• Guest Post Feature: Edifix Converts Unstructured Bibliographies to BibTeX

    Posted by Caitlin Gebhard, Inera Inc. on January 25, 2017

    BibTeX is a great way to manage references and bibliographies in a LaTeX authoring environment. It allows authors and publishers to format bibliographies into a variety of styles with ease and consistency. Powerful LaTeX authoring and editing tools—such as Overleaf—offer you the option to create high-quality LaTeX manuscripts with an easy-to-use WYSIWYG editor and drag-and-drop upload of your BibTeX files.

    However, there is a common challenge when it comes to BibTeX. Many of us have research materials or reference lists that may not have originated in BibTeX. This creates a problem: text-based, unstructured bibliographies, such as those created in Microsoft Word, must first be converted to BibTeX before they can be used in a LaTeX project.

    One way to solve this problem is to create a BibTeX file (.bib) from scratch. There are some online resources that can teach you to do this, but manually working with BibTeX is a time-consuming and error-prone process. Your time could be better spent perfecting your content—not wrangling with BibTeX syntax.

    You could also export your bibliography as a .bib file from your favorite reference manager, such as EndNote or Zotero. But those are databases, and like all databases, they require structured input. If your reference list already exists in a Word or PDF document, you must first enter each reference into your reference management tool, manually identifying the reference elements and filling in a multitude of fields.

    There's no easy way to convert an unstructured, text-based reference list to a format digestible by reference managers. While there are tools available that extract reference metadata from your plain text bibliography, they can require time and effort to set up; some examples include manual code changes or complicated installation packages. The bigger problem is the output from such tools. The generated .bib file may be riddled with errors that can affect the final format of your references.

    Edifix is an exciting new solution that employs a unique and patented heuristic parsing system to analyze references and create structured data from unstructured, plain text bibliographies. It converts your reference list into a variety of formats, including BibTeX. Unlike other text-to-bib converters, Edifix can also link your cited sources to Crossref and PubMed.

    In addition to converting references to BibTeX format, Edifix can improve your references by correcting them with data obtained automatically from PubMed and Crossref. Edifix can insert missing reference data and correct incorrect information so you can be assured your references are accurate. Crossref and PubMed links are preserved in BibTeX as doi and pubmed fields, which provide an additional layer of confidence and discoverability to your finished bibliography.

    Edifix is a cloud-based web solution designed for quick and easy usability; no installation or technical expertise is required. To get started, just sign up for an Edifix account online. If you have an unstructured reference list—say from an HTML web page, PDF, or Word file—you can simply copy and paste the reference list into Edifix, press a button, and get structured (and corrected!) BibTeX back for use in LaTeX tools such as Overleaf.

    How to get BibTeX bibliography with Edifix

    To get started, sign up for an Edifix account at https://www.edifix.com. There’s a free 30-day trial that includes full access to Edifix’s reference-processing tools for up to 100 references.

    Once you have signed up for an account, click New Edifix Job at the top of the Edifix.com page to submit a new list of references for Edifix to process.

    First, select the reference style template that meets your editorial style. In a LaTeX workflow, the editorial style of your bibliography is ultimately defined in the LaTeX manuscript. However, every editorial style includes different reference elements—for example, different styles require a different number of listed authors. You should select the style in Edifix that fits best.

    Edifix style selection dropdown

    If you want your references corrected and linked to PubMed or CrossRef, select PubMed and/or CrossRef Linking and Data Correction.

    Linking and Data Correction

    When you have finished selecting your Edifix options, paste your unstructured references into the Input References box. For best results, there should be no line breaks within individual references, and the reference list should be either numbered or in alphabetical order as they would typically appear in print.

    When you are ready to submit your references, click Edifix Your References.

    Input References

    When Edifix is finished, your results can be displayed in three different views:

    1. The References Only view displays your references without hyperlinked PubMed IDs or Crossref DOIs and does not include Edifix comments.</.li>
    2. The References + Links/Comments view displays your references and the hyperlinked PMIDs and DOIs that Edifix inserted. This view also displays comments from Edifix—such as a warning when a reference has been retracted—highlighted in yellow.
    3. The Show Changes view displays your references, links, and comments, as well as any changes that Edifix made to the content.

    4. Show changes

      To export your Edifixed bibliography to BibTeX format, select "BibTeX" from the Export menu, and then click Export. Your reference list will be exported and saved as a BibTeX .bib file.

      Export BibTex

      Then, import your BibTeX reference list into Overleaf

      Once you have an Edifixed bibliography saved as a BibTeX file, you are ready to import your bibliography into your LaTeX project.

      First, Open the Project pane to manage your project files. Then, click Files… and select Bibliography.

      Overleaf project pane

      To import your Edifix bibliography, click Upload a .bib file.

      Upload a .bib file

      Drag-and-drop or browse to and select the .bib file you downloaded from Edifix, and then click Open to add the file to your project. You can then view and manage the BibTeX file within Overleaf.

      Add the file to your Overleaf project

      Once your .bib file has been added to your project, you can reference your bibliography using standard LaTeX syntax, for example:

      \bibliographystyle{apalike}

      \bibliography{JMS-1_edifix_BibTeX.bib}

      See the LaTeX Wikibook for more detailed information on managing bibliographies using LaTeX.

      Conclusion

      If you need a BibTeX bibliography, and you only have an unstructured reference list, there is an easy solution. Edifix will not only convert your unstructured bibliography into BibTeX, but will also offer corrections based on the authoritative metadata extracted from PubMed and Crossref. You can work safely in your editor, knowing that you can always convert your research notes back into a format that’s compatible with the LaTeX environment. The results are accurate, the sign up is fast, and the export options are numerous. Sign up for an Edifix account here and start now for free.