Reference Management Workflows

Publications and products are increasingly needed in various places in the research lifecycle. References are used in writing papers, but researchers also need to reference their own work on websites, research portals, sponsored funding applications, and CVs as just a few examples. For this reason, it is suggested that researchers and their administrative staff consider where they should create a workflow that will reduce the amount of work to get the information in the right formats in the right locations on an ongoing basis.

This document serves as an overview of reference management software and provides a framework on how do decide what is needed for a workflow within the context of sponsored programs. Finally, an example walkthrough on how to apply a workflow using Zotero software is provided.

Reference Formats and Citation Managers

References can be displayed in many different formats, such as MLA, APA, or Chicago. Historically, researchers would need to meticulously format citations to comply with these rulebooks. Today, computers are able to automate much of this work through database entries. By maintaining a reference database, the user can automatically format a given reference according to the rules that the user chooses in the moment.

The database formats used to store this information can vary, and common citation file formats include BibTeX (.bib) and RIS (.ris). In some cases, references can be transferred with more common formats, such as .csv or .txt.

Zotero

The BU Libraries maintains general information on Citation Managers available to the community. This guidance will specifically look at using one of these tools within the context of how publications are used in sponsored activities. Recommended by both BU Libraries and BU Sponsored Programs, Zotero is an open-source application that makes it easier to manage publications. It is a robust application for importing and exporting information. It also has strong searching and organization capabilities.

After reviewing the questions that will assist in generating a custom workflow, a walkthrough on how to create a customized workflow in Zotero using this framework will be provided.

Framework for Creating a Workflow

When deciding on a workflow for reference management, a few key decisions will need to be made to streamline your efforts. To get started, consider asking the following questions:

• Which system will we use, MyNCBI or ORCID?
  • Consider specific sponsor requirements that may influence this choice
• Who will add publications to the systems?
  • Do they have access to the systems? Do they need to be entered as a delegate/trusted user?
• Will we upload data or manually enter data?
  • Which file formats will we need to do this?
• How often will we update the data?
• How will we know if there is a new publication to enter?
• Are there other repositories or reports we are already maintaining publications for?
  • Am I a MyCV user (which connects to ORCID)?
  • Will it be easy to submit to OpenBU? [Note: MyCV can submit to OpenBU. More information is available at the OpenBU site.]
  • Can we streamline our process to keep one publication process?

Here are two example workflows that could result from this process. Notice how similar questions need to be decided (Where will be store all publications initially? Where will my data end up?) and also how the sponsor systems dictate additional steps.

NIH-focused Researcher

1. Keep track of publications in MyNCBI’s My Bibliography for easy access for NIH RPPRs.
2. Add citations into biosketches from MyNCBI in SciENcv.
3. Export citations from My Bibliography when needed for other projects or to submit to OpenBU.

NSF and DOE-focused Researcher

1. Keep track of publications in Zotero; populate initially from Google Scholar.
2. Export data as needed to upload to ORCID.
3. Add citations into biosketches from ORCID in SciENcv.
4. Ensure publications populate into MyCV and OpenBU.
5. Export citations from Zotero when needed for other projects.

Example Zotero Walkthrough

Step 1: Setting up a Group

Researchers are often using administrators or lab members to help with publication data. In this case, setting up a Zotero Group can make it easier to manage the data together. Once you make a Zotero account and are logged in, create a group specifically to manage the publications used for sponsored activities. As a reminder, this is a separate repository that is used only for sponsored grants and contracts. Zotero provides documentation on how to complete and manage groups.

Step 2: Adjust the Client Settings

Once the Zotero application is downloaded, log into the application with your Zotero account and ensure data syncing is enabled. File Syncing should also be enabled to make use of the search capabilities of PDFs.

Step 3: Add Publications to the Group Repository

Zotero has four main ways to add publications to the repository with different levels of efficiency:

1. Least Efficient: Enter each publication by hand using the form.
2. Somewhat efficient if PDFs of all publications are available: Use the PDF Metadata to create items in Zotero via drag and drop. See documentation on the Retrieve PDF Metadata feature.
3. Somewhat efficient and more complete: Use the browser extension to scrape a publication’s meta data from a website along with the pdf of the publication (if it’s available). You can also add an item by identifier if you have it (ISBN, DOI, PubMed ID, arXiv ID, or ADS Bibcode).
4. Very efficient, no file attachments: Upload publication data from another location, e.g., Google Scholar or PubMed. This data will be of varying quality, and in some cases, it may be required to review all relevant publications and ensure the data is correct and available. This is particularly the case when PMCID/PMID numbers, or other persistent identifiers are required.
   1. To export publications from your own Google Scholar profile: Login using the account that is tied to the profile. Navigate to the Google Scholar profile. Select the articles you’d like to export – or check the box next to the “Title” column header to select all articles in your profile – and click the “Export” button. Follow the prompts to download a BibTeX, EndNote, RefMan, or CSV file. BibTeX is recommended for Zotero.
   2. If attachments are not automatically imported, use Zotero’s “Find Available PDF” feature. It uses the Unpaywall service to automatically find and attach a legal, full-text article to your publication if available.

Step 4: Review Data for Accuracy

Some researchers will have too much data to review; however, the last 4-5 years of publications, or ones that are routinely used in proposal documents (e.g. biosketches), should be evaluated to make sure the data is high quality. Ensuring the co-authors and dates of publication are accurate will also help in the process of making other documents, such as creating a co-author list for the NSF Collaborators and Other Affiliations (“COA”) document.

Step 5: Organize with Tags and Collections

When importing publications, they may come with many tags. Delete tags that are not useful and consider making tags that are useful to the sponsored research activities. See documentation on tags.

Collections look like folders but function more like playlists. In this way, items are not duplicated but instead may appear in multiple collections. See documentation on collections.

Ideas for organizing your repository:

• Make a collection based on a theme of publications, e.g., a biochemist may have some publications that lean towards a biology-focused project and others that are more chemistry-focused. A third project could be very interdisciplinary. This is helpful for biosketch creation, as biosketches require products that are “most relevant” to the proposed work. This can make it faster to find worthy candidates.
• Tag publications with the award number for a grant or contract. This can make it easier to search for publications that need to be referenced in a progress report (“RPPR”).
• Tag publications with a status, such as “In PubMed” or “In PAR” to help keep track of what has been submitted to public access repositories.
  • To review the requirements for depositing publications in the Public Access Repository, see the handout for NSF’s PAR system and documentation for NIH’s PubMed Central system.

Step 6: Create Saved Searches

Saved searches function like a smart playlist. They will automatically update as new items meet the criteria of the search. Examples of saved searches that may help your workflows:

• Search based on a tag, such as an award number or project name.
• Search for publications based on a status-based tag, such as “Add to PubMed” or “Add to ORCID”.
• Search based on a co-author, if publications with this collaborator should appear on biosketches for applications that they appear on.
• Search for publications based on dates, such as in the last four or five years to generate a co-author list for the NSF COA documents.

Step 7: Export Publication Data

Once the data is in Zotero and is clean and accurate, then the data can be reliably exported for use in a sponsored application, such as My Bibliography or ORCID. If needed, a search can be performed using a saved search or using the search bar. Either select the specific items for export or use the “Export Collection” or “Export Library” options. See the documentation on exporting.

Exporting formats will vary depending on where the information will be uploaded. NIH’s My Bibliography uses RIS, but ORCID uses BibTex.