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Short Term Educational Experiences for Research in Environmental Health (STEER): Starting Library Research

Welcome to the Library Session for STEER!

Dinosaur in VLSB; click image for library home page

Presented by Michael Sholinbeck (


Agenda for today's session:

  1. Introduction to the scientific literature.
  2. Critically evaluating information.
  3. Thinking about your topic.
  4. What about indexing?
  5. Databases: PubMed, Web of Science, and more.
  6. Citation management: Zotero and more.
  7. Lit review help.

The Scientific Literature: Books, Handbooks and Protocols, Articles

When a topic is new to you and you need an overview of the topic, encyclopediae and textbooks are great at giving an overview or introduction.

Use UC Library Search to find encyclopediae and textbooks.

For more detailed exploration of a topic, books provide the focus you want. UC Berkeley has millions of books!

Use UC Library Search to find books on your topic.

For lab research, handbooks and lab protocols provide information on the materials and procedures for experimental work.

The next format type is journals. They report on the findings of current research studies, offering the most up-to-date and detailed information on a topic.
A single journal issue will have many articles, and each article is devoted to a research study. There is a standard pattern in how journal articles are written, and knowing this pattern will help you find the information you need:

  • An article’s introduction explains the context of the work and the importance of the research;
  • The materials and/or methods section describes the experimental procedures;
  • The results report on the data and the outcomes of the work;
  • The discussion section interprets the results, whereby the authors explain the meaning and the implications of the research;
  • Lastly, there are references to the scholarly works (other articles, etc.) used by the authors.

Finally, databases are what you use to find journal articles. Databases let you search across many (often millions) of journal articles to find the papers relevant to your research topic.

The Library catalog

Books, handbooks, videos, and much more may be found in UC Library Search, the UC Berkeley/UC library catalog +.

Critically Evaluating What You Find

"Research users are not passive recipients of distilled wisdom, they are active agents of critique and creative analysis."
- from "How to 'QuantCrit:' Practices and Questions for Education Data Researchers and Users," W. Castillo and D. Gillborn, 2018.

"It is better to be vaguely right than exactly wrong" - Carveth Read, 1898.

Evaluation is about determining the quality, value, or importance of something in order to take action. It is underpinned by the systematic collection of information and evidence.

What is evidence?
All research is (potentially) "evidence" and there are no "perfect" studies. 
Critically evaluating what you read will help any unearth biases or methodological shortcomings that may be present.
Examples of problematic methods descriptions. From: T. Greenhalgh. How to Read a Paper: The Basics of Evidence-Based Medicine and Healthcare. John Wiley & Sons, 2019.

Is there an agenda (bias)?
It is doubtful that any study of humans is without some kind of bias, either in the study design, or in the author's pre-existing beliefs. How bias in methodology was controlled and the significance of bias in any particular study is what is relevant. Also relevant is whether the researchers addressed their biases intentionally.

Things to consider:

  • The question being addressed: What kind of research gets funded?
  • Publication bias: Research that shows no effect tends not to get published.
  • Conflict of interest, author affiliation, source(s) of funding: Does the researcher have a vested interest in the outcome? Many authors do not disclose industry payments.
  • Documentation and assumptions: Are all stated "facts" referenced?
  • Peer review: Peer review refers to a process whereby a scholarly work (ie, an article) is reviewed and critiqued by experts to ensure it meets some standards of acceptance before it is published. Does this process make for better science?
  • Authority: Does the researcher have the knowledge to work in this area?
  • Significance of a single study: Science is an incremental process; one study rarely "changes everything."

Who pays for science? Does it matter?  (There is evidence that it does matter).
Research is usually funded by:

  • Government;
  • Industry/trade groups;
  • Private foundations/associations/educational institutions.

This article (PDF) discusses the "manufactured uncertainty" created by industry groups that sponsor research and publishing on chemicals.

Is qualitative research "evidence"?

If your goal is to understand beliefs and meanings in the group with whom you are working, then qualitative studies can be important.

Reliability and validity
Reliable data collection: relatively free from "measurement error:" 
Is the survey written at a reading level too high for the people completing it? 
If I measure something today, then measure it again tomorrow using the same scale, will it vary? Why? 

Validity refers to how well a measure assesses what it claims to measure:
If the survey is supposed to measure "quality of life," how is that concept defined? Is it measurable?

What to consider when looking at survey or estimated data:

  • Beware of spurious precision.
  • Look at sample sizes and survey response rates - representative of your population? Enough responses to be valid?
  • Who was surveyed? Are they representative of population being compared to? Include group you are interested in? Is the sample "WEIRD"?
  • Were the survey respondents from heterogeneous groups? Do the survey questions have a similar meaning to members of different groups?
  • How was survey conducted? Via telephone? - Many people only have cell phones. Random selection or targeted group?
  • What assumptions and methods were used for extrapolating the data?
  • Look at definitions of characteristics - Does this match your own definitions?
  • When was the data collected?

How is race/ethnicity reported in the studies you read?:

  • Who identified race/ethnicity of respondents/participants?
  • Does the language in the article impart bias?
  • Is race acknowledged as a social construct?
  • Are differences reported as associated with "race" or "racism"?
  • Are participants' identities disaggregated?

About Your Topic

What to consider when thinking about your research topic
Much current research in environmental health is interdisciplinary.
The terms you use when searching PubMed, Web of Science, or other databases may need to include concepts from different fields of science.

Is your topic researchable?

  • Effects of vehicular emissions from 1995 Toyotas on elderly women in Berkeley;
  • Health effects of seasonal variation in PM2.5 levels in the San Francisco Bay Area;
  • Air pollution in the United States.

What is a good Research Question? It is a question that:

  • identifies a relevant issue in your field;
  • pursues relatively uncharted research territories to address the problem;
  • piques the interest of others.

This blog post has tips on how to write a good research question, including examples of bad, good, and great questions.

Information on chemicals/substances:
Before you delve into the research literature on a topic, it can be helpful to get some basic information on the substance(s) of interest.

  • PubChem
    PubChem mostly contains small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. Includes information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others, on millions of substances, compounds, and more.

Let's talk about indexing!

  • Do you want articles on HIV (a virus) or articles on HIV diseases?
  • Do you want articles on nanofibers or articles on nanofibres?
  • Is lead a noun or a verb?

Indexing means a controlled vocabulary (a finite list of terms) is used to assign subject terms to articles.
Controlled vocabulary schemes are often hierarchical; any given term will have broader and (possibly) narrower terms. Example:

  • Environmental Pollution > Air Pollution > Indoor Air Pollution

Subject terms tend to have a single, unambiguous definition. Example:

  • Air Pollution: "The presence of contaminants or pollutant substances in the air that interfere with human health or welfare, or produce other harmful environmental effects. The substances may include gases particulate matter, or volatile organic chemicals."

Subject terms may also be called thesaurus terms, descriptors, or (in PubMed) Medical Subject Headings (MeSH).

Literature Review Tips Handouts

Write about something you are passionate about!

Ten simple rules for writing a literature review.
Pautasso M. PLoS Comput Biol. 2013;9(7):e1003149. doi:10.1371/journal.pcbi.1003149

Conducting the Literature Search.
Chapter 4 of Chasan-Taber L. Writing Dissertation and Grant Proposals: Epidemiology, Preventive Medicine and Biostatistics. New York: Chapman and Hall/CRC, 2014.

A step-by-step guide to writing a research paper, from idea to full manuscript. Excellent and easy to follow blog post by Dr. Raul Pacheco-Vega.

Off Campus Access to Library Resources

Off-campus access is limited to current UC Berkeley faculty, staff and students. Choose one of the following methods:

Library Proxy (aka EZproxy):
When you click on a link to an article, database, etc., from a library web page. you will be prompted to authenticate via CalNet.
If you click on an article (etc.) link found via a search engine or a non-UCB Library webpage, you should use this bookmarklet to access the licensed resource.

Virtual Private Network (VPN):
Download and install the VPN client to allow access the UC Berkeley licensed resources.
Make sure you select Library Access - Full Tunnel VPN when you log on.

Students: Problems setting up Library Proxy or VPN? Contact your librarian, or Student Technology Services: (510) 642-HELP, or