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CDL Database Transitions

June 27, 2002 Author: CDLCategories:

a. BIOSIS Previews in Ovid (Beth Weil, Resource Liaison for BIOSIS Previews)

UC access to BIOSIS Previews will be available on Monday, July 1, 2002 from http://gateway.ovid.com.  Then click on the “Start Ovid” button; no login or password is necessary. Access to BIOSIS Previews via CDL (1985-present) is expected to continue until 12/31/02.  Ovid provides BIOSIS Previews data from 1969 to the present.  Links to holdings, electronic full text are available through the UC-eLinks service.  The Ovid version of BIOSIS Previews greatly enhances our access by providing 15 years of additional data and new searching capabilities.  A short guide to searching BIOSIS on Ovid will be available at [http://www.cdlib.org/libstaff/comm/outreach/OvidBIOSIS.doc]

What’s new for UC Users?

  1. Data back to 1969
  2. Data is in one file, instead of two
  3. Adjacency operators allows greater precision in searching
  4. Volume and/or issue number are searchable, which can assist in verifying citations
  5. Truncation options have expanded
  6. Direct importing into EndNote 4 and 5

What has changed for UC Users?

  1. BIOSIS significantly changed their subject and organism indexing in 1998.  They reissued the data back to 1993 following their new indexing scheme.  CDL masked these changes in the data so UC patrons would not need to modify they way they searched.  We now must learn the new field structure.  This particularly affects the way searching for organisms works.
  2. BIOSIS also modified the format of author names.  They used to just include the authors’ last name and initials.  Now they are including the first name and   middle initial if available.  This means that there are frequently many variants (including typos) of an author’s name (e.g., d wake, d.a. wake, David Wake, David A. Wake, etc.) which need to be marked. Generally putting the last name and first initial only is the best starting point to see all variants of a name.
  3. Phrase searching is the default for keyword searching.  Because Ovid defaults to adjacency, if you want to do a word search you must enter Boolean operators (i.e., AND, OR, NOT) between the keywords.
  4. Alerts (Updates) are in beta test and will be available soon.
  5. Command line access devotees will need to learn Ovid command line syntax.  (These are generally very similar to old BRS commands.)  A summary of commands is listed in Ovid’s help under advanced searching.  See http://gateway1.ovid.com:80/ovidweb.cgi?S=IDNJHKLGKFADLK00D&HC=syntax& .
  6. The pound sign (#) truncation symbol stands for only 1 character truncation.  The dollar sign ($) is equivalent to the # in the CDL system.
  7. Call numbers and full text URLs can no longer be printed, emailed or imported into personal bibliographic software (such as EndNote).

Below is a more detailed view of the BIOSIS Previews database on Ovid and the upcoming changes.

BIOSIS Previews is the world’s most comprehensive reference database for life science research.  It covers original research reports and reviews in biological and biomedical areas.  Coverage includes traditional areas of biology, such as botany, zoology and microbiology, as well as related fields such as biomedicine, agriculture, pharmacology and ecology. Biochemistry, biophysics, bioengineering and biotechnology are also included.  Nearly 5,500 serials are monitored for inclusion.  In addition, the database covers content summaries, books and meeting abstracts, papers and posters, U.S. patents from 1986 to 1989 and from 1999 on, and meeting reports from 1980 to present.

Searching Options

Ovid offers two searching options, Basic and Advanced. Basic mode supports Author and Subject searching with a few limits.  Advanced mode allows the user to specify fields, and Boolean or adjacency operators either by using the main search tool bar or by specifying commands in the search box.  The search history is displayed in the Advanced mode.  Although the search history is not displayed in Basic mode, Ovid does maintain it and you can easily see previous searches done in Basic mode by clicking on the Advanced mode button on the main search page.  A list of commonly used fields in BIOSIS Previews is available in the BIOSIS Previews on the Web (Ovid) Quick Reference Guide at [http://www.cdlib.org/libstaff/comm/outreach/OvidBIOSIS.doc].

Truncation

Truncation is greatly enhanced in the Ovid interface.  There are 3 truncation symbols.
$ or : retrieves unlimited suffix variations (e.g. bacteria$.ti.)
# replaces a single character within or at the end of a (word wom#n.ti)

Note: You must have at least two characters in a word before any wild card or truncation.

Author Searching

BIOSIS has changed the way they enter author names. Recent years include the author’s first names and middle initial if available.  Earlier years only contain the initials. It’s important to check all of the variant forms of the name in the author index for a complete search.

Journal Searching

Enter a few words of the journal title, just enough so that Ovid can take you to the correct part of the journal index display. Do not use abbreviations.

Subject Searching

Enter your Subject Keyword or Keywords (linked with a Boolean operator or as a phrase), in the main search box and click on the “Perform Search” button.  All subject headings are included in this index with the exception of Taxa Notes, the new name for Supertaxa, the very broad systematic classifications.  Without a Boolean operator, terms will be searched as a phrase.  To retrieve all relevant records, include every possible way an author might have described your concepts (e.g., phage or phages or bacteriophage or bacteriophages or lambda, etc.).  You will need to use truncation ($), synonyms and to consider spelling variations.

BIOSIS added a large number of specialized subject indexes in 1998 and remastered the data back to 1993 for some of them.  It is important to remember that only 3 indexes, Concept Codes, Supertaxa (formerly called Biosystematic Names) and Taxa Notes (formerly Supertaxa) span all years.

The Tools Menu contains lists of Major Concepts, Super Taxa, Organism, Taxa Notes, Geopolitical Locations and other fields containing controlled vocabulary.  However, to browse a list of these tools you have to type in something that exists in one of the lists.

Pluses (+) by a term indicate that there are narrower terms underneath it.  Click on the plus to see more terms. Frequently you have to navigate down a couple of layers to actually see data.

Under the “Search Fields” button, it is possible to display the indexes which will show everything BIOSIS has put in a field. Because many fields combine both controlled and uncontrolled vocabulary, the Display Fields feature is of limited use for most fields.  This is, however, the only way to see the complete list of Concept Codes.

In general it is best to do subject searching using the keyword index without mapping turned on.

Organismal Searching

There are now 3 fields: Super Taxa (Content changed!), Taxa Notes and Organism.  Super Taxa and Organism Fields are included in the keyword (mp) index.  Taxa Notes, unfortunately, are not included at this time.

Taxa Notes: Taxa Notes are basically equivalent to the pre-1993 Super Taxa; 65 terms reside under the Tools menu.  In the Tools menu, type a valid entry (i.e., Bats) and use the Tree option.  You will see the entire list of Taxa Notes.  Taxa Notes are usually not scientific names (use “birds” instead of “aves”; “chordates” instead of “chordata”).

Super Taxa: Super Taxa are now basically equivalent to the pre-1993 Biosystematic Code taxon terms.   The numerical codes no longer exist.  The Super Taxa field contains over 950 higher level taxonomic terms which can be found by using the Tree search under the Tools Menu.

Organism Field: This taxonomic field contains the particular genus, species, or common name of an organism.  Because this field only goes back to 1993 and is included in the keyword field, comprehensive searches on genus/species and common names should be done in the keyword (mp) index.

Major Concept: 168 broad subject categories comprise the Major Concepts in BIOSIS Previews.  These are equivalent to the very broadest of the pre-1993 Concept Codes.  Major Concepts can be found through the Tools Menu.  Use the Tree command in the Tools menu to see a list of the 78 broadest Major Concept Terms; then type in a valid entry (try “ecology”).  This will take you to a list that includes terms such as Biochemistry and Molecular Biophysics, Evolution and Adaptation, Genetics, Parasitology, Systematics and Taxonomy, Toxicology, etc. Some Major Concepts have narrower terms beneath them (e.g., Biochemistry and Molecular Biophysics) and may be exploded to pick up these narrower terms.  Generally these terms are best used to limit a search where keyword searching is too imprecise.

Geographic Searching

Geopolitical Location: Broad geographical areas are listed in the Tools menu many are explodable. Browse through the Tree search in the Tools menu to see the possibilities; for non-thesaurus locations search by location (Sacramento.ge) Data exists in this field from 1993-.  For earlier records use all possible geographic variants in the keyword index.

Publication Type

To limit your search to journal articles amend the phrase “article.pt” or “journal article.pt” to your search. Both need to be included to get all journal articles.  Checking off “review” on the Main Search pages searches for citations with literature review in the publication type or review in the title. “Literature review.pt” can be used to limit your search to review articles.  The retrieval is a bit different than using the check box on the Main Search screen.

Managing your Results

Citations can be emailed, printed or downloaded using the Citation Manager found at the bottom of each screen display of records.  The Citation Manager in Advanced mode provides a great amount of flexibility regarding which fields are included, which citations are included and the method of delivery.  Primary and secondary Sort functions are also available.  The Print function from the web browser must be used to print.

Personal Bibliographic Software (i.e., EndNote)

Patrons who wish to import data in EndNote have several options; however, you must be in Advanced Mode to utilize them. Users of EndNote 4 and 5 can use Ovid’s Direct Export option if they are searching Ovid from a machine which has EndNote.  It is also possible to email or save files for importing into EndNote at a later time.  The reprint/Medlars format in the Citation Manager should be used for either of these options.

Telnet Searching

A telnet searching option is available in Ovid.  It can be reached by telneting to Ovid.com and pressing Return in response to the next two prompts.  The telnet access is not user-friendly. For those of you looking for a fast command language system we do not recommend telnet access.  Using the Ovid command language will be considerably more satisfying.