Ecology and evolution of infectious disease in a changing world

BIO 2N - Spring 2017 - Instructor: Erin Mordecai

This guide outlines key resources for conducting biological research.

 

Finding books and book chapters

SearchWorks

Use SearchWorks (https://searchworks.stanford.edu/) to find books and ebooks available at Stanford.

SearchWorks find books

Tips for using SearchWorks

  • SearchWorks finds books, ebooks, journals, ejournals (not journal articles), Stanford dissertations, databases, and other items owned by the libraries at Stanford.
  • All fields works well to find books on a topic.  To search by title or author, pull down the list of search fields.
  • Use the facets on the left of the search page to limit to books and online in order to find ebooks.
  • In a list of results, click on a title to display the full record.
  • On the left side of the full record, find library locations and availability of e-versions.
  • If the item is at SAL3, click on Request to have it sent to your library.
  • At the bottom of the full record, browse similar items.

xSearch

xSearch searches multiple resources at one time.  More than 250 resources are covered by xSearch, including abstracts and indexes, full-text ejournals and ebooks, patents, technical reports, and reference sources. 

X search

To find book chapters:

  1. On the search page, under Categories/Subcategories, click Plus sign next to Multidisciplinary.
  2. Check the box next to Books, Reports, & Theses.
  3. Enter your search.
  4. On the Results page, click on the Books tab.

You can also search books from specific publishers. For a search that is focused on specific resources:

  1. On the search page, under Categories/Subcategories, click Plus sign next to Multidisciplinary.
  2. Click Books, Reports, & Theses (not the box next to Books, Reports, & Theses).
  3. From the list, select resources to search.
  4. Enter your search.
  5. On the Results page, click on the Books tab.

Finding journal articles

The libraries provide access to hundreds of databases that index journal articles, meeting abstracts, technical reports, book chapters, and other literature.

To find journal articles on ecology and evolution of infectious disease, parasites, and vectors, search Web of Science Core Collection, BIOSIS Citation Index, Google Scholar, or PubMed.  Databases can be found by searching SearchWorks:


SearchWorks catalog search all fields search


Web of Science Core Collection

Web of Science Core Collection indexes a selected set of important journals across all scientific disciplines.  A key feature is cited reference searching, described in a separate section.  Search for journal articles from 1900 to the present by topic, author, author address, or publication name.

Web of Science Core Collection search page

Web of science search page

Tips for searching Web of Science Core Collection:

  1. On the Basic Search page, click on Add Another Field for more complex searches.  Place different concepts on separate lines.
  2. Use truncation (*) to find variations in word endings.  Connect synonyms with OR: zika and (transmi* or epidemiol*) and (brazil* or amazon*).
  3. Added index terms are minimal in Web of Science Core Collection, and many records do not have abstracts.  Topic searches find words mainly in titles and abstracts.
  4. Singular and plural forms are searched automatically, but consider adding irregular plural forms: alga or algae.
  5. On the basic search page, pull down the list of indexes to search for authors or publications.
  6. On the results page, click on Find it SU to see the full article.
  7. On the results page, click on Save to EndNote Online to save to a citation management program.
  8. On the results page, click on Search History to create an alert and get an email alert when new articles match your search request.
  9. For best results in author searches, select the Author index from the pull-down list of indexes, then click on Select from index. 

Web of Science Core Collection subject search example

Finding articles on effects of climate change on the evolution of malaria:

 Web of science malaria search

BIOSIS Citation Index

BIOSIS indexes journal articles, meeting abstracts, and some book chapters in life sciences.  It covers literature published from 1926 to the present.  Indexers add index terms to each article using a complex system of terms.  Organism names are particularly well indexed.  Search by topic, author, author address, or publication name.

BIOSIS Citation Index search page

Biosis citation index

Tips for searching BIOSIS Citation Index:

  1. On the Basic Search page, click on Add Another Field for more complex searches.  Place different concepts on separate lines.
  2. Use truncation (*) to find variations in word endings.  Connect synonyms with OR: zika and (transmi* or epidemiol*) and (brazil* or amazon*)
  3. The entire taxonomic hierarchy is very well indexed in BIOSIS but you can mix general and specific terms or taxonomic names with common names for better results: mosquito or aedes or anopheles or culicidae.
  4. Singular and plural forms are searched automatically, but consider adding irregular plural forms: alga or algae.
  5. On the basic search page, pull down the list of indexes to search for authors, author address, or publications.
  6. In a list of results, click on a title to view the full record.  On the right side of the full record, find cited references and citing articles.
  7. On the results page, click on Find it SUto see the full article.
  8. On the results page, click on Save to EndNote Online to save to a citation management program.
  9. On the results page, click on Search History to create an alert and get an email alert when new articles match your search request.
  10. For best results in author searches, select the Author index from the pull-down list of indexes, then click on Select from index.

BIOSIS Citation Index subject search example

Finding articles on climate chage on mosquito transmission of diseases in Brazil:

Web of science malaria search example

Google Scholar

Google Scholar indexes journal articles and other literature across all disciplines.  Like Web of Science Core Collection, Scholar offers cited reference searching, described in a separate section.  Search for journal articles by topic, author, author address, or publication name.  Dates of coverage vary, depending on content that is available digitally.

Google Scholar search page

Google scholar

Tips for searching Google Scholar:

  1. Enter words or author names in the basic search box or use the pull-down menu for more options on the Advanced Scholar Search page.
  2. For best results in a topic search, enter a few words that best describe your topic: zika climate change.
  3. In a list of results, click on Find it@Stanford in the right column to view the full article.  If you do not see the Find it@Stanford link, click on the down arrow in the upper right, then on Settings to set your library link.
  4. Also under Settings, you can opt to show links to import to EndNote or another citation manager.
  5. To create an alert and receive updates via email, on the results page, click on Create Alert.
  6. See Google Scholar help: http://scholar.google.com/intl/en/scholar/help.html.

Google Scholar subject search example

Finding articles on Zika epidemiology in Brazil:

Google scholar search example

 

PubMed

PubMed indexes journal articles in medicine, basic biomedical sciences, health care, and related areas, including epidemiology.  An important feature of PubMed is the use of Medical Subject Headings (MeSH), a standard set of index terms, to index nearly all articles. 

PubMed search page

PubMed search

Tips for searching PubMed:

  1. On the Basic Search page, use AND, OR, and parentheses for more complex searches.
  2. Use truncation (*) to find variations in word endings.  Connect synonyms with OR: zika and (transmi* or epidemiol*) and (brazil* or amazon*)
  3. Click on Advanced to enter a more complex search.
  4. To take full advantage of MeSH, on the Basic Search page, pull down the menu under All Databases and select MeSH.  Use MeSH to find the best terms for searching PubMed.
  5. To find an author, enter the last name and the first initial with no punctuation.  Click on Help for more information.
  6. In a list of results, click on a title to view the full record.
  7. On the results page, click on Find it SU or Lane to see the full article.
  8. On the results page, use the check boxes to select articles of interest.  Click on Send to in order to download a record to a citation manager.
  9. On the results page, find the link to Create Alert.

PubMed subject search example

Finding articles on the epidemiology of zika in the United States:

PubMed search example

Finding review articles

Review articles are longer articles that review the current state of knowledge on a topic.  Usually an extensive bibliography is included.  Review articles are an excellent starting point for research on a topic.

Web of Science Core Collection

Web of Science Core Collection indexes a selected set of important journals across all scientific disciplines.  A key feature is cited reference searching, described in a separate section.  Search for journal articles from 1900 to the present by topic, author, author address, or publication name. 

Finding review articles in Web of Science Core Collection:

  1. On the Basic Search page, pull down the list of indexes to the right of the search box and select Document Type.
  2. Select Review from the list of literature types.
  3. Click on Add Another Field.
  4. Enter search terms in the new search field.

Web of science review

BIOSIS Citation Index

BIOSIS indexes journal articles, meeting abstracts, and some book chapters in life sciences.  It covers literature published from 1926 to the present.  Indexers add index terms to each article using a complex system of terms.  Organism names are particularly well indexed.  Search by topic, author, author address, or publication name.

Finding review articles in BIOSIS Citation Index:

  1. On the Basic Search page, pull down the list of indexes to the right of the search box and select Literature Type.
  2. Select Literature Review from the list of literature types.
  3. Click on Add Another Field.
  4. Enter search terms in the new search field.

Biosis literature review

Google Scholar

Google Scholar indexes journal articles and other literature across all disciplines.  Like Web of Science Core Collection, Scholar offers cited reference searching, described in a separate section.  Search for journal articles by topic, author, author address, or publication name.  Dates of coverage vary, depending on content that is available digitally.

To find review articles in Google Scholar, add review to your search terms.

Google scholar search disease ecology

PubMed

PubMed indexes journal articles in medicine, health care, basic biomedical sciences, and related areas.  PubMed covers literature published from 1946 to the present.  A key feature of PubMed is the use of Medical Subject Headings (MeSH), a consistent and well-developed list of subject headings.  Often MeSH can be used to improve search results.

Finding review articles in PubMed:

  1. Enter a search in the Basic Search or Advanced Search box.
  2. On the Search Results page, click on Review under Article types in the list of facets on the left side of the page.

PubMed zika epidemiology

Cited reference searching

Cited reference searching allows the searcher to find more recent literature that cites an item of interest.  Web of Science Core Collection is a good database for cited reference searching in the sciences.  Other databases that offer this feature are: BIOSIS Citation Index, Google Scholar, and Scopus.  These databases index different overlapping sets of the literature, and different results will be found in each.

Web of Science Core Collection

Web of Science Core Collection indexes a selected set of important journals across all scientific disciplines.  A key feature is cited reference searching, described in a separate section.  Search for journal articles from 1900 to the present by topic, author, author address, or publication name. 

Cited reference searching in Web of Science Core Collection:

  1. To find articles that cited a known article, use Basic Search to find the article.  On the right side of the results page, click on the number next to Times cited.

    Web of science cited reference search

  2. For more options, on the Basic Search page, click on the down arrow next to Basic Search and select Cited Reference Search.  Find all articles that cite an author or articles that cite a selection of an author’s papers.

    Web of science cited reference search all articles
  3. Search for cited authors using last names or last names with initials.
  4. Results of a cited reference search are presented in a table.  Use the check boxes to find the citing articles of interest.
  5. Because articles can be cited in different ways, the same cited article can be represented on different lines of the table.

Web of science cited reference table

What to do if the item you need is not available

  1. If you are working off campus, review Connect from Off Campus (http://library.stanford.edu/using/connect-campus).
  2. Search the book or journal title in SearchWorks (https://searchworks.stanford.edu/).  Do not search for articles in SearchWorks.  If you cannot find the book or journal in SearchWorks, it is probably not available at Stanford.  If you find the title in SearchWorks, click on the title in the list of results to view the full record.  On the left side of the full record, find information about availability of print or digital versions.
  3. Send a message to the library.  We will investigate availability.
  4. Use Google to determine whether a free version of the item is available.
  5. Request the item through Interlibrary Borrowing (http://library.stanford.edu/using/interlibrary-borrowing).

Finding research groups

Finding a research group whose interests are similar to yours can lead you to unpublished research or to literature that is not well indexed in traditional journal article databases.

Finding research groups through journal literature

  1. Search for a topic in BIOSIS Citation Index, Web of Science Core Collection, Google Scholar or PubMed.  Find a recent article on your topic.
  2. Display the full record and find the author address field.  Focus on the first and last authors.  The first author is the primary author and the last author is frequently the principle investigator.
  3. Search Google for the author in combination with the author’s institution: Deborah Gordon Stanford
  4. The author’s web page may list collaborators or published or unpublished research.

Finding research groups through Federal Research in Progress

Federal Research in Progress (FEDRIP) provides Information about ongoing federally funded projects in the fields of the physical sciences, engineering, and life sciences.  Project descriptions generally include: project title, keywords, start date, estimated completion date, principal investigator, performing and sponsoring organizations, summary, and progress report.

  1. Find Federal Research in Progress through SearchWorks.
  2. Enter a topic search in the search box.  For an item of interest, display the full record and find the investigators and the performing organization.
  3. Search these in Google to find the research group’s web page.

Finding research groups

 

 

Citation management

As you accumulate literature to support your research, you will want to save items for future reference and to store citations for use in bibliographies.  Many people do this by saving PDF files in folders, but this is very inefficient.  Citation management tools streamline the task of managing both citations and your access to literature of interest.  Citation tools can import references from journal article databases, allow you to search for articles in your personal database, link to full articles, facilitate sharing of articles among your research group, and output references in any format you need as you write.

Citation management tools

Of the many citation management tools that are available, most Stanford users rely on one of the five listed below.  See the Citation Tools Comparison Chart: https://stanford.app.box.com/s/qo4rs7eyhma5pl5pxacrg3arcze8boex

The libraries also offer Bibliography Management http://library.stanford.edu/research/bibliography-management, a brief guide to citation management software.

RefWorks 2.0 https://searchworks.stanford.edu/view/5053841

RefWorks is a web-based citation tool that is available to Stanford users via a library subscription. 

EndNote X7 and EndNote X8 http://www.endnote.com

EndNote is an individual software program that is available for purchase.  See the EndNote Online User Guide http://endnote.com/support/online-user-manual/x7

EndNote Web

EndNote Web is a web-based citation tool that is available to Stanford users as a part of the library’s subscription to Web of Science.  It is integrated with Web of Science Core Collection, BIOSIS Citation Index, and other Web of Science databases.  See the EndNote Online User Guide http://endnote.com/support/online-user-manual/x7

Zotero www.zotero.org

Zotero is free, open-source software for citation management.

Mendeley https://www.mendeley.com/

Mendeley is a free reference manager and an academic social network.  Join the Stanford Mendeley Group https://www.mendeley.com/groups/2444891/stanford-university/ for more storage.  See the Mendeley Fact Sheet https://stanford.app.box.com/v/mendeleyfactsheet

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