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Open Access Research Publishing: Home

This is a guide to open access pubilshing in the heatlh services.

What is Open Access?

Open Access is an academic publishing model which makes research freely available to read, avoiding subscriptions or paywalls. First articulated in the Budapest Open Access Initiative of 2002, Open Access is transforming a publishing world dominated by multinational corporations and expensive subscription arrangements.

Many Open Access journals are funded by the payment of Article Processing Charges (APCs), while others do not charge for publication, instead funding their operation via organisational subsidies.

Open Access offers a number of benefits. It allows authors to retain copyright and other intellectual property rights over their work, unlike subscription publishing. It allows researchers and ‘citizen scientists’ to access research that was previously beyond their means. It increases the visibility and citation frequency of published research, boosting the careers and reputations of its authors. And it addresses a long-standing inequity of research publishing: that publicly-funded research should be available to the public funding it.



Open Access and Lenus - a quick video introduction by Dr Greg Martin

Green vs Gold Open Access

  Green and Gold 

"Green" OA refers to the archiving (or self-archiving) in a repository of the corrected, peer-reviewed draft of an article which the author receives prior to final formatting and publication.

"Gold" OA by contrast is the immediate universal availability of an article following payment of an APC.



Open Research

In recent years Open Access has expanded to include the related concepts of Open Data and Open Research. According to the Department of Public Expenditure and Reform,

“The concept of open data is about making the data held by these public service bodies available and easily accessible online, for reuse and redistribution… The positive impacts of open data are wide-ranging and cover political, social and economic spheres. These can range from improving transparency and efficiency of government, potential for business innovation and a vast array of social and personal benefits.”

Open data involves making available both the large datasets held by public bodies (with obvious exceptions for reasons of privacy and commercial sensitivity) and the data gathered or generated by researchers in the course of their work. By also including any software or protocols used in the research, we move from Open Data to Open Research. OR allows for greater validation and reproducibility of research, and potentially faster scientific progress.

A coalition of European research funders, cOAlition S, has produced a plan (“Plan S”) for all scientific scholarly output to be published in an OR forum by the start of 2021. Science Foundation Ireland is a member of cOAlition S. In July 2019 the National Open Research Forum (NORF) published a framework document outlining the technological and regulatory requirements to make OR a reality.

Scholarly Communication

Health Library Ireland offers a range of resources and advice on aspects of scholarly communication, enabling researchers to navigate the pitfalls of the research publication process.

Repositories: repositories are long-term storage facilities for research. Unlike websites they allow for stable preservation of research and assign persistent identifiers that allow items to be uniquely located and described. They also function as a ‘shop window’ for published research, increasing its visibility. Most research-producing institutions have a repository – the HSE’s repository is Lenus, managed by the NHLKS.

Copyright / Intellectual Property: One of the benefits of Open Research is that it allows authors to retain control of their work, and the conditions under which they make it available. Conversely, authors publishing in a non-OR forum who make their research available online (e.g. on Researchgate) are often violating copyright law in doing so. The NHLKS offers advice to researchers on copyright issues, so that they can stay within the law. The Sherpa / RoMEO website also enables authors to check the Open Access policy of a journal to see if it meets the requirements of Plan S.

Predatory journals: the rise of OA journals funded by Article Processing Charges (APCs) has inevitably led to a form of online scam known as predatory publishing. Predatory journals set up websites purporting to publish peer-reviewed OA journals. In reality they provide no such peer review, and exist only to take money from unsuspecting researchers. Predatory journals are not just a waste of money, however. A researcher’s reputation can be damaged by having their research published in a predatory journal, and they will be unable to publish the research elsewhere.

Many people have compiled lists of predatory journals to alert researchers to the dangers they pose, but such lists are of dubious value. Disagreement exists over what constitutes ‘predatory’ as opposed to just low quality, and some predatory publishers attempt to evade detection by taking over legitimate journals to use as ‘front’ operations.

So how can a researcher ‘stay safe’ online? A number of tools are available to guide you through the journal evaluation process:

Directory of Open Access Journals (DOAJ): a regularly updated list of Open Access journals which meet an agreed set of quality criteria.

ThinkCheckSubmit: a site that helps researchers choose the right journal for their research, and to assess its trustworthiness.

Sherpa / RoMEO: this site allows you to check the Open Access policy of a journal.  

HSE Open Access Publishing Statemment

The HSE is very much to the fore in advocating Open Access in Ireland. Its 2013 statement notes that the organisation "is committed to sharing the findings of its research as widely as possible to enhance its use and its impact on the population it serves."



How to add items to Lenus - basic submissions

Irish health documentation, reports, guidance etc can be manually added using this process. One-off items or independent parts of a series can also be added this way. Such items are normally harvested by the Lenus manager from a list of monitored pages and periodically added to the ‘Items to be catalogued in Lenus’ folder on the shared drive. The list is by no means exhaustive however, so if you come across an item not in the folder, or feel a certain site should be monitored, please suggest it.

  1. Log in.
  2. Click ‘Communities’ under the map icon and again for the appropriate sub-community or collection.
  3. Once you’re at the collection level, click “submit a new item to this collection”.
  4. Ignore ‘choose import source’ prompt and click ‘next’.
  5. Fill in as much metadata as you can. More metadata means better discoverability and increases the usefulness of the item.
  6. At the bottom of the page click ‘next’.
  7. Under ‘File’ click ‘browse’ and locate the file you want to upload.
  8. Review your metadata and make any corrections necessary. Click ‘Next’.
  9. Click through the ‘license type’ screen – this is rarely needed.
  10. Click the ‘I grant the license’ box and finish.

The completed item will go into a queue to be reviewed by the collection administrator and you’ll be notified when this is done. Review is a necessary part of the quality control process. If you have another item to add to the same collection, click ‘submit another item’. Otherwise return to Communities to find a new collection.

How to add items to Lenus - importing items from PubMed

 There are many full-text Open Access items in PubMed which can be easily imported into Lenus. They are mostly peer-reviewed journal articles. We save these as a list of references in the Lenus folder on the shared drive.

  1. Go to PubMed and locate the reference for the article you’re adding to Lenus.
  2. Select the PMID from the reference.
  3. Click on ‘affiliations’. If one or more of the authors is affiliated to a Republic of Ireland institution, proceed. If not, refer to Lenus manager.
  4. Log in to Lenus.
  5. Go to the Lenus collection matching the author affiliation (or the appropriate subject collection).
  6. Click “submit a new item to this collection”.
  7. Click ‘choose import source’ and select PubMed.
  8. Click ‘next’.
  9. Paste the PMID into the search box and click ‘search’ (hitting return won’t do).
  10. Click ‘import’.  If the item is already in Lenus, a notice to this effect will display.
  11. Scroll down to the imported reference and click ‘next’.
  12. PubMed imports to Lenus usually don’t include the abstract, so copy this across manually from PubMed. Likewise if there are no subject headings, you’ll need to choose one or two yourself.
  13. When you’re happy with the imported record click ‘next’.
  14. Download the article full text from PubMed.
  15. On the Item Submission screen in Lenus click ‘browse’ to attach the article, and navigate to wherever you keep downloaded files. Attach the file. Scroll down and click ‘next’.
  16. Review your submission, scroll down and click ‘next’.
  17. Ignore the license screen and click ‘next’.

Click the ‘I grant the licence’ box and then ‘complete submission’.

Note: if you're using the list of PubMed articles on the shared drive as a source, remember to delete each reference after completing the import procedure.

How to add items to Lenus - adding new versions of an item

A particular form of submission to Lenus is version control. Version control allows us to store successive versions of an item in a single record. It has become routine during the Covid-19 pandemic due to the number of clinical guidance documents being issued, and the frequency with which these change. Version control is a cumbersome process, but one-to-one training can be arranged for anyone interested in learning how to do it. 

  1. Got to the record of the item for which you’re adding a new version.
  2. From the Context menu on the left of the screen, click ‘create version of this item’.
  3. In the ‘Reason for creating new version’ simply type ‘updated to vX.X on [date]’.
  4. Click the ‘Version’ button.
  5. Review the existing metadata for this version and click ‘Resume’.
  6. Click ‘Skip import’.
  7. Make the required changes to the metadata for the new version. These are usually just the version number and publication date, but may include title and abstract changes.
  8. Click ‘Next’.
  9. Under ‘File’ click ‘Browse’ and select the file for the new version. Before you do this, change the file name to include the version number, e.g. ‘v2.1SampleDocument’. This is important to avoid it getting lost in a series of similarly-titled files.
  10. Click ‘next and complete the submission as normal.
  11. Delete the file from your drive.
  12. The collection administrator will approve the item. If you are not the collection administrator you’ll need to contact them to expedite this.
  13.  When the item is in Lenus (it will be at the top of your ‘archived submissions’), select it and click ‘Edit this item’ from the left side Context menu.
  14. Click the ‘Item bitstreams’ tab and look for the file group ‘Bundle: ORIGINAL’. These are the files associated with the record.
  15. Locate the new version file and click the move up button on the right. Repeat this until it is at the top of the ‘Bundle: ORIGINAL’ group. This will ensure that it is the file displayed with the metadata record (the other files are under ‘view more files’).
  16. Click the ‘Item status’ tab, then click ‘Authorizations’.
  17. Find the ‘Policies for Bundle: ORIGINAL’ section. These govern access to the files.
  18. Click the READ policy for the second-newest version (the one that just been superseded).
  19. Under ‘Select a group’ change Anonymous to Administrator. This locks the version from public view.
  20. Click ‘Save’ to return to the previous screen.
  21. Once again, locate the Policies: BUNDLE section and scroll past the current version and the one you have just locked. If there are older versions they will have an Anonymous policy attached, and these will need to be removed. This is done by simply ticking each Anonymous policy you want to remove.
  22. Scroll down to the bottom of the screen and click ‘Delete selected’ and ‘Delete.’
  23. Click ‘return’ until you’re back at the metadata record for the item. You can now see the new version displaying at the top (the older versions will be under ‘view more files’).
  24. Click ‘Return’ and ‘Return’ again to exit.

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