Thursday, May 08, 2025

Academic publishing tools tripping up AI's automation of bibliography processes

By Mary Harrsch 

Lately, I've been working very hard to consolidate the six articles I wrote, "Isolation and Climate Change Factors in Delayed Technological Development of the Ancient Americas" into a single narrative-style article complete with citations and extensive illustrations. I've also included additional information and the file is now 72 pages long including a 23-page bibliography.

College student compiling a bibliography. Image generated by Adobe Firefly with a Robert Griffing painting used as a style reference image.

It is obviously too big to share directly in Facebook or even post to one of my blogs so ChatGPT suggested I submit it to Zenodo (https://zenodo.org/), a site developed by CERN to provide storage for Open Access research articles and assigns DOIs if your article doesn't yet have one. It also suggested I obtain an ORCID so my work would never be confused by any other author with the same name (Yes, there is another Mary Harrsch out there and I bet you thought I had to be one of a kind!)

So, yesterday, I decided to establish an account on ORCID then on Zenodo to accomplish this. Obtaining an ORCID was not a problem. I just had to spend about an hour populating it with my education and certificates information, professional memberships, public service activities, etc. Then, I set up an account with Zenodo and prepared to upload my paper that is now titled "The Paradox of Plenty: How Isolation and Abundance Stalled Innovation in the Ancient Americas."
The upload form for Zenodo is not very user friendly and labels fields rather strangely (at least from my American perspective). First of all, it appears to require you to submit your paper to a "community" for approval. I since learned this is not required despite its appearance and it will slow down your submission approval by several days. I also hate gatekeepers! So, DeepSeek told me not to assign a community in the future and if I get tired of waiting for approval, just remove my submission and complete another submission request without a community selection so it will be published right away and I can obtain the DOI assigned to it.
Next, there is a field labeled "Creator". Below it is a field labeled "role". When I scrolled through the roles I saw "author" was not listed so I chose "researcher" and an error message immediately popped up. I checked with DeepSeek again and it said to just enter your name and leave the "role" field blank. Then there was a field to enter an identifier like ORCID so I entered by assigned ORCID and another error message popped up. This may have been the result of me setting up my Zenodo account with my ORCID to begin with. ChatGPT told me to link my ORCID in my user settings and leave the field blank on the form. When I checked my settings, it already showed I had linked to my ORCID account.
Then I got to the "References" field. Even though my article contains inline citations and a complete bibliography at the end, Zenodo expects your bibliography submitted as a .bib file. OK, DeepSeek told me I could create a .bib file using a tool at Text2bib.org. I had already each of my bibliography entries for proper APA format so I was given the following instructions:
Copy APA formatted bibliography from Word
Paste into Notepad to remove Word formatting
Save as .txt carriage return delimited file
Login to text2bib.org
Submit .txt file for conversion
Be sure to select "carriage return" as the delimiter type
Check for errors using either the website's correction interface with buttons and a popup correction form or
Download .bib file
Open in Notepad and check entries for accuracy.
Text2bib provides a GUI interface with buttons and a popup form to correct entries but it is so time consuming I prefer to download the .bib files and scan them myself with Notepad because it is so much faster for me. Years ago, I used to write programs in .html and .php so I am relatively fast at spotting errors in lines of code.
I was also told about a tool called Zotero. It can import .bib files and create a library of citations for you that can be used in multiple related projects and can create bibliographies in whatever standard you prefer like APA, MLA, etc.
Both ChatGPT and DeepSeek can provide inline citations and related bibliography entries for all information sources used in your writing. However, they struggle a bit with making the entries completely format compliant.
I use APA format because it is considered acceptable for multidisciplinary research. The citations provided by ChatGPT and DeepSeek are useful but in APA format, both article titles and book titles are to be formatted in sentence case. Some of the citations provided were in Title case so I had to manually correct those. (By the way, even though I have Word 2021, it seems to refuse to let me use its case icon and change Title case to sentence case! ??)
AIs sometimes have problems identifying the type of source, too - book, journal article, etc.) A number of my 307 citations were also missing DOI links for journal articles so I had to paste the citation into Google Scholar and search for the page where I could obtain the DOI. Chat GPT admitted this is a problem for AIs because there appears to be no real standard across online academic sources as to where the DOI is located. Journals like "Science" display it on the main article page. Others may label the link "cite" that you must click to reach a page where the DOI link is listed.
It took me a little over an entire day to chase down the DOIs which, in my opinion, is a real waste of time. I know there are academics who seem to think the ability to produce a compliant bibliographic entry demonstrates your academic rigor but to me it's just an annoying clerical task, usually delegated to research assistants. I described my process to ChatGPT and it admitted it should be a task than an AI could accomplish in seconds but with the nonstandard format of academic journals, it would be difficult to automate. Sigh...

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