May 15, 2018

Why We Love Our Journal Database (And You Should, Too)

In August 2016, we wrote a little ode to our beloved Journal Database, which at that time contained just over 42,000 journal titles. We’re revisiting this topic now as we close in on an important milestone: the 50,000 title mark!

The Journal Database: A Band of Unsung Hero(in)es

If you’ve read our previous post, you know that when you run eXtyles Reference Processing, the Journal Database does a lot of the heavy lifting.

What we call “the Journal Database” actually consists of several database files, including

  • JrnAbbr, listing journal titles (e.g., New England Journal of Medicine) and their standard abbreviations (e.g., N Engl J Med)
  • BadJrnAbbr, listing a wide variety of variant titles and incorrect but frequently encountered abbreviations (e.g., NEJM).

During Reference Processing, eXtyles uses these data sources in

  • identifying which bibliography entries refer to journal articles, so that they can be appropriately styled and copyedited
  • identifying, styling, and formatting journal titles
  • correcting errors in journal titles
  • abbreviating or spelling out journal titles, depending on your editorial style
  • looking up DOIs on Crossref and PubMed
  • Whether you’re using eXtyles or Edifix, the journal name is one of the most fundamental pieces of data used to query PubMed and Crossref!

The Journal Database is also what enables another very visible process—alerting you via Word Comments when an apparent journal title is not found in the database (see below)—as well as an invisible one: adding the appropriate ISSN as an XML attribute when you use eXtyles to export XML from your Word file.

eXtyles error flag: Unrecognized journal title

That’s one reason why, when you submit a journal title via journals@inera.com, it’s a helpful bonus to include both the title and the ISSN.

But that’s not all!

Did You Know…

To celebrate the upcoming 50K milestone, here are some less-well-known facts about our Journal Database!

What Else Can the Journal Database Do?

  • As well as the database files discussed above, the Journal Database includes

    • A file that looks for incorrectly abbreviated words (e.g., “Agr” for “Agric”; “Hort” for “Hortic”; “Intl” for “Int”), allowing eXtyles to check whether substituting the correct abbreviated word helps to resolve an unrecognized journal abbreviation
    • A file that can contain start and end publication dates for particular journals, helping eXtyles to disambiguate identically or similarly named journals based on article publication date
    • A file that includes information on journals that have no volume numbers, or issue numbers rather than volume numbers, or no volume or issue numbers. This can allow these references to be processed even when otherwise critical information is missing, and avoids redundant warning comments.
  • Depending on the reference template settings, eXtyles can be set to construct an abbreviation from an unrecognized full journal name, using lists of standard word abbreviations.

  • The Journal Database also includes files used to process references to books, including lists of book series, publishers, and publisher locations. If your book or chapter reference was not correctly restructured, it may be because the publisher and/or location were not listed, or because the book series to which it belongs was not included in our database—so please forward references like this to references@inera.com.

If the Journal Database Is So Great, Why Does It Sometimes Get Things Wrong?

  • Journal databases such as the NLM Catalog require a unique name for each journal, so they may add, for example, a journal’s place of publication or its launch year to disambiguate two or more journals with the same title (for example, our database includes 5 journals called Anticipation, 6 called Environmental Geology, and 9 called Vital Signs). The first journal with a given name may not now be the best known, but it typically has the “honor” of using the name unaltered, while a later, now better known journal has to be identified by adding its place of publication or launch year. These modified names may not be widely used in the journal’s own discipline, so they may “look wrong.”
  • Journals may also have similar titles that reduce to identical abbreviations; for example, Advanced Science and Advancement of Science both abbreviate to Adv Sci, and in this case they’re distinguished by adding the place of publication to the abbreviation for Advanced Science so that the journal name is rendered “Adv Sci (Weinheim).” If eXtyles can’t determine with confidence which of two or more journals a title or abbreviation refers to, you’ll get a Word comment asking you to investigate further.
  • Similarly, academic disciplines tend to have their own internal shorthand names for journals, which don’t translate well to other fields. For example, researchers in biochemistry and related fields will use “JBC” to refer to the Journal of Biological Chemistry, but JBC could also be used for the Journal of Biological Control, the Journal of Breast Cancer, or the Journal of Business Communication. This means that eXtyles can’t always confidently associate a non-standard abbreviation with a single journal name.
  • A handful of journals have names that make automated reference restructuring difficult or impossible because they can be mistaken for other reference elements; examples include October, 1199 News, boundary 2, and 1999.
  • A journal may go through several names in its lifetime, but authors—and even publishers!—don’t always respect those name changes. (For example, the current journal name is sometimes applied to all issues of a journal when back issues are digitized and made available online.) Using the wrong name for the right journal may prevent eXtyles from matching the reference on Crossref and PubMed.
  • Every so often, a journal changes its name without getting a new ISSN! This can cause difficulties because eXtyles can associate only one “definitive” journal name with each ISSN.
  • Many non-English-language journals also go by an English “parallel title,” but the parallel title often doesn’t have its own ISSN. If the two titles share an ISSN, eXtyles must be configured to decide on one language or the other; typically we’ll opt for the title used in the NLM Catalog (to allow PubMed linking and correction to work correctly). But that may not may not meet your needs, so if you need a local override, let us know!
  • A journal published in two languages may have different pagination in each language, which can lead to confusion even for humans.
  • We typically add between 100 and 200 new journal names per month, but there are still thousands more journals out there that we haven’t added yet, with new journals starting publication all the time!

So How Can I Help?

If you’re an eXtyles or Edifix user, you can do a couple of things to help make eXtyles Reference Processing work better.

First, if you’re an eXtyles user, remember to update your Journal Database regularly! (We recommend updating at least once a month.) That way, you’ll be using the most complete and correct version of the database when you run Reference Processing.

  • Are you an Edifix user? You’re in luck: because Edifix runs in the cloud, you’re always using our most up-to-date Journal Database!

Second, when eXtyles tells you it doesn’t recognize a journal title you know to be correct, send us the reference! Most of the new journal titles we add come from eXtyles and Edifix users like you! And every new journal name we add improves performance for everyone.

With that in mind, we have a few tips to make sure your submissions can be added as quickly as possible:

  • Choose the appropriate target for your email: journals@inera.com for new journal names to be added; references@inera.com for entries that you believe eXtyles should have handled better.
  • When submitting a journal name, please send us the correct full title and, if you have them, the ISSNs associated with that title (most journals have both print and online ISSNs).
  • When submitting a mishandled reference, please send us both the original (very important!) and processed entries, so that our developers can try to reproduce the problem.
  • When submitting a reference, please do not send us a PDF of the cited article!
  • When submitting a new journal name, please do not send us a PDF of journal content!

Your feedback helps make eXtyles and Edifix work better for everyone! We appreciate every submission, and we hope you’ll keep them coming. :)


Link: http://www.edifix.com/blog/blog/Journal-Database.html