Open source bibliographic reference management


Recently I’ve been looking around the internet for bibliographic database software (for Windows). Years ago I used a great program called Papyrus which was fantastic (and now free if you want it) and which I can still get to work in a DOS/ Command window. But this really isn’t terribly practical anymore. Yes, there are paid reference management tools such as EndNote and others. There’s also Zotero Standalone (looks good but imports imperfectly set up library classmarks exactly as there are input by the libraries themselves – not Zotero’s fault to be fair) and lots of them in the cloud. However, none of these quite suit my purposes. The features I want include:

  • Must be able to export to XML, csv, or similar;
  • Must be able to insert library name and classmark for any item;
  • A note field would be handy;
  • Would like to be able tick an item when I’ve read it;
  • Not really pushed about PDFs but this seems to be an important feature in most software;
  • Ability to cite item while I’m writing isn’t actually that vital as I can just insert a placeholder instead;
  • Obviously must be able to generate a full bibliography at the end in the style I need (e.g. Chicago);
  • Not in a paid cloud.

Having looked at Zotero Standalone which was pretty neat I realized that I needed something more flexible. Then I came across Aigaion which is open source and very useful for groups. If you’re comfortable running Apache, PHP and using MySQL databases then this one is pretty good. In addition, you’ll probably be able to customize it yourself. This is definitely worth a look (and installation won’t mess up your machine). I’ve also looked at Jabref/BibTex.

After all this I decided to create an Access database. I’m very familiar with this software and know how to import and export data in a way that suits me. I’m not attempting to replicate proprietary reference management software here as bibliographic databases are very complex to design. What I really want is something: a) to track my reading project; and b) have the data in digital format that I can cut and paste.

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For anyone who’s interested these are the fields I’m using:

  • RefID – the table autonumber
  • Surname – of author/ editor: use for sorting records
  • Reference – the full reference in the style that you’re aiming for (I know, I know you might no idea about this yet but if you’re doing a big project then decide this now)
  • RefType – dropdown list that includes book, article, chapter, manuscript, etc. This is useful to know for library reading lists as the journals are usually located in different places than books
  • Read – checkbox if I’ve read it or not so that I know what remains to be read
  • Cited – checkbox if it’s cited, this will be used to generate final bibliographic references
  • Library-Archive – the name of the library or archive where the item is located
  • Classmark – the location id of the item in the library or archive
  • I’ve also got 2 other fields that are directly applicable to my research, e.g. Area to indicate geographic area that the item relates to

I might add other fields later on as my thoughts develop on this.
I’ve created the basic table with related tables for RefType, Library-Archive and so on. There’s also a nice form for data entry and edit, and different queries with appropriate reports where I can generate searches by author, area, library-archive (really useful if you’re doing a research trip), or unread items.
When I’m writing I’ll have Access open and just copy the reference from the Reference field to my footnote. I might have to edit it further but that’s ok with me.
The most important report will be the final one to create the finished reference list. This will query the Cited checkbox field and then generate a simple list of records that I can import into Word or other processor.
Like all data it’s important to backup the data file regularly.

That’s it!

01-01-2018 Edit: I was still unhappy with the lack of features in my own system so I looked into Zotero Standalone again. I’ve now discovered that if you’re using the Chicago style (which I am) it is possible to create an annotated bibliography by inserting the annotation in the ‘Extra’ field, then download the Chicago note – annotated bibliography style to create the export file. This is a game changer for me as I need to create annotated bibliographies for my research.
I also discovered that every item in Zotero can have a note added to it – so that’s that issue ticked off the list.
Another feature I was looking for was a tickbox to indicate that I had read/not read an item; as a workaround I’m now inserting a tag ‘read’ or ‘unread’ so I can search for these.
I’ve also created several collections and numbered these ’01-Primary Sources’, ’02-Secondary Sources’, ’10-Maybe useful’, etc. so that they appear in the order I’d like. I’ve noticed that if you want to save a reference or webpage using the browser connector (Chrome in my case), it’s useful to click on the collection name you want the reference to be saved to first and then it’ll be saved there thus saving having to move it afterwards.
I’m also using the collections feature to create ‘folders’ for each time I create an annotated bibliography so that I know there won’t be duplicates between them (i.e. these bibliographies aren’t incremental but are recording what I’ve read since the last one was created).
As regards backup, the Zotero folder in Windows (harddrive/Users/username/Zotero) that contains a ‘sqlite’ file is the one to backup in its entirety.

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The one major defect in my eyes with Zotero is the lack of customisation of reports. There was an extension available but this doesn’t seem to work with version 5.0.33. I really need to generate lists of references with library class marks so that I can go to a library with these in hand. In the meantime, I might do a workaround by creating collections, search by tag (that is a library name) and generating ‘bibliographies’ from these rather than ‘reports’ (but I’ve yet to figure out how to include the ‘Call Number’ field in the printout).

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