Journal Title Abbreviations in Zotero and a ChatGPT Story
Updated: Aug 1
Everyone, it seems, has a ChatGPT story. Here's mine.
In my last post, I detailed how Zotero revolutionized my approach to reference editing. In fact, I hardly edit references anymore. It's usually easier to save the reference in Zotero and generate it, then replace the author's version with Zotero's. There are reference items that are almost correct to begin with, and these are the only ones I edit nowadays. They are, however, few and far between. Most of the reference lists I get need serious doctoring, and a transplant is much faster than intricate surgery.
One problem I discovered while using Zotero was that journal titles were not being abbreviated even when the style mandated it. This puzzled me. Was the user expected to enter abbreviated titles by hand? Why could Zotero not abbreviate the titles automatically? I turned to the Web for answers, but a full explanation was not forthcoming. I posted my question to the Zotero Forum, and the response was swift. Zotero could abbreviate journal titles automatically, but it was the Word add-in that did it. Outside the Word add-in, the "Journal Abbr" field would have to be used.
Now, I had used the Zotero Word add-in during my first brush with Zotero, and I wanted to avoid it. It's great for authors building their reference lists while they're writing their paper, I'm sure, but not for copyeditors wanting to edit reference lists. Generating a bibliography item in the add-in requires more than one step. So, I pinned my automation hopes on the "Journal Abbr" field (see the field in Zotero below).
This field could be filled in manually, but I wanted it filled automatically. The follow-up question I posed in the Zotero Forum was this: "Is there a way to populate that field automatically?" While I waited for the answer, I had a brainwave. Why not put the question to ChatGPT? I'd tried to ask it questions earlier, only to be rebuffed by the "I'm currently overloaded!" error message each time. This time, however, I crashed through the gates. I now had to frame the question. This is what I came up with: "How is the journal abbreviation field in Zotero populated?"
The answer came in a flash: "The journal abbreviation field in Zotero is populated using a database of journal titles and their corresponding abbreviations. When a journal article is imported into Zotero, the software matches the journal title in the article's metadata to the journal title in its database and automatically populates the journal abbreviation field. If the journal title is not found in the database, the user can manually enter the abbreviation or search for it using a built-in tool."
Wow! I was floored. However, when I examined the answer carefully, I was more puzzled than enlightened. I did want the journal abbreviation field to be automatically populated, and the process ChatGPT said Zotero used to achieve this sounded plausible, but Zotero wasn't working like that for me: it was not automatically populating the journal abbreviation field. I also noticed that there was no mention of Zotero's Word add-in, which the human expert on the Zotero Forum had mentioned. I was intrigued by the "built-in tool" for searching journal title abbreviations. The human expert had not mentioned this tool. I needed to probe deeper.
So I asked ChatGPT a follow-up question: "What is the built-in tool used to search for journal abbreviations in Zotero?" The answer was crystal-clear: "The built-in tool used to search for journal abbreviations in Zotero is called 'Abbreviation Index'. It can be accessed by clicking on the 'Tools' menu and selecting 'Abbreviation Index'."
I was onto the Tools menu in Zotero in a jiffy, but alas! There was no option called "Abbreviation Index" in the Tools menu.
Wait! Maybe it was an add-on? I eagerly clicked "Add-ons", only to see this:
This was a cruel disappointment! I had fallen for ChatGPT's confidently spun make-believe. It had led me up the garden path.
A little later, the human expert posted that for medical journals (I'd asked about abbreviations for AMA style), PubMed was the best source. Indeed, I found that the Zotero browser add-in automatically filled in the journal abbreviation field when I saved papers into Zotero from PubMed. I wonder if other disciplines have their own field-specific databases that will do this.
Someone on the Zotero Forum pointed me to https://www.issn.org/services/online-services/access-to-the-ltwa/ as a source of journal abbreviations for nonmedical journals, but this seems to be for filling in the journal abbreviation field manually. I suppose there is always the last resort: the Zotero Word add-in will automatically generate journal title abbreviations for CSL styles that have container-title-short or container-title form=short (examples of such styles are ACS and AMA). Zotero will first look for MEDLINE abbreviations. If it doesn't find the journal there, it will use ISO-style abbreviations (which MEDLINE is patterned on; thanks for this tidbit, adamsmith of Zotero Forums). I have just tested it, and it works. Here's what I did.
I first searched for the paper titled "Determination of the natural abundances of krypton and xenon isotopes using mass spectrometry: A demonstration of isotopes and the basis of atomic mass" in Scholar Google, and imported it into Zotero as described in my previous blog post. This is how the paper should look in Zotero:
Note that the Journal Abbr field is empty.
Now open a Word document, and load the Zotero Word add-in. Click on "Add/Edit Citation". The following windows appears:
Notice that the ACS style is selected. Ensure that the "Use MEDLINE journal abbreviations" is checked. Click OK.
The Zotero search box loads. Enter "Blauch " inside it, and press Enter. Zotero shows the Blauch entry it has found in our database.
Hit the Enter key. The Blauch citation appears.
Notice that a superscripted "1" has been inserted in the Word document, which is the numerical citation style that ACS uses. Click on the "1" and select the option "Add/Edit Bibliography" from the Zotero add-in. Zotero will ask if you want to replace the citation. Hit the Enter key, and the bibliographic item replaces the numerical citation. It is in ACS style.
Because this is a chemistry journal and not a life sciences journal, it's likely not present in the MEDLINE database. Therefore, Zotero must have used ISO-style abbreviations to generate this abbreviated journal title.
And, finally, where does all this leave ChatGPT? A friend had a similar experience with ChatGPT. He asked it a question about an unclear sentence, and the answer he got was similar to mine: it sounded plausible, recited known facts indirectly related to the question, but got an important detail wrong. These answers rang a bell. What did they remind me of? I finally got it. They remind me of what some students serve up when they don't know the answer to an examination question: the main ingredient is a regurgitation of whatever they know about a topic that is tangentially connected to the question, liberally laced with the jargon of the field, and garnished with one or two small doses of outright invention in the hope that the examiner will swallow them unexamined. The whole concoction is infused with the kind of swaggering confidence that brooks no rebuttal.
ChatGPT and similar tools need human supervision. Lots of it.
Oh, I almost forgot to credit the image that heads this post. It was created by the text-to-image engine DeepAI with the text prompt "ChatGPT".