Bookends For The Lazy Newbie

[eastgate]

Jon’s fascinating guest appearance at this week’s Tinderbox Meetup reminded me of a need that you’ve doubtless filled — but I don’t know where you filled it!

In the chat, there were inevitably two distinct threads:

1. “How do I handle this esoteric and complex citation puzzle, using this tricky workflow?”
2. “Can Bookends do this very simple thing?”

One of the latter is: what are the best ways to avoid or streamline the chore of typing references into a new, empty database?

My current Bookends database got started in 1991, as I was writing (heading for Bookends)

Bernstein, M., Bolter, J. D., Joyce, M., & Mylonas, E. (1991). Architectures for Volatile Hypertext. In Proc. ACM Conference On Hypertext (pp. 243-260). San Antonio: ACM.

(Confession: I was using Endnotes first, and switched to Bookends after the second or third Endnotes sale....). So, I’ve got a pretty good database. I seldom need to hand-enter a reference. Anything from a book comes from the Library Of Congress Online. Most technical papers come from the ACM Digital Library, which has handy downloadable BibTeX and RIS. So, I hardly ever need to hand-enter a new reference.

But if I were just starting out now, the task of retyping all my references might be daunting. Is there a page somewhere that gives an overview of the best way to get your citation store up to speed?

[Jon]

My advice to people starting from scratch would be to try to acquire the references from online sources as much as possible. Bookends has dedicated searches with importing capability to a number of free sources for biomedical sciences (PubMed, PubMed Central, Semantic Scholar) and other sciences and the humanities (Google Scholar, JSTOR). For books there is Google Books, Library of Congress, and JSTOR. And of course with Bookends Browser you can search any site and often import directly in the browser, or by downloading the metadata as RIS or BibTeX and importing that.

You can often obtain the PDFs via these sites, too, if you have privileges.

If you have the PDF and want the metadata, drop it on the library window. If Bookends finds a DOI or other unique identifier, you'll be notified and Bookends can fetch it for you. If it doesn't, you can still attach it to a new reference and Bookends will assist you in autocompleting the metadata (that is, find it online with a bit of help from you. These are covered in this video tutorial

https://www.youtube.com/watch?v=maiGZ_FTBOI

Another way to get reference metadata is from friends, colleagues, and others. If they have them in a reference manager, on any platform, they can export them in a format that Bookends can import. These are usually EndNote XML, RIS, EndNote refer, and/or BibTeX.

Of course you can enter the references from the keyboard (in the edit pane on the right). But that's to be avoided if possible.

Does this answer the question, or is there something deeper I'm missing?

Jon
Sonny Software

[DrJJWMac]

From my experience, I agree that the best way to generate a bibliography in Bookends from scratch is to use on-line search tools.

Another way to get reference metadata is from friends, colleagues, and others.

This can also be a good way to establish a library metadata, especially for example when a project mentor has an established database in the field. FWIW, as a general rule, with defined exceptions, one is not permitted to send a journal article PDF file itself to someone else. Perhaps this goes without saying but I also hope no harm is done in repeating it.

[Dellu]

Thank you for reminding us about the meeting.
And, very pleased to hear that Jon is a fellow academic. I never knew. But, I should have suspected it from the temperaments to get into details; and from the patience for dabblers.

[Jon]

@DrJJWMac

I was careful to say metadata, not copyrighted material. Metadata (author, title, etc.) cannot by copyrighted or trademarked, and is offered freely by thousands of online sites. The export/import methods I mentioned deal with those data, not PDFs of the full article.

With regard to PDFs -- in the sciences, at least, the move to make the full text available for all makes most copyright issues moot. Any article published by a scientist in the federal government has always been free (the government owns the copyright, not the journal, and the US government wants the information made public immediately upon publication. Now, in 2023, any US (NIH)-funded research papers must be made available to the general public for free at least 6 months after publication. PubMed Central, Unpaywall, Google Scholar, arXiv and other preprint servers and repositories, etc. allow one to freely access PDFs that are not under any restrictions. In addition, sites like ResearchGate, which scrupulously abide by the rules, allow authors to distribute their full text PDFs to individuals that request it if they check some disclaimer box saying it's for academic use only. The old publishing model where journals profit by restricting access to material that they didn't create is dying, if not dead. And it's about time. The warning that one can distribute PDFs only with carefully defined exceptions is a bogeyman.

Jon
Sonny Software

[DrJJWMac]

@Jon

Apologies. Your first point is duly noted, and I've amended my post accordingly.

I agree about the harm caused by the grossly distorted the business model that publishing houses follow. I also agree that no one will be knocking on any one person's door at any time soon to check on whether you have or have not been sharing PDFs from journal articles. I only disagree on one point. Yes, the old business model is dying, but its replacement is still not one that gives anyone permission to share a PDF with anyone else. I retain copyright on a published article even when it is published in an open source. As such, you may distribute a reference to the open source for someone else to obtain the article. You may not distribute the article itself. The fact that an article is no longer behind a restricted paywall is not granting you or anyone else liberty to act as a point-to point distribution source, even if only for a one-time occurrence. I am also at liberty to send a journal article of my own authorship to anyone who asks *even without signing a waiver*. As to the "waiver for academic use only", I might say that I see this is a clever way for ResearchGate to make up for their past abuses, where posters would simply attach journal articles to comments. Copyright also defines one aspect of fair use (not academic use) as your right to reproduce or reuse another person's work for educational purposes, not as your right to redistribute that work to someone else just because they signed a waiver that they will use it for educational purposes. Said differently, should push ever come to shove (see my second sentence above), the onus will likely be on you to prove that the other person did use the article that you sent them for educational purposes only, ResearchGate waiver be damned.

Finally, as to all this, I spend significant time trying to teach undergraduate and graduate students about the right and wrong ways to manage distribution of journal articles with copyright (as well as how to manage the companion issues of academic misconduct). In the end, the simplest answer is this: If you want a journal article that I authored or co-authored and cannot get it through proper channels, send me an email request. I will send the article. I have permission to do so, and no waiver is needed.

In summary, the restriction on point-to-point distribution of a journal article that you did not author or co-author is not a bogeyman. The restriction remains, as it is a core part of a copyright statement. Copyright does not disappear simply because the distribution of said journal article on its source location is free versus paywalled.

[Jon]

This is an interesting discussion (off topic, but interesting).

In the many examples I gave for the sciences, the US government or the publisher, whomever holds the copyright, has agreed to let it be distributed without restrictions immediately of within a certain time after publication. Just because an article is copyrighted (they all are) doesn't mean that distribution is restricted. And at least for the conventional journals with which I am familiar, you (the author) cannot assert any rights that limit distribution, either. Of course in real life that is never an issue because the whole point of publishing your results (or reviews, or whatever) is to have them disseminated as widely as possible. But in the hypothetical case that you do, I do not believe you have that power. And in the US, if you have used grant money from the NIH I know you do not have that power. I suspect this applies to grants from other agencies of the government. I see the NSF has a similar policy (free access after 12 months is mandatory). https://www.nsf.gov/pubs/2016/nsf16009/nsf16009.jsp#q1.

Note that I am speaking about academic journal articles in major disciplines including medicine and biology and the "hard" sciences like physics, astronomy, etc. I'm not talking about creative writing, where intellectual property is a concern. In my examples the goal is to get the information into as many hands as possible at no charge (costs underwritten by whomever funded the research).

And back to the context of this thread -- for many if not most Bookends users, the exchange of articles that publishers have made freely available (i.e., not behind paywalls) is entirely legal and in fact to be encouraged. This is obviously not the case for PDFs of articles or books for which the publisher asserts their copyright protections. Bookends uses are obviously highly skewed to professionals, and they understand what is and what is not the standard in their field (and can instruct the occasional Bookends-using grad student in their lab).

To summarize: a copyright does not imply that use of a PDF is restricted in any way. That is only the case if the publisher asserts such a protection. For Bookends users in many disciplines these protections are never asserted or are asserted only under certain conditions (e.g., no distribution by 3rd parties for the first 6-12 months). It's up to the user to understand what is and what's not allowed, which I suspect the vast majority of Bookends users already do. This thread would go differently for apps aimed at high school or college students, for example.

I suspect that I''m obligated to mention that I'm not a copyright lawyer, so don't rely on this post in a court of law!

Thanks for the give and take. If anyone wants to continue this I suggest that it be in a new thread.

Jon
Sonny Software