Berkeley Connect: Computational Biology: Cite sources

Citation elements

Citations should include enough information to enable someone else to find your source. The basic elements of a citation to an article include:

1. Author name(s): the names of the authors of the article
2. Publication year: the year the article was published
3. Article title (e.g., "Approaching a state shift in Earth's biosphere")
4. Journal title: the name of the journal in which the article was published (e.g., Nature, Ecology, or Journal of Arid Enviroments)
5. Volume number: journals are often divided into volumes that indicate that they have been published in a specific time period (e.g., if the volume numbers change annually, "volume 17" would indicate that the issues in that volume were published in the journal's 17th year of publication). Volume numbers for different journals can change after different time periods: annually, semiannually, quarterly, or even monthly.
6. Issue number (omitted for many citation styles in the sciences): Each volume is often subdivided into specific groupings of articles that are published at regular intervals (e.g., if the journal is published monthly, issue 1 may include the articles published in January, issue 2 the articles published in February, etc.).
7. Page numbers (for articles published both in print and online) or article number (for online-only articles)
8. For articles published online: URL or DOI (omitted for some citation styles)

Try this example:

Freeman LA, Kleypas JA, Miller AJ. 2013. Coral reef habitat response to climate change scenarios. PLoS ONE 8: e82404. doi:10.1371/journal.pone.0082404

Click on the "Find an article using a DOI" link above, copy and paste the DOI into the "Resolve a DOI" box, and click "Go." (Don't include the characters "doi:") Were you able to access this article?

Citation Styles

A citation style is a specific way in which the elements of a citation are combined and formatted. There are hundreds of different citation styles.

The following examples provide in-text and reference list citations to the same journal article in each of three citation styles: AMA (American Medical Association), APA (American Psychological Association), or CSE (Council of Science Editors):

AMA

In-text citation: Residential segregation impacts the ecology of urban landscapes.¹

Reference list citation:
1. Schell CJ, Dyson K, Fuentes TL, et al. The ecological and evolutionary consequences of systemic racism in urban environments. Science. 2020;369(6510):eaay4497. doi:10.1126/science.aay4497.

Guide: Purdue OWL: AMA Style
Guide: AMA Manual of Style: Minimum Acceptable Data for References

APA

In-text citation: Residential segregation impacts the ecology of urban landscapes (Schell et al., 2020).

Reference list citation:
Schell, C. J., Dyson, K., Fuentes, T. L., Des Roches, S., Harris, N. C., Miller, D. S., Woelfle-Erskine, C. A., & Lambert, M. R. (2020). The ecological and evolutionary consequences of systemic racism in urban environments. Science, 369(6510), eaay4497. https://doi.org/10.1126/science.aay4497

Guide: Purdue OWL: APA Style

CSE name-year

In-text citation: Residential segregation impacts the ecology of urban landscapes (Schell et al. 2020)

Reference list citation:
Schell CJ, Dyson K, Fuentes TL, Des Roches S, Harris NC, Miller DS, Woelfle-Erskine CA, Lambert MR. 2020. The ecological and evolutionary consequences of systemic racism in urban environments. Science. 369(6510):eaay4497.

Guide: UW-Madison Writing Center: Council of Science Editors Documentation Style

Citation managers (also called reference managers or bibliographic management software) offer a way to save, organize and manage references. Many work with word processing software to format in-text citations and bibliographies for papers and theses, allow you to share references, and enable you to attach or link PDFs to a citation record.

Citation managers supported by the UC Berkeley Library:

• Zotero guide [UC Berkeley Library]
• Zotero documentation [Zotero.org]
• Free Zotero workshops [UC Berkeley Library; offered in the Fall and Spring semesters]
• Free desktop program with browser connector; 300 MB storage (can be synced with Google Drive, Berkeley Box or Dropbox for greater storage--see Zotero guide for details)
• Sync Zotero to access your library from any computer with internet access
• Insert citations and automatically format reference lists in Google Docs/bDrive, MS Word and LibreOffice
• Capture citation data from PDFs and web pages
• Share and collaboratively edit folders of references

• Mendeley guide [UC Berkeley Library]
• Free software/web hybrid for PC, Mac, Linux
• Format bibliographies in MS Word
• Sync PDFs to your web account for online access
• Capture citation data from some PDFs
• Read and annotate PDFs
• Share and collaboratively edit folders of references

• EndNote guide [UC Berkeley Library]
• Desktop-based software and online EndNote Web
• Desktop program requires purchase; EndNote Web is available without cost to UC Berkeley students, faculty and staff
• Format bibliographies in MS Word
• Capture citation data from some PDFs
• Annotate PDFs
• Find the full text of articles from within desktop EndNote
• Share lists of references with other EndNote users

For additional options: Wikipedia comparison of reference management software