Berkeley Connect: Computational Biology: Reading scientific writing

The range of formal and informal writing in the biological sciences encompasses:

• Articles, letters/short communications, commentaries, editorials, opinion pieces and news published in scientific journals
• Preprints of scientific articles posted to repositories
• Conference presentations
• Dissertations and theses
• Reports from governmental or non-profit organizations
• Articles published in industry/trade publications or newsletters
• Articles published in newspapers or general circulation magazines and newsletters
• Scholarly monographs and technical manuals
• General interest books
• Textbooks, handbooks and encyclopedias
• Information shared on social media
• Messages posted on interest-group boards or email lists

Publication Types

Primary literature

In the sciences, the primary literature:

• presents or comments upon the first-hand results of research activities
• often includes analyses of data collected in the field or the laboratory
• is very current and highly specialized.

Examples of primary literature in the sciences include:

• research articles published in peer-reviewed journals
  More about peer review
  Identifying peer-reviewed primary research articles
• dissertations and theses
• technical reports
• conference proceedings

Grey Literature: Dissertations and theses, technical reports, conference presentations, and other documents are considered grey literature (or gray literature), defined by GreyNet as "multiple document types produced on all levels of government, academics, business, and [other] organization[s] in electronic and print formats. . .where publishing is not the primary activity of the producing body." Grey literature may have editorial or committee oversight, but does not necessarily undergo the process of peer review. Nonetheless, it may have significant scientific value.

Secondary literature

The secondary literature is a good place to start when you are investigating a new topic, because secondary sources:

• summarize and synthesize the primary literature
• are both broader and less current than the primary literature
• are useful for getting an overview of a research area
• are useful for finding citations to more information on a topic.

Examples of secondary literature in the sciences include:

• literature reviews (or review articles) - More about literature reviews
• monographs (books or book chapters dealing with a specific area of research in the sciences)

Tertiary literature

The tertiary literature:

• deals with broad, discipline-level topics in the sciences (like biochemistry or evolution)
• is a useful starting point for background information on a research topic
• reports well-established facts in the scientific literature
• is often not as thoroughly referenced as primary or secondary literature

Examples of tertiary literature in the sciences include:

• encyclopedias
• textbooks
• handbooks

How to read a primary scientific research article

To read primary scientific articles effectively requires dedicated time. If you encounter unfamiliar words or undefined acronyms, pause and look them up immediately. If you are struggling to understand the paper's context, finding a relevant encyclopedia entry, textbook chapter or review article can provide helpful background.

Your reading should answer the following questions:

1. What is the major research area of this study? What system is it investigating?
2. What is the specific research question being investigated by the authors? Why is it important? Are the authors testing a hypothesis?
3. How did the authors try to answer the research question? What experiments did they perform? (You don't necessarily have to understand the experiment in close detail, but it is important to understand the basic steps and methods involved.)
4. What data were collected by the authors? How did they analyze and present the data?
5. Do the results seem to support the authors' conclusions?
6. What are the limitations of the study?
7. Does the paper suggest any follow-up studies, additional experiments, or future areas of inquiry?

To get a general sense of the question or system studied and the conclusions drawn:

1. Read the Title: Does it seem relevant to your topic? If so,
2. Read the Abstract: This will give you a summary of the content of the paper. If it seems relevant,
3. Read the Introduction: This will give you more detail about the question or system studied. If it still seems relevant,
4. Read the Discussion/conclusion: This will describe the scope and significance of the results; at this point you may also want to look for any potential conflicts of interest in the Acknowledgements.

To get more detail about the experimental results and methods,

5. Read the Results: This will detail the data and analysis used by the authors to draw their conclusions.
6. Look carefully at the figures and data tables and read the captions: These will show you what data was gathered and how it was analyzed and interpreted. Additional figures and data may be included in the supplementary or supporting information.
7. Read the Methods: This will provide the specifics of the experimental procedures followed such as where samples were gathered and how measurements were taken.

To find additional relevant resources,

8. Look at the References.

The first four steps will give you a good picture of what the paper is about and what conclusions can be drawn from the study. Steps 5 through 7 provide essential details for in-depth understanding. Step 8 will point you to the earlier work on which this study was based.

How to read a literature review

1. Read the Title: Does it seem relevant to your topic? If so,
2. Read the Abstract: This will give you a summary of the content of the paper. If it seems relevant,
3. Read the Introduction: This will give you more detail about the topic under review, with citations to earlier relevant studies. If it still seems relevant,
4. Read the conclusion for a summary of the findings and suggestions about future research directions.
5. Read the sections of interest to get more detail.
6. For additional resources, note citations to specific references that seem especially relevant.