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Integrated Workflow for Publications and Datasets: Manuscript Acceptance

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

Acceptance with Revisions

Congratulations! You have received confirmation from your chosen publication that your research output has been accepted for publication. You will now complete any revisions as required following the peer review process. Following completion of any revisions, it is crucial that you save a copy of the author accepted manuscript (AAM) for uploading to the Pure record.

Open Access Publishing (OA)

At this stage
  • Save the version of the manuscript which incorporates all changes following the peer review process, before it has been formatted and copy-edited by the publisher. This version is known as the Accepted Author Manuscript (AAM).

  • If you created a record for the prospective publication in Pure at manuscript submission stage, then you should now update the record to include the full date of manuscript acceptance and upload a full-text copy of the AAM. At this point, the Open Access Team will complete the record with any missing metadata and validate it.

  • If you have not already created a record of the publication in Pure, you must do so now. Remember to include the full date of manuscript acceptance and to upload a full-text copy of the AAM. The date of acceptance and AAM are necessary to ensure compliance with the REF Open Access policy.

  • At this stage the publisher will offer you the option to select the most appropriate route to Open Access, 'Gold OA' or 'Green OA'.  

  • If you choose the Green Open Access route, then you do not need to take any further action at this stage. The Open Access team will check each record and apply any applicable embargo to the AAM as per the publisher's policy. Once the embargo period has been defined (if/where applicable), the publication and its associated metadata will be transferred to the Strathprints repository.

  • If you plan to select the Gold Open Access route, then you should contact the Open Access Team at to check (if not done so earlier) if the accepted manuscript is eligible for Gold Open Access funding from the library (ideally forwarding the acceptance notice). Once this has been confirmed, you may then select Gold OA for your paper on the publisher's site.

  • The Open Access team will assess and confirm eligibility for Gold Open Access funding on a case-by-case basis and, where appropriate, arrange for processing of the Article Processing Charge (APC).

How to Identify an AAM

How to identify an AAM

Copyright and Permissions

Copyright Transfer Agreements

Following manuscript acceptance, it is likely that you will be asked to sign an agreement with the publisher detailing ownership of copyright and permissions for re-use. Many publishers of traditional subscription journals will require you to transfer copyright to them as a condition of publication. Please read any publication agreement carefully before signing it to ensure that you are happy to accept the terms. If your research is funded and you are subject to research funder Open Access policies, then you should ensure that any agreement that you sign is compliant with these. 


You can check details of publisher copyright agreements and permissions via the SHERPA/RoMEO database.

Creative Commons Licensing

You can retain copyright and choose the conditions under your research is reproduced and re-used by applying a Creative Commons licence to your work. Work published via the gold Open Access route is often published under a Creative Commons licence. There are six different licence types, with the most permissive being the CC-BY (Creative Commons Attribution) License and most restrictive being the CC-BY-NC-ND (Creative Commons Attribution Non-commercial No Derivatives) licence. The licences allow you to specify if you wish your work to be used for commercial purposes and if you require the person re-using your work to share it under the same licence, or if you are happy with derivative works being created from your work. 

Please contact the Open Access team at if you have any questions regarding copyright transfer or permissions.

[some content above is adapted from Secker, J. [n.d.] 'Copyright for Researchers: Creative Commons'. Available at: under a CC BY NC licence (Accessed 6/4/2021)]

Research Data Management (RDM)

At this stage [view timeline]
  • You will have created and saved a Datasets record in Pure, which should currently be at "entry in progress"
  • You wil have recieved a 'place-holder' DOI from RDMS staff
  • You will have created a Data Availability Statement using the place-holder DOI and added this to the appropriate section of the manuscript
The Place-holder DOI

The reason an inactive or 'place-holder' version of the DOI is initally provided is because once the active version of the DOI has been minted, no changes can be made to the metadata or data held in the Pure dataset record. The DOI serves as a authentic time-stamped snapshot of the data and metadata in a Dataset record, providing systems and administrators with a means of establishing the intergity of the data and measuring any changes made to the record. Providing a place-holder DOI means a viable Data Statement can be added to the publication in good time while also providing the opporunity for any changes to be made to the record or data as a result of the review of the publication.

In Pure, once the DOI has been minted and the record validated, any attempt to update the record or the data will result in a re-validation request. Unless the re-validation request is minor in nature (e.g a typo) then the request will be rejected and a new dataset record and DOI will be required as the revision will be viewed as a 'new' version of the dataset. Such restrictions are in place so that the data integrity can be verified if required and protect against accusations such as data tampering. It is therefore important not to request a DOI be minted until you are certain that no further changes will be made to the data or the metadata.

In a situation where you are required to provide access to the data supporting a publication during the review process and prior to publication then the sharing options provided by Office365 OneDrive or Strathcloud should be employed (note that the 'direction of travel' within the university is towards Office365 and away from Strathcloud).

On acceptance from Publisher
  • Complete the metdata fields in the Pure dataset record, remember to:
    • Decide on the visbility options for the data and/or the record itself. Even if you wish to restict or embargo access to the data files the recommendation is that a public Knowledgebase record is still made available to record the data deposit and so a viable DOI can still be issued
    • Ensure you upload the final version of the data, including any revisions resulting from the peer review of the publication
    • Create and upload a comprehensive Readme file which describes any of the more technical aspects of the data being deposited
    • If the research is the result of a funded project (e.g. EPSRC/UKRI) then this should be added in the section 'Relations to other content' using the "Projects" button, just select from the available options. Adding the project provides the university with valuable compliance data on research funding

  • When you are satisfied that all relevant metadata fileds have been completed and all final data has been uploaded send the record "For Validation" using the Status drop down menu and the very bottom of the record.
  • The Pure record will then be reviewed by RDMS staff, if the minimum standard for completeness has been reached:
    • The active version of the DOI will be minted
    • The Pure record will be validated.
    • A public Knowledgebase record will automatically be created from the metadata contained in the Pure record. The visibility options set in the Pure record will determine whether the data you have uploaded will be made publicly available from Knowledgebase or not
    • Only at this point will the 'place-holder' DOI issued at the beginning of the deposit process become active
  • The Data Deposit is now complete.
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