DOI (Digital Object Identifier) for Systematic Reviewers and other Researchers: Benefits, Confusions, and Need-to-Knows

DOI: Digital Object Identifier

I had this question asked so many times I'm fed up with my repetitive patchy answers. Today, I listened to Professor Severus Snape: "Control your emotions! Discipline your mind!" and I wrote this post to refer my students and colleagues to it. Briefly:

PDF, DOI, XML, preprints, and clouds are the most impactful developments in the academic and professional publishing industry during the past 30 years.

What is DOI?

DOI or Digital Object Identifier is a unique number that a publisher, a journal, or a content repository assigns to an online digital object/document. To make it more comparable, it is like ISBN for books and ISSN for journals, DOI could be assigned to a book, book chapter, a video, an image in the paper, a journal, a paper in a journal, an appendix, and so on; however, it has many other good uses and different functions otherwise it would be a duplicate to other IDs. Although DOI was introduced in 2000, the publishers started assigning DOIs to the papers published before 2000 as well!

Read on, and I promise you'll enjoy :D

What is the structure of a DOI?

As a unique alpha-numeric character string, DOI has a prefix and a suffix:

  • The suffix starts with 10. to identify the string as a DOI;
  • It continues with the publisher's identifier (anything between 10. and the first slash /);
  • The suffix (anything after the first slash /) identifies the digital object. Some publishers use journal abbreviations or ISSN, year, and paper number for suffixes; others use meaningless sequences of characters.
  • DOIs are case-sensitive and work only if the object is on the internet with a publicly available file (webpage, PDF, audio, video, etc.).

Benefit 1. Finding the paper or digital object via 'DOI Link'

Just add the DOI at the end of https://doi.org/ or https://dx.doi.org/ in your browser's address bar to create a DOI Link and directly end in the origin of the paper or a digital object. This link is usually called the DOI link because it converts the DOI into a hyperlink, but many mistake the link with DOI and call it a DOI.

Benefit 2. Automatically downloading the full texts

If you can find the source of the paper via DOI Link and the paper is open access or your institute has access to it, you can download the full text, but two more alternatives can help you find full texts of the papers automatically:

A: Citation managers: in EndNote and Zotero, there is an option for automatic full-text finding when your citation includes a DOI. It may not necessarily get you the PDF, but if the access is clear, you'll get the PDF as an attachment to the record in your library. EndNote can search for full texts of 250 records at a time.

B: Sci-Hub: if the paper is not freely available and you have no other 'legal' choices to get the full texts, [use at your discretion] Sci-Hub is where you may paste the DOI and get the PDF most of the time. I have seen emergency doctors who have used Sci-Hub to get a full text and decide on a patients' choice to live or researchers and scientists from low- or middle-income countries who has no other options than WHO HINARI and Sci-Hub. Many from high-income countries also use Sci-Hub with justifications! Working from home, you may have to go through several clicks, VPN, remote desktop, and logins to get the PDF legally, but via Sci-Hub, it is faster.

Shame on access solutions not creating user-friendlier and faster ways to access the full texts from all locations for authorised users. Accessing a paper from home through OpenAthens and Shibboleth is like you simply pay for a cup of coffee in advance but to get the coffee you should climp up a ladder, squeeze thorugh a toilet’s window and swallow a frog! Sometimes you may have to kill a dragon on the way and it is not a creature to find easily in 21st century. Not fair, we need more dragons.

Some universities have blocked Sci-Hub; however, I am not here to discuss or advertise if it is safe, secure, legal, logical, or ethical; it is your judgment call. Again, use it at your discretion. If interested, watch the paywall movie or read the Abused Academics to help you decide.

Benefit 3. Finding the duplicate records

Obviously, and since the DOI is unique per digital object, it is an excellent meta-data to find duplicate records during the systematic reviewing process. However, many citation managers currently do not use the DOI field to match and find the duplicates. EndNote has been a disappointment.

Regardless, when you have two records that look similar in terms of title and one has no volume or page number, checking the DOI could be an option to find if one of the two records is duplicate if they both have the same DOI.

Benefit 4. Updating incomplete reference information in EndNote or publishers' submission systems

Since the meta-data for the digital object is being registered in a DOI server, it would mean that specific programs can retrieve or fetch this information. If you right-click on a reference with DOI in EndNote and try Update Reference Information, you can see how the magic works. This is pretty important for the systematic reviewers for duplication detection when they need to fetch page numbers and volume and supply enough information for journals before publication. Some publishers do not accept reference/citation to e-published journal articles in the reference misses volume or page numbers unless they have DOI.

Some of the journal submission systems will automatically fetch and update the reference information for your manuscript only if you use DOI [if available] for each reference to assure the data accuracy for each reference in your manuscript.

CAUTION: During automatic updating of the reference information in EndNote or submission systems, please check the updates for each record and update the Empty Fields Only if appropriate. Some DOIs are not specific/unique for one record and may retrieve the information for an entire journal issue; some DOIs may be entered incorrectly and find wrong paper's information. In addition, if you are using batch updating — selecting multiple records to update their information together with fewer clicks — be careful with the EndNote option that asks if you want to use the retrieved updates for all the selected records in the batch! The existence of such an option is another disappointment for EndNote.

Benefit 5. Creating an 'almost' a permanent link to a paper or a digital object

Yes, adding DOI at the end of https://doi.org/ will take you to the source of the digital object or paper so it can be a permanent link to the paper 99% of the time. Try this: https://doi.org/10.1016/j.jclinepi.2021.02.002

This link connects to DOI sever where the correct URL/Link to the paper/digital object has been registered and then re-directs you to that URL/link. It is the publishers' responsibility to keep that link updated, and if the online address of the digital object changes, the publisher should update it to the new online address in the DOI record in the server. That way, the DOI link will always work, and it is usually the shortest trusted link to the paper — as opposed to TinyURL.

Benefit 6. Detecting the predatory publishers and journals

Maintaining data and meta-data on DOI servers are costly and requires administrators, security, and server costs. Certain publishers or journals who won't pay or won't be able to pay:

A: Predatory publishers/journals: these are the publishers/journals that publish with the primary purpose of earning profit at less or no economic cost and any legal or ethical cost! No cost means spending no resources (time, skilled people, money). So they accept and publish anything as long as you pay; they do it rapidly as long as you pay; they will not have any/little editorial checks or peer-review to save time. The final papers will not have proper designs because a designer costs. And last but not least, most predatory journals either do not have DOI or their DOI will not work if you add it after https://doi.org/

B: Poor/unaware publishers/journals: these are usually journals with little or no sources, so they cannot afford the costs of DOI or design. Volunteers usually manage them, and no one gets paid. They may also not be professional publishers to be aware of the benefits of DOI.

C: Unfair economic sanctions: if the publisher or the journal is from countries affected by economic sanctions, they either are unable to pay, or they are unable to transfer money.

I have a reply email from late Norman Paskin — founding director of the International DOI Foundation (IDF) — who replied to my DOI request email that since you are from a country affected by economic sanctions, we cannot allocate DOIs to your journal! The North remembers.

Benefit 7. Citation detection purposes

Using DOIs in all references makes it easier for citation indexes and databases to use linked data technologies and detect and display the citations to the papers. Such a feature is also helpful in identifying more relevant papers in some of the information retrieval systems and search engines. For systematic review purpose, tracking such citations are considered a complementary search method to systematic searching.

Benefit 8. Updates on the changes to the publication

A: Updates to bibliographic information: Imagine a paper gets published as 'online first' or 'early online' without final volume, page numbers, and year of publication, and you use/cite it in your research or your systematic review; however, your review or research takes time to complete and by then that online paper might be published within a fully paginated volume of the journal. Clicking CorssMark sign — you might have seen CrossMark in some of the PDFs and websites — you can access the latest version and update information/meta-data for the paper.

CrossMark

B: Retaction or corrigendum/corrigenda or erratum/errata:

  • people may publish the research findings based on the research that never happened;
  • they may fabricate or falsify the data
  • they may manipulate the interpretation of the data to serve their interests (conflict of interests);
  • they may publish the same paper in more than one journal;
  • they may commit plagiarism;
  • they may use unethical guest/ghost authorship;
  • and if you want more, visit the Committee on Publication Ethics (COPE).

Such academic dishonesty may be revealed, and the paper may be retracted! DOI and, in particular, the meta-data in the CrossRef server would get such change via DOI. Zotero can detect some of these retractions automatically and efficiently if a retracted paper is in your Zotero library.

Occasionally, people also may have unintentional typos and errors that may be detected and corrected after publication. Such changes appears as erratum/errata or corrigendum/corrigenda. As the magic of linked data works, CorssMark from the CrossRef server would show you if you are seeing or holding the most updated copy of the document, and if not, you can click the link to see/find the latest version.

Benefit 9. Creating a reference record using only DOI

Imagine you are reading a journal article in PDF format and you want to add it to your EndNote library to cite it later. All you need is to copy the DOI and paste it into the DOI field in a new reference record in EndNote and save it, then right-click on the record and find updates to populate all the bibliographic information. Done.

Benefit 10. API purposes

I'm not a programmer, but I know software programmers/coders can create programs that can fetch, integrate, link and create new products out of the meta-data only if they could have these DOI numbers or any other useable open IDs.

Why may a DOI link end with an error?

The problem is that sometimes these DOIs do not work for several reasons, such as having special characters that the browser cannot convert typos or publishers forgetting to register/update the DOI in the server. Then if you click the DOI link, you may get the 'DOI for found' error which is when CrossRef would receive these errors.

DOI Not Found

Common reasons for such errors:

  • A DOI is published/distributed but hasn't been registered yet;
  • A published DOI doesn't match the registered DOI;
  • A link (URL) was formatted incorrectly (a . at the end of a DOI, for example);
  • A user has made a mistake (confusing 1 for l or 0 for O, or cut-and-paste errors).

Can I have a DOI for my unpublished works, please? YES!

You cannot make up a DOI out of the blue; they need to be registered in a DOI server to function properly.

Many institional repositories, preprint servers (arXiv, medRxiv, bioRxiv), and research networks (ResearchGate) allow you to have a DOI if and only if you upload a free copy of your work to their server. It is also possible to upload the same work into several of these sources and get several DOIs which is against DOIs uniqueness philosophy!

Two Types of DOIs!

In my work, I have seen two types of DOI!

  1. Type I: they support all the benefits I described above. Professional publishers usually assign them to academic journal papers.
  2. Type II: they are only good for taking you to the paper via DOI link; you can get one immediately and for free via publishing public preprints or submitting works for public availability in repositories such as ResearchGate, medRxiv, or DOIs used by many Chinese journals. Such free DOIs encourage open access to science but can't necessarily support the other functions, and you can delete your work and its DOI permanently in many cases!

Misuses and abuses

  1. Different DOIs for the same work: Some love to share their unpublished works in as many DOI-assigning repositories as possible, so they get many different DOIs for the same work! Examples of repositories that give you free DOI are ResearchGate, Open Science Framework, and medRxiv. This confuses and divides the citations because citation indexes use DOI to indicate that each object with a DOI is unique. In systematic reviews, we count all such reports as a single study; this process is sometimes called studification.
  2. Assigning a single DOI for an entire conference proceeding or several conference abstracts: Some publishers are not professional enough to know that using one DOI for an entire supplementary issue of the journal or an entire conference abstract is against the discoverability philosophy of DOI. This also causes issues when finding updates for records in EndNote. It is easy to make a mistake and replace the bibliographic information of a single conference abstract with bibliographic information assigned for all posters or oral presentations in the journal issue. Each conference abstract published in an issue of the journal should have a separate page and separate DOI. Professional publishers usually use a unique DOI for each conference abstract, but some publishers save money and their DOIs!
  3. Fake DOIs: fake publishers and journals or their copycats may use fake DOIs; either DOIs don't work (after adding at the end of https://doi.org/), or if they work, they should take you to the original journal's page, not the copycat's page! Some publishers/journals — unaware of professional publishing — think that DOI is something like a page number that you should creatively create and assign to papers, and they have no other uses. Hence, they generate a string and call it DOI. They don't work!
  4. Wrong Direction: imagine that you have access to a paper via institutional access. Then, the publisher's DOI links re-direct you towards a webpage that shows you purchase and subscription options rather than download! Guess who? Elsevier!

So I found this paper in PubMed, and I can either click the Elsevier's logo or click the DOI link (Figure 1); both would take me to the journal's webpage where my options are Purchase or Subscribe (Figure 2)! Then I copy the paper's title into the search box in Elsevier's ScienceDirect.com, and voila! I can download it for free via institutional access (Figure 3)! Why would Elsevier do such a thing? And Why am I not surprised people using Sci-Hub to get the papers with fewer clicks!

Figure 1. Elsevier Style Confusion via PubMed DOI Link
Figure 2. Elsevier's DOI link's landing pager asks for purchase or subscription!
Figure 3. But I can download the same paper from Elsevier's ScienceDirect.com via Institutional Access!

Conclusion

DOI enhances the accessibility, discoverability, trustability, and interoperability of digital objects and serves the openness and visibility of professionally published content. While I am not a DOI expert, I know about it because I use it a lot in my profession. I believe DOI will play a significant role in the automation of literature reviews. More than it does now.

It is the responsibility of librarians, information specialists and other information professionals to raise awareness about the benefits of DOI. DOI is one of the best developments in the snail-paced developing publishing industry. If you behave, I will write about XML next time :D

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A Proper Information Scientist/Professional with a Pinch of Career and Life Lessons

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Farhad

Farhad

A Proper Information Scientist/Professional with a Pinch of Career and Life Lessons

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