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Comment by westcort | Hacker News Reader

I write a lot of academic papers and never use this kind of software. EndNote creates uneditable references and slows down Word, Zotero had some limitations after which they charge a monthly fee, and none of the reference libraries are easy to share with external clients.

Most other medical/technical writers I know only use these tools as a “reference library.” It might be useful for someone writing a thesis, but almost all professionals avoid these because they slow things down, break, and require updates that cause issues.

I use API requests to get formatted references direct from PubMed, and use FileLocator Lite to search multiple PDFs in reference folders with RegEx. QPDF is useful for unlocking PDFs. This system has worked quite well for me and I don’t have to worry about my data getting locked into aging or unsupported software platforms.

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Only if you want to sync pdfs using the Zotero server does Zotero cost money. Anything else is completely free, including syncing your db (without pdf attachments). If you want to sync your pdfs you can point Zotero to a webDAV server, this has worked flawlessly for me.

You can use something like Nextcloud to run your own webDav server, if that's something you are okay with. I haven't tried this, but I believe you can then share out files using Nextcloud via a unique link. Actually, I know the sharing works, just not sure if it's easy to do with a Zotero back-up of PDFs.

The most valuable workflow is the one you have been using and happy with. I wouldn't wish a changed workflow on anyone in this state. I would only suggest another way for someone who is unhappy and already regularly changing. Stick with what works.

Fair enough, but not every client is going to want to use the same operating systems, processors, be allowed to install third party software, etc. This might work in a strictly academic setting with few stakeholders, but in professional publishing, interoperability makes these systems unpopular. Downvoting that won’t change reality. I guess there is not much interest in feedback or possible routes to improvement.

You're getting down voted because you comment seems uninformed. AFAIK Zotero is available on every OS that Firefox runs on, for example. Also you talk professional publishing, what does that exactly mean? Zotero is a reference manager, so largely aimed at academic writing (because they tend to be the ones who cité and use references the most). I would be surprised if any other setting has more stakeholders, scientific articles often have lots of coauthors, from different groups and I can sayas an academic keeping track of thousands of papers by grepping through PDFs is not really feasible.

So maybe your use case does not match what a reference manager is for, but you also have not brought any informed criticism.

Let’s say you are working on a paper with 6 coauthors for a major medical journal, hypothetically. Dr. So and so in Russia, another in Japan, a third in California, and a few others. Would you mind reviewing this draft? Oh, yeah, by the way, you need to install Zotero before you can edit the references. How do you think that is going to go? How about dealing with a graphic designer in Hungary who can’t copy the text out of the document because there are weird hyperlinks that copy out with the references and don’t work with the InDesign. Oh, and the PM at DDB says the citation manager crashed and could you please resend the PDFs. I have worked with some big name journals and there are major interoperability issues that make this software undesirable for publishing in many scenarios.

For what it's worth, I've seen the same sort of interoperability issues with all similar software. Author A wants "the latest copy of the Endnote file" but nobody's using Endnote; Author B insists on emailing PDFs as attachments and uses their email as their personal literature database; Author C has set up a Dropbox full of PDFs but nobody uses it; Author D has created a shared Google spreadsheet with links to each paper but it's always out of date; etc etc etc.

These aren't issues with any one piece of software, they're issues with coordination, as are the examples you mention.

Yes, I think that makes a lot of sense. Maybe the issues I am referring to are more to do with the general frustrations of putting together a paper with multiple authors and less to do with specific software.

This is why I just use Google docs and Google scholar... when i need to do the refs, I just alphabetize in a sheet. Frontiers has low barrier citation expectations. If I have to do ACM numbering I do it in word, as last step.

This is the way. Numbering should happen right before submission.

I'm not really seeing it. In most of the workflows I've used, one person is responsible for maintaining most of the document including the bibliography. The other coauthors will add in notes requesting to add in a new item, etc.

Zotero is used primarily for managing the PDF library, the actual writing will happen in Word, LateX, etc. The reference list produced by Zotero is just text.

I don't see any real requirement that everyone working on a project would need to actually use Zotero, though I guess it would be handy to keep a coordinated shared library of papers.

Maybe I'm wrong and it is a very valuable tool I should be using. I just haven't seen it used in my industry over the past 2 decades. All I have heard about are major problems arising with use of this kind of software. Surely that experience has to count for something? I don't have any problem with others using it. I am just saying that when I submit a paper to a major journal, these kinds of tools generally are not used because of interoperability issues that inevitably come up when multiple people work on a project.

Maybe it actually is something I should try and it sounds like there have been some major improvements over the past few years. I dislike EndNote, but that doesn't mean the same issues exist with Zotero, so maybe I will give it a try. I should also define my terms better. When I talk about professionals publishing, I am referring more to corporate publishing houses, agencies, and pharma and chemical industry publishing. Academic publishing is probably the most professional type of publishing of all, so I should clarify that.

What reference library is easy to share with external clients then? Also, what do you mean by "external clients"?

Clients, editors, etc. Internal clients might be an editorial department within a holding company that works across agencies, for example. I know I am getting downvoted, but it’s a reality that these systems have caused issues for companies like mine and have not been widely used in professional publishing, mostly due to interoperability issues.

Zipped folders of PDF files sent via e-mail.

Sharing zipped files of PDFs amongst people is quite possibly a copyright violation. Do you have distribution licenses for all the material you ar referencing?

I am curious as to how you share PDF files with others ensuring that you have distribution licenses for all of the files. Not even RightsLink from the Copyright Clearance Center automatically purchases those distribution licenses. What I do know is that other ways of sharing files do not have the same privileges of communication applied to e-mail in the law, so that is the reason why this is still the most commonly used strategy.

Interested to hear more about this, so how do you create citations and bibliographies? How do you format the bibliographies according to each journal’s style?

It is true that there is no good tool for editing references collaboratively. Previous attempts at this have resulted in some poor sod having to redo all the citations.

In my field, we typically just use plain bibtex files. With a proper bibtex file and a decent journal latex template, the template should do the vast majority of the work towards formatting the bibliography the way the journal wants.

Typically there are some remaining warts (both due to suboptimal templates and to limitations of bibtex itself and its community/ecosystem like the address vs. location conundrum, those who have found it will know what I'm referring to), but often they are insignificant enough to just deal with them in the typesetting stage, and when they aren't they don't require much manual work, to me it's not even near the top in the ranking of inconveniences of publishing a scientific paper. And I'm not sure this kind of software would solve such nuances anyway.

Some years ago I tried several of this kind of referencing software, including Mendeley and a couple others (not Zotero because at that point it was Firefox-only IIRC, which was a red flag for me, I'm particular about using the browser I like) and to be honest I found them more trouble than they were worth, although seeing the general positivity here towards Zotero I think I'll give it a try now.

Of course, fields that use Word instead of Latex are a totally different world where probably nothing of my comment will apply.

A RegEx-based parsing system in JavaScript helps with the reference formatting. EndNote makes references uneditable (unless you also have a copy of EndNote) and often cannot adjust to a particular journal's idiosyncrasies...but I can do that easily with home-built software.

Zotero may be great, and I cannot really make an assessment one way or the other. All I know is that hardly anyone in my industry uses it. It's really a nonstarter. Often, people need special permission to get access to open-source software and IT departments do not look kindly on installation of these tools.

Not to mention, I can't think of one piece of software or database I was using in 2003 that I can still access and use except for plain text files. This kind of software has no longevity. For these reasons, the academic publishing industry has not really standardized the process.

After a copy of RefMan broke, following the EndNote acquisition, I remember a time when I had to reverse engineer the database so I could still access the contents. It was a big tabular file and there was a much easier way to make it work with a simple browser-based tool and a few lines of code. I made it work and showed it to my boss, who summarily rejected the solution, even though it worked much better than the original (broken) software and broken database files for hundreds of prior projects. He emphasized that he wanted a paid solution. I still don't understand the logic. These are the kinds of nightmares that I associate with any kind of proprietary software solution. Often, in publishing, we need something that will work now and will still be accessible in twenty years. That's hard to do with free software.

I see, so you wrote your own solution which you have to maintain and extend for each different citation style… pros and cons to that obviously.

Why is it so important that a citation system works in 2003 and in 2021? Papers once published become historical artefacts essentially.

I am thinking of one particular journal that had a problem with historical reference libraries under RefMan that all broke after the EndNote migration. A library of thousands of purchased articles, including pivotal trials that are commonly referenced, essentially became inaccessible after RefMan was purchased by EndNote. I believe EndNote also remotely inactivated the software and engaged in some other chicanery. That experience turned me off of reference manager software. Maybe Zotero has gotten it right this time! I don't know. I just know that few things last in tech and least of all libraries of data housed in software that may or may not be updated or supported by future systems.

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