Contribute: How to add references

The references for the field guide are managed using a Zotero group library - HumanGenomicsFieldGuide. This library is openly accessible for read-only access but only members of the group can edit references. To add members to the group, go to the member admin page. Here you can send invitations to new members and adjust the roles for each member.

Each time the website is built, a script to extract all references from Zotero and save as a bibtex file (_bibliography/references.bib) in the repo is run via GitHub actions.

Adding references to bibliography

Note: Ensure you have Zotero installed with the appropriate browser addon and the ability to add references to the Zotero group library, if you need to be added as a member, please contact the HGI team.

Open the Zotero desktop app
Go to the webpage of the publication you want to add to the group library
Use the Zotero browser add-on and ensure the reference is added to the correct group library i.e. HumanGenomicsFieldGuide

Next time the Human ‘Omics field guide is updated, the new reference will be automatically added to the _bibliography/references.bib file.

Adding citations to a page

Any citation in the _bibliography/references.bib file can be referenced using its identifier. This is done through the use of the Jekyll Scholar extension.

To find out the identifier of the article you want to reference:

Open the references.bib file in a text editor or in a browser.
Search for the article in the file by using keyword or author names
Once you have found the article, copy the article identifier, the first part of the entry, just after the @article{. It is usually a combination of the first author, a key word from the title, and the year of publication. e.g. zappia_exploring_2018
Open the markdown file of the page where you would like to add the citation
At the location where you want to add the reference, use the identifier to create the following code:

{% cite $identifier %}

So using the example above, this would look like

{% cite zappia_exploring_2018 %}

When the website is built, this will be rendered into a reference like this: (Zappia et al., 2018)

Adding reference list to a page

If you would like to have a list of the references that have been cited on a page at the bottom, simply use the following code:

{% bibliography --cited %}

Using our example reference, this would look like this:

Zappia, L., Phipson, B., & Oshlack, A. (2018). Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. PLOS Computational Biology, 14(6), e1006245. https://doi.org/10.1371/journal.pcbi.1006245

If you want to list all references that are in the entire references.bib file, remove the --cited tag. This is what is displayed on the References page.

Modifying citation and reference style and appearances

The overall style and format of citations and references is determined by the scholar block in the _config.yml.

You can modify what is displayed in the reference when it is listed by editing the _layouts/bib.html file.

More information about how to edit the configurations can be found in the Jekyll Scholar Documentation.

Contributors