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Library Resources for the UC Berkeley Bridges to Baccalaureate Summer Research Program, Summer 2014

Presented by Michael Sholinbeck and Jeffery Loo

URL for this web page: www.lib.berkeley.edu/PUBL/SPH/b2b.html


The UC Berkeley Science Libraries: Location, Reference, and more

Science Libraries @ UC Berkeley
  » Includes links to the individual libraries (Bioscience, Chemistry, etc.)
  » Information on email reference and 24/7 chat reference services
  » Scanning, printing, copying services
  ... and more!

How to set up off-campus access to library resources (databases, online journals, etc.)

Information on UCB Wi-Fi Options, including AirBears

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The Scientific Literature: Books, Handbooks, Articles

With 8 science libraries on campus, we have many information sources to help you in your research. Let’s review these sources.

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

For more detailed exploration of a topic, books provide the focus you want.

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

All of these materials can be found at Berkeley by searching our library catalog, OskiCat. You’ll find which library owns the item and whether it is available for borrowing, or online.

The next source 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:

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

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Critical Evaluation

What is evidence?

Peer review
Peer review refers to a process whereby 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?
» Read Editorial peer review for improving the quality of reports of biomedical studies (Cochrane Database Syst Rev. 2007 Apr 18;(2):MR000016)

Who pays for science?
Most scientific research is funded by government grants, companies doing research and development, and non-profit foundations. Because science is attempting to get at some "truth," the source of research funding shouldn't have a significant effect on the outcome of scientific research, right?
» Read Industry sponsorship and research outcome Cochrane Database Syst Rev. 2012 Dec 12;12:MR000033).

Oops! I made a mistake (or ... was it cheating..?)
Occasionally, scientists make mistakes, and sometimes those mistakes affect the conclusions of a published article. Articles may be retracted if the mistake is significant. This is a formal process where the author or journal publishes a statement outlining the error. Sometimes, however, retraction is the result of fraud, plagiarism, or other bad acts.
» Read Retraction Watch.

Reliability and validity
Reliable data collection: relatively free from "measurement error."
  » Is the device used to measure elapsed time in an experiment accurate?
Validity refers to how well a measure assesses what it claims to measure
  » How accurately can this animal study of drug metabolism be extrapolated to humans?

What to consider when looking at survey or estimated data:
Adopted from information on the UCSF Family Health Outcomes Project web site

Other things to consider
Do the conclusions of the article follow the evidence that's presented?
Are opinions or notions posited as facts? (Search "As is well known..." in Google Scholar.)
Publication bias: Studies where nothing happened are less likely to get published.
CV boosting: Does this study add to the body of knowledge, or is it just something the author is doing to add to his/her list of publications?
Significance of a single study: Science is incremental. Beware of any study that's proclaimed to be a "breakthrough."

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Starting the Library Research Process

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

Examples of interdisciplinary research with contributions from UCB scientists:
  » Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination (Biology and Engineering)
  » Galvanotactic control of collective cell migration in epithelial monolayers (Biology and Engineering)
  » Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics (Biology and Physics)
  » DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 (Chemistry and Biology)

Is your topic researchable?
  » Growth and development of viruses
  » Growth and development of DNA viruses
  » Growth and development of Adenoviridae
  » Growth and development of Adenoviridae in outer space

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?
  » Does electrophysiology describe the effects of electricity on living organisms, or is it what electrophysiologists do?

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.
    eg, Viruses, DNA Viruses, Adenoviridae, Aviadenovirus
Subject terms tend to have a single, unambiguous definition.
    eg, Aviadenovirus = a genus of Adenoviridae that infects birds
Subject terms may also be called thesaurus terms, descriptors, or (in PubMed) Medical Subject Headings (MeSH).

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Searching PubMed

PubMed: Citations to over 23 million journal articles and books, with links to full text via Getting Started with UC-eLinks

PubMed top tips for better searching:

  1. Combine terms with AND or OR
  2. Use Filters (eg, Publication date, Language, etc.)
  3. Search for your term as a word in the title or title or abstract (using Filters, Advanced Search, or Field Tags)
  4. Use truncation (with a *)
  5. Use MeSH (Medical Subject Headings - PubMed's subject terminology), with subheadings
  6. Use the Related Articles link, once you find a set of relevant citations
  7. Always keep in mind the question you are trying to answer when creating a search strategy and when reviewing the articles you find

» PubMed Quick Guide: Basic search help. (From the UCB Bioscience Library)

» Searching PubMed exercise set (PDF):

» Combining search terms with Boolean operators (AND, OR, NOT - remember Venn diagrams?)

» Filters: Limit your search by language, age group, publication type, publication date, and more.
   Also use Filters to restrict your search to words in the article title, abstract, or Medical Subject Heading (MeSH).
   Note that Filters stay in effect until you clear them.

» Use Medical Subject Headings (MeSH):
» Saving citations temporarily using the Clipboard

» My NCBI:

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Searching Web of Science

Web of Science
Searching the Web of Science database will find journal articles across a wide range of scientific disciplines from health through astronomy and beyond. It offers powerful search and analysis tools to hone into the relevant articles for your research. The in-class exercise explores these tools.

» Web of Science Quick Reference Guide (PDF)
» Searching Web of Science Exercise (PDF)

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Other Scientific Databases and Sources of Scientific Information   Getting Started with UC-eLinks     access paid by UCB

Remember those PubMed "Top Tips"?
Most are applicable to the databases below, as well as several other databases you may find yourself using.

BIOSIS Previews
Coverage includes traditional areas of biology, such as botany, zoology and microbiology; biomedicine, agriculture, pharmacology, biochemistry, biophysics, bioengineering and biotechnology are also included, as well as instrumentation and methods. Includes citations to articles, books, meeting abstracts, and more.
» BIOSIS Previews Quick Guide

Encompasses civil, structural, and mechanical engineering disciplines, as well as related fields in science and management.
» Compendex Quick Guide

Indexes scholarly journals, conference proceedings, books, reports, and dissertations in physics, electrical engineering and electronics, computers and control, and information technology.
» INSPEC Quick Guide

Citations in psychology, behavior, cognition, and related disciplines; includes citations of journal articles, conference proceedings, books and book chapters, reports and dissertations.
» PsycINFO Quick Guide (PDF)

Google Scholar
Citations on all topics, fast & free. Use Advanced Search by clicking on the ▼ in the search box, then search for title words to reduce your search results.
    Be aware that Google Scholar lacks what the databases above have:
    » the ability to use iteration in developing search strategies,
    » any indexing (ie, a controlled vocabulary),
    » bulk downloading or saving of records,
    » a complete description of its contents.

Use the library catalog to find books, reports, etc. on your topic.
Over 11 million volumes; maybe there's one on your topic:
» OskiCat: UCB library catalog  |  OskiCat Help

The above are but a sample of the many databases available to find article and other citations.
See the Science Libraries @ UCB Databases A-Z web page for more.
Ask a librarian for help if you are having trouble with your topic.

Molecular & Cell Biology Resources

Chemistry Resources

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Citing and Keeping Track of Citations: Mendeley, Zotero, RefWorks, EndNote

Citation Guides: A list of online resources to help you with consistent citing.

Mendeley, Zotero, RefWorks, EndNote, and other bibliographic management programs (aka reference management software) will:
    - Let you create a database of citations you find;
    - Let you organize your citation database by criteria of your choosing;
    - Link to PDF files, or store PDF files in your database;
    - Work with Word to correctly cite citations into your document.
Information on a substantial student discount for EndNote is available from the Cal Student Store; call 845-1226 ext 8470 for details.
RefWorks is licensed by the UCB Library and is free to use while you are here.
Zotero and Mendeley are free.
» Comparison of reference management software (from Wikipedia)

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