5 ms·

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 aft

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.

medstrom 5y ago
What reference library is easy to share with external clients then? Also, what do you mean by "external clients"?
- westcort 5y ago
  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.
- westcort 5y ago
  Zipped folders of PDF files sent via e-mail.
  - cycomanic 5y ago
    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?
    - westcort 5y ago
      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.
akjssdk 5y ago
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.
- westcort 5y ago
  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.
  - cycomanic 5y ago
    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.
    - westcort 5y ago
      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.
Gatsky 5y ago
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.
- westcort 5y ago
  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.
  - Gatsky 5y ago
    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.

medstrom 5y ago

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

westcort 5y ago
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.
westcort 5y ago
Zipped folders of PDF files sent via e-mail.
- cycomanic 5y ago
  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?
  - westcort 5y ago
    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.

akjssdk 5y ago

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.

westcort 5y ago
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.
- cycomanic 5y ago
  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.
  - westcort 5y ago
    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.

Gatsky 5y ago

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.

westcort 5y ago
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.
- Gatsky 5y ago
  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.