Sonny Software

My thesis chapters are written in MS Word and I had hoped that Word could now could handle large docs, which is not the case. Everything is being transferred to LyX which leaves me with the problem of how to generate the bibliography. I have made extensive use of Bookends and I would like to generate the reference section from some of these data. I see there are several options and any comment / suggestions of a working approach would be very helpful as I am a newbie to this environment and my deadline is looming. (MacBookPro, Big Sur (the OS version is not an issue)) Thanks

Hm, LateX is not the easiest thing to move to on a deadline (I tend to recommend a Markdown workflow with Pandoc which is simpler and far more flexible).

Nevertheless, Bookends is an excellent choice for LaTex companion. Here is what I would do:

1) If you haven't done it yet go to Settings ▸ BibTeX and enable it. The User1 field becomes the Citekey field. You can set it up so copy citation copies the citekey but perhaps LyX will do this?

2) Choose your citekey format -- Author + Year is the simplest and creates smaller citekeys (if there is more than one a letter is appended, e.g. doe2022a doe2022b), but you may prefer longer and more unique keys if you use multiple databases etc.

3) If your Citekey fields are empty you need to populate them. Select all references and Refs ▸ Generate Citekey.

4) Use the File ▸ Sync Linked BibTeX File option to create a one-way sync of your Bookends database to a BibTeX file. I've not used LyX but you should be able to point it to this .bib file so it can be used.

The next steps depends on if you will use BibTeX or BibLaTeX as they may use different formatting in the document. I would always prefer BibLaTeX which LyX seems to support: https://wiki.lyx.org/BibTeX/Biblatex — as far as I can glean LyX should allow you to insert refs from the linked BibTeX file and you should be good to go...

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Conversion: if you were using Word, I assume you already had many embedded references in your documents, how are you going to convert them? It may be possible to use a search + replace script to autoconvert Bookends temporary citations, so:

{Wilberry and Schwartz, 2002}

would become

\cite{wilberry2002}

If you choose to use the author + year citekey format for example?

I would add a few additional notes to what @londol posted. But first some questions ...

* Are you using one Bookends library or multiple libraries? I assume the former.

* Is your one library containing all references on the dissertation research, including those that may not be used in your dissertation? Or is your library already pared down to be only those references that are to go in your dissertation? I presume the former.

* Are you comfortable using groups and/or labels in Bookends?

* Are you just starting the process to embed the citation sets, or have you already started? I might hope the former rather than the latter.

In the meantime, follow what @landol suggests to set up citekeys for all references in your library. But do not export/sync the library to a BibTeX file just yet until you have answered my questions above. Especially when your library contains significantly more references than you will use in your dissertation, and when you are only now starting to embed / adjust the citations through the document, you might save some administrative troubleshooting later by doing some administrative set up at the front end.

Also, obtain a copy of BibDesk (https://bibdesk.sourceforge.io). It can be used to troubleshoot the .bib file itself.

First I must apologise for not replying sooner, I have finally produced a lyx document with text and graphics using a local Thesis template. My references are in a single library where the Thesis references are a subset ofthe whole I estimate I have used 100 to 200 references and the Bookends library has 1100 references. , I have not used either the lable feature or the group features of Bookends. Also I have embeded the citations in the Thesis text and have used the Author, 2001 or Author and Author, 2001 or Author et al., 2001. I have not started creating the Bibliography in the document. My next step is to extract the citation details for the reference used. There is a function in Bookends File > Link To> Lyx -- could I tag the citations in Lyx with this and then extract? Some reference managemnt systems can scan a PDF for references (Mendeley ?) which I guess would mean transferring everything out of Bookends for this to work (except the attachments). I looked at other apps - Zoltero etc I have come to the conclusion that I will need to go through my Thesis and tag each reference I have used in Bookends and produce an extract for this unless there is another option? I have not set up the cite keys yet.

My reading on Lyx suggests that you have to determine which bibliography package you will use. Two common ones are natbib or biblatex. Your processing options follow accordingly. From my experience with LaTeX (not Lyx) using natbib.

* Create citation keys for all references in your library. Use the menu Refs->Generate Cite Keys
* Parse through your thesis and use \cite{CiteKey1, CiteKey2, ...} syntax to insert the references paired by the appropriate cite key in Bookends.
* Use the Bookends menu Biblio->Scan Document to scan your thesis using the BibTeX format. The citations that appear in your thesis using \cite{CiteKey...} will be marked in Bookends and will appear in the Hits list.
* Review the Bibliography file (in the Bibliography Window) to see that citations are being collected in a reasonable manner.
* Select all the Hits and move them into a Static Group (e.g. Thesis Citations). This allows you to return to them later without having to keep them on the Hits list.
* Rerun the Scan action and save the bibliography to a file.
* Use the appropriate call to incorporate the bibliography in your document. For my case

%% Preamble
\usepackage[sort&compress]{natbib}
%% Document
...
\bibliography{bibliography filename}

* Run BibTeX on the document to bind the bibliography.