open Access" webpage but you may prefer to drop us a line.

  • If you are funded by the Wellcome Trust, please contact the Open Access team at at the earliest opportunity for advice regarding routes to compliance with their Open Access Policy and to determine which pathway is most appropriate for your research. You can use the Journal Checker Tool to check if your preferred journal enables you to comply with the Wellcome Trust Open Access Policy and, if so, which route you should use.

  • You should create a record for the publication in Pure, including basic information such as the title of the output, the co-author network, the type of publication and the intended publication destination (typically journal or conference).

  • The Open Access team will check the basic details and contact you if any further information is required. Once checked, the repository team will validate the record but, as the publication is still in preparation, the visibility of the record will be restricted to Pure users only at this stage.

Research Data Management (RDM)

At this stage [view timeline]
  • You will have decided if you will deposit data in Pure or with an external repository. If you do decide to deposit externally check that the external body will provide a DOI for the data.
  • Select and review data which supports the publication. Data should be well organised and formatted, if the dataset contains complex data or has been created using proprietary software then a Readme file should be created which describes the characteristics of the data and be uploaded with the data to the Pure record.

  • Data must be reviewed to ensure that it is legal to re-distribute. Check the data for any legal, ethical, copyright or IP constraints.  Even if there is good reason to restrict access to the data this should be no barrier to the data being deposited. A public record of the deposit can still be made public even if the data itself is restricted in some way. All rights and permissions should be cleared before any data is uploaded.

  • Be familiar with the data upload requirements of Pure. For example Pure does not retain folder structures so files of similar format or content should be saved in an appropriately named folder and compressed into a single zip file and then uploaded. Note that the largest single file size for upload to Pure is 20GB.

  • Create a basic dataset record in Pure. Before a DOI can be issued a basic dataset record in Pure must be created and saved, the full record does not need to be completed immediately nor any data uploaded. The minimum requirement for a Pure dataset record is:

    • A title

    • A 'creator' (usually the person creating the record)

    • Add this year's date to 'Date made available'

  • Save the record as 'For validation' using the 'Status' drop down menu at the very bottom of the record.

  • A 'place-holder' DOI will be issued to you by RDMS staff. The 'place-holder' DOI is an inactive version of, what will be, the final active DOI. However all you need is a copy of the DOI at this stage so that it can be used to create a Data Availabilty Statement for the publication.

  • Add the 'place-holder' DOI to a Data Availabilty Statement (either in the Acknowledgements or Data Availability section) in the article manuscript prior to submission. If the data will be openly available then the Data Availability Statement will look like this:

    • "All data underpinning this publication are openly available from the University of Strathclyde KnowledgeBase at [paste University of Strathclyde dataset DOI here]"

  • Once you have added the Data Availability Statement to the publication the first main step in making your data FAIR is complete.

  • Return to the Pure dataset record and complete the relevant metadata fields and upload the appropriately selected data. Details on completing the dataset record can be found on the RDMS website and the guide "Describing your dataset in Pure" (DS login required)

  • Keep the record at 'entry in progress' until you have heard back from the publisher on the publication's acceptance.


Preparing Your Manuscript and Dataset

This is the first stage in the Open Research Lifecycle. At this stage, you will be taking the initial steps in transforming your research idea into tangible outputs. You will identify suitable venues for publication, prepare your dataset, and create records in Pure for both the publication (in preparation) and any supporting dataset(s).

The DOI (Digital Object Identifier)

Through out this LibGuide reference is made to a "DOI". A DOI is part of a suite of permanent identifiers and have been adopted for data publication, enabling data citation and reuse. See this short Open Access blog post for further details on how DOIs are employed at Strathclyde. DOIs are now also considered as an integral element of FAIR data and their use have become a mandatory requirement of many research funding bodies. Two key features about DOIs to remember:

  • Once 'minted' a DOI can never be deleted. Unlike a broken URL link, a DOI must always resolve to a landing page, even if the landing page declares that the data no longer exists. Unlike URLs, DOIs are monitored and managed, in the case of Strathclyde data DOIs by Datacite via the British Library.
  • Once minted no changes can be made to the metadata record or the data the DOI is citing. The DOI therefore helps to promote the data integrity of the deposit.
Consult Funder Policies

The deposit of supporting datasets is encouraged for all publications. However, authors should be aware that if their research is externally funded there may be additional compliance requirements on what, when and even where to deposit data, so funder open access publishing guidelines should be consulted. The EPSRC for example expect, at a minimum, that sufficent metadata relating to and describing a data deposit will be freely published on the internet and will contain a "robust digital object identifier" such as a DOI. The corresponding published research paper must include the DOI in a Data Access Statement describing how and on what terms any supporting research data may be accessed.

External Deposit

Pure is not the only data repository available to researchers at Strathclyde, but it is often the most convenient. There may be good reason to deposit with an external data repository; funder compliance (NERC funded research data should be deposited in a NERC data centre), format support and version control (GitHub for software and code). Note that if you do deposit data externally, a 'regsitry' record which documents and points to the external deposit, but where no data is uploaded, must also be created in Pure.


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