Journal of Cheminformatics - Abbreviation

Gregor Simm

When importing articles with the Firefox plugin, Zotero (5.0.96.3) does not populate the "Journal Abbr" field in the corresponding bibliography entry for articles in the Journal of Cheminformatics https://jcheminf.biomedcentral.com/. The journal abbreviation I would expect is "J. Cheminf."

In contrast, when importing from the Journal of Cheminformatics and Modeling https://pubs.acs.org/journal/jcisd8, the field contains the correct abbreviation (J. Chem. Inf. Model.).

As I am frequently encountering the problem of Zotero not abbreviating certain journals titles, I would be thankful if one of the developers could document here where to change that so we can create PRs in the future.

adamsmith

How are you generating the citation? Journals are only auto-abbreviated when using the word processor add-on

Gregor Simm

Thank you for the quick response, and please excuse the imprecise problem description. I updated my post accordingly.

In summary, I am referring to the Journal Abbr field that is not being populated.

Gregor Simm

@adamsmith, are there any updates regarding this issue? I would like to contribute to the Zotero project by documenting how to fix incorrect journal abbreviations. Thank you.

adamsmith

What gets imported as a journal abbreviation depends on the site you're importing from and the metadata they provide.
To fix this, you'd have to see if the journal abbreviation us anywhere in the metadata of the site it's not importing from and then modify the import script (translator) in Zotero. In many cases, however, it's just not going to be available.

But I am also wondering about the use case here? Why aren't you using the word processor add-on?

Gregor Simm

I see, so it's not the case that Zotero looks up the abbreviations when importing new items with the browser plugin but extracts them from the website's metadata somehow.

Could you point me to the piece of code that I would need to update? I looked through the translator's development guide, and I didn't understand what I needed to do now.

I am using BBT to generate bibliography items. I am interested in resolving this problem because I would like my Zotero database to be as complete and correct as possible.

adamsmith

I'm pretty sure there is a setting in BBT to use Zotero's auto generated abbreviations

There is no one place in the code. This would have to be done separately for each translator that doesn't import journal abbreviations. The translator code is on GitHub, I assume you have found that?

Gregor Simm

My goal is to change Zotero such that the field "Journal Abbr" is populated correctly every time I import a new item using the browser (Firefox) plugin.

I figured out that this is related to the translators but I don't know how they operate precisely. I read the documentation, but it is unclear how the abbreviations are determined.

1) How do I work out which web translator is active for a particular site (e.g., https://jcheminf.biomedcentral.com/)?
2) I checked the https://github.com/zotero/translators repository and couldn't find much on the journal abbreviations despite the fact that Zotero gets the abbreviations right most of the time. What am I missing?

adamsmith

1. Hover over the Save to Zotero icon
2. Most publisher translators will find one of three common metadata formats (Embedded metadata, RIS, or BibTeX) on a site and then import and clean that. So you would have to figure out what they use and if it has the journal abbreviation in a given site and then continue that. The specific metadata format used is not set in stone, though it's typically used for a reason.

All that said -- while I assume we'd take patches, I don't think this is a particularly good use of time. Abbreviations can be reliably generated from the journal title, which is what Zotero doesnin the word processor andnwhatnBBT uses, so why bother?@

Gregor Simm

Thank you for clarifying, @adamsmith. The translator for https://jcheminf.biomedcentral.com/ is (unsurprisingly) BioMed Central. From the source code of this translator, I can see that it downloads a RIS file and extracts the information from there. I understand that there is little point in tweaking the code to accommodate this use case. Nonetheless, it would be nice if there were infrastructure that would allow modifying the automatically scraped information.

DWL-SDCA

The metadata provided by many (if not most) journal publishers _worldwide_ includes abbreviations that are non-conforming with the NLM-Medline model or even the LTWA. Abbreviations of law journal titles follow a different standard. Many engineering journals follow what seems to be a standard (but I've never spent the time to find it). Other journals have abbreviations that have no basis other than the whim of the original editor or the publisher.

For each imported record, Zotero uses the publisher-provided abbreviation when it captures metadata from the web. It seems to use the LTWA or Medline standard when auto-abbreviating from titles.

Except within the discipline of law (Blue Book) I don't recall seeing anything in journal guidance for authors about abbreviation standards. Other style guides (APA, MLA, etc.) provide different instructions for how to represent journal names.

The point of all my verbiage is that you need to tailor your abbreviations to conform with the style guidelines of the publisher that will receive your manuscript.

edit:

I use Zotero to capture metadata from publisher websites, hand edit the Zotero records to conform to my needs, export the Zotero records in MODS format and through a parser import the MODS file into another database that is the basis of an online bibliographic indexing service. The parser uses an ISSN-based look-up table to standardize the journal abbreviations. The table is updated by hand as unknown journals are identified. The index includes journal titles (all that are in common use, including acronyms [JAMA]), and LTWA derived abbreviations. For selected journals, we also include other abbreviation standards as journal title synonyms. The purpose here is to allow naïve searchers to find what they are seeking without knowledge of official abbreviations and titles. If a Zotero user imports a record from my online database they will only receive the LTWA abbreviation. A purpose of Zotero is to expedite manuscript preparation and Zotero (or any other current software) cannot know the abbreviation requirements of the publisher an author must please. (Very early CP/M and DOS versions of the now defunct Reference Manager allowed up to four journal abbreviations to be assigned to a journal title.)

Gregor Simm

Thank you for chiming in, @DWL-SDCA. You're right; it's practically impossible to cover all the different standards. There's no point in even trying.