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Writing in BIOSC 1540 - Oakland Campus

This guide is intended to assist students in the Computational Biology course, BIOSC 1540, with the research and writing for their project.

Basic Search

For a basic search enter your search terms in the box. Search terms can be relevant subject terms, author names, protein names, terms identified from other records, or even journal names.

As you type, PubMed will show suggestions for possible search terms based on matches to MeSH headings (standard subject headings created by the National Library of Medicine) and on previous searches done in PubMed.

 

PubMed will search for the terms you entered as keywords in the article title, abstract, author names, indexing terms, and journal name.

To search for an exact phrase, use quotation marks around the phrase:     "protein folding"

To search for the root of a word with different endings, add an asterisk at the end of the root:   fold*

For more on how to structure database searches, check the Search Tips tab.

Advanced Search

Advanced Search lets you combine your search terms in a variety of ways and select the sections of a record that will be searched for each term. This gives you more control over the search and therefore over the results that will be displayed.

  • Click on Advanced under the Basic Search box, and then enter your search terms in the Builder boxes.
  • Use the pull-down menu on the left to choose the field, or section, of the record where you want the term to be searched. Click on Show Index List on the right to see a list of the terms that appear in that field.
  • Use the pull-down menu on the far left to specify how the terms in the different boxes will be combined (AND, OR, or NOT).
  • You can combine terms with AND, OR, or NOT within a Builder box 

 

 

In this search adding the truncation symbol * after model finds more endings than PubMed will process. You can see exactly what terms PubMed searched and how they were combined by checking the Search Details window to the right of the results and clicking on See more . . .

You might want to search a few selected terms instead:        model   or   models   or   modeling   or   modelling

By default the search results will display chronologically, most recently added records first. You can change the sorting order to display by most relevant first. Relevance is based on the number of times search terms appear in the record, where they appear in the record, etc.

 

 

For more on how to combine terms and structure a search in general, check the Search Tips tab.

 

Finding Review Articles

Here are two ways to find review articles in PubMed.

Limit your results after a search - While viewing the search results list, click on Review in the Article Type section of the leftmost column. This applies to both basic searches and advanced searches.

 

Include "review" as a search term in an advanced search -  In the search builder use the pull-down menu on the left to select Publication Type and enter review as the search term. Clicking on Show index list will give you a list of the possible terms to search in that field.

PubMed Search Tips

Author Searching

Enter the author's last name and initial, initials, or first name. Separate the last name with a comma if needed to distinguish between the first and last names:           crick f                  watson jd                      james, john

If entering the last name only, add the tag [au] after the name to search only in the author field:        wilkins [au]

or use Advanced Search to search in the author field. In Advanced Search you can also choose to search specifically for a First Author, Last Author, or Corporate Author, (e.g, an organization or institution).

PubMed will automatically truncate an author name to find all possible combinations of initials and names:                                                                            crick f,     crick fc,     crick fh,     crick francis

Use quotation marks to search for an exact name:           "willkins m" [au]

 

From 1966 - 1984 and from 2000 to the present, PubMed indexed all author names, so they are searchable. From 1984 - 1995 indexing was limited to the first 10 authors, and from 1996 - 1999 the limit was 25 authors.

 

Journal Title Searching

You can search for a specific journal by entering the full title, the journal abbreviation, or the ISSN (an international standard identification number for the journal) in either a Basic or Advanced Search.

  • journal of computational biology
  • j comput biol
  • 1557-8666

 

Automatic Term Matching

PubMed automatically checks untagged search terms against various tables, including MeSH headings, journal names, and author names. If it finds a match, PubMed will search the terms in the corresponding field as well as doing a search in all fields. You can see exactly what terms were searched and where by checking the Search Details box on the right side of the search results screen.

Exporting References to EndNote

You can export references of interest from your search results to EndNote or other reference manager software.

  • Select each reference of interest by clicking on the box at the left
  • Click on Send To and choose Citation Manager as the destination
    • If no references are selected, you will be asked how many references to send to the file and which reference to begin with
  • Create the file
  • Save the file to your computer, and then export the file to your reference manager
  • OR  If the desktop version of your reference manager is loaded on the computer you are using, try opening the file with your reference manager software to export the file directly to it.