THIS GUIDE IS OUTDATED --
TO FIND MORE UP TO DATE GUIDES GO TO:
http://www.lib.uchicago.edu/e/su/chem/ucbeil.html
and look for the section on "User Guides"
URL for this document: http://www.lib.uchicago.edu/~atbrooks/beilfact.html
Beilstein CrossFire Fact Searching
Contents of this document:
Note:
This guide was written for use with version 3.2 of the Beilstein
CrossFire client. For a more recent version (4/28/99) of the document written
for use with version 4.0 of the client, point your browser to:
http://www.lib.uchicago.edu/~atbrooks/fact40.html
The Beilstein database contains information on approximately 7 million
organic substances. Records in the database include structures, data
on chemical and physical properties such
as melting point, boiling point and spectral identification, and over
5 million reactions, as well
as references to the chemical literature published from 1779 to date.
The information in this database has been compiled by Beilstein
Information Systems, Inc., publishers of the Beilstein Handbook of
Organic Chemistry.
Commander and CrossFire
The Beilstein database is searched using Commander, a client-server
graphical interface that provides access to the CrossFire search and
retrieval software. The database may be searched for substances using
structures and/or property information. There are over 30 million
numeric and text reports in the database arranged in some 300 fields
that can also be used to construct a seearch for a particular compound
or class of compounds. For example, Chemiical Abstracts Services
(CAS) Registry Numbers, chemical names, molecular formulae and values
of physical properties may be used to search. In addition, the
database is searchable for reactions and literature citations. This
document is intended to introduce new users of the database to some of
the basic searching techniques; those who have complex searches will
find additional documentation in the manuals provided by Beilstein
Information Systems, Inc (copies of these manuals available at the
Chemistry Library). Users at the University of Chicago may use
Beilstein CrossFire at selected Library workstations, or by
downloading the client for the World-Wide Web. For more information
on either means of access, contact the Chemistry
Librarian or visit the Chemistry
Library Subject Page.
Use the mouse to point to the Commander icon on the screen and double
click the mouse. (see below for graphic of Commander icon)
The Commander introductory screen will display. Click on the
CrossFire button (two red crossed arrows; seen in Figure 2) to bring
up the CrossFire login screen (Figure 1). Type in at least one
character on the User ID and Password lines and press
("x" and "x" are used in Figure 1). If the login attempt times out, simply click once more on the CrossFire button. A successful login to the Beilstein server at the University of Wisconsin is indicated by the CrossFire button being "pushed in".
Figure 1. CrossFire Login Screen
The Commander main screen will reappear (Figure 2). The top of the screen
displays a menu bar and a function bar; the function bar allows quick
selection of frequently used system features. The status bar at the
bottom of the screen provides information on the status of the
session. To begin searching pull down the Task menu and select
Fact Editor to construct a search based on facts such as
chemical name, molecular formula, etc.
Figure 2. Commander Main Screen
After Fact Editor is selected a window will open with the
heading Fact Editor and a menu bar, function bar and form to
enter facts (Figure 3). The form has three columns headed
Operator, Field Name and Value. Over 350 fields are
available for searching can be displayed by choosing List Field
Names from the Edit menu or by clicking on the List
Button (see Figure 3). After an appropriate field name is
selected and copied into the Fact Editor form, enter a search
term in the Field Value column. Again, the List Button
may be used to select an appropriate term. Boolean operators AND,
OR and NOT can be used in the Operator column to
construct multi-concept searches.
Figure 3. XFIRE Fact Editor
Tips for using the XFIRE Fact Editor screen:
- Use the left
column labeled Operator to enter a Boolean operator
(AND, OR, NOT) to specify the relationship between facts on the
adjacent lines.
- The search statement in the box at the bottom can be edited and copied back into the the form above by clicking the
up arrow button found at the lower left of the window.
- The Clear
Line button erases input on the line in the form where the cursor
position; use correct a typing
mistake.
- The tab key is used to move from box to box through
the columns of the editor form.
- Fields available for searching can be browsed by positioning the
cursor in the field name of the column and pressing the function bar
button labeled List Field Names. Copy a particular
field code to the search form by double clicking on the field of interest.
There MUST be a valid field
name label entered to proceed with the search.
To enter a known registry number, select from the list of fields or
type "RN" (the valid field name for CAS Registry Number) in the Field Name column, move the cursor to
Value column and enter the number including any hyphens.
Registry Numbers have not been entered for all compounds in the
database. If a Registry Number search is not successful, try another
type of search such as chemical name or molecular formula.
To search
a molecular formla, type the code "MF" in the Field Name
column and enter the formula (in Hill order: carbon, hydrogen,
followed by all other elements in alphabetical order) in the
Value column. For example, to search for cubane, type "C8H8";
the search statement "MF=C8H8" will appear in the box at the bottom of
the window.
Searching the chemical name field is done using either the systematic
International Union of Pure and Applied Chemistry (IUPAC) name as in
the Beilstein Handbook or with names that appeared in original
publications indexed by Beilstein. Sometimes other names are also
searchable; typically, common or trivial names may be successful but
trade names are less likely to retrieve records.
Complete names are indexed as units in the "Chemical Name
(CN)" field, but are also broken into fragments at punctuation marks
and spaces in the "Chemical Name Segment (CNS)" field. Right and left
truncation of fragments is allowed using the * operator. For example,
the search statement "CN=*fluoxetin*" defines a search for any
compound whose name contains the term "fluoxetin" no matter how the
name starts or ends. The search statement "CN=fluoxetine" will
retrieve the record for that specific compound, but the search
"CNS=fluoxetine" will retrieve records for any substances whose names
contain that segment.
The name and name segment indexes can be browsed by typing "CN" or "CNS" in the
Field Name column and positioning the cursor on the Value
column. Click the List button in the function bar to
display the index for the specified field. Scroll or drag to move
through the index or type a few characters into the input box at the
bottom of the window to move to the desired section of th e index.
Double clicking on an entry copies it to the search form where the
term may be edited, if desired. Entering least common fragments of a
long complex name connected by Boolean AND operators will often
produce a small set of hits that can be reviewed for further
selection.
After defining a fact search, click on the ->BC button (see
Figure 3). The search statement will appear on the left side of the
screen in the Fact box. When the search has been transferred
to the Commander main screen, click the Search button in
the function bar. A small graphic of a pacing figure will appear in the upper left corner of the screen. Commander/CrossFire will search the database and
report how many compounds match the search criteria, i.e., how many
"hits". Click the Display Hits button (see
Figure 4) in the dialog box to review the items retrieved in either
full or short display; the default display mode is the full record.
Figure 4. Search Results
The Display Hits
window in full display mode (see Figure 5)shows the structure of the
compound in a smaller window labeled with the Beilstein Registry
Number (BRN), the system's unique identifier. The larger window
displays all available fields in the record and can be scrolled
through using the right hand scroll bar.
Here are some tips for moving through
the hitset:
- Underlined numbers in various colors seen in
many records are hyperlinks to the Beilstein record for a compound, reaction or citation
referred to in the hit. To move to the linked record click on the
highlighted number.
- To move to the previous or next record, use the
center two arrows in the upper left part of the screen.
- Use the outer two arrow buttons (the ones pointing to a vertical line) in the upper left part of the screen to
move to either the first or the last hit.
Figure 5. DisplayHits
Screen
There are a number of ways to maneuver through a CrossFire hitset.
Many records in the database are extremely long. The display can be
customized to show only the information of interest (e.g.,
preparations, NMR spectra, toxicity, etc.) for each compound in the
hitset. To customize the display of hits open the Options
menu, choose Define User View (Figure 6). A window will open
with a list of all available fields on the left side of the screen;
the right hand side may contain a list of fields from a previous user.
Clear the right hand box by clicking Remove All. Highlight the
fields desired and click on Copy to define preferred view and
then click OK.
Defining a Preferred View
Then select User View from the
View menu. To go back to full display at any time, simply
choose All Fields from the View menu. Alternatively,
the brief record (which shows only the molecular structure and
Beilstein Registry Number) may be used to identify hits of interest
among a large set.
Records in the database are often several printed pages long and take
longer to print than a regular text file of the same length. To avoid
printing lots of unwanted information, define a User View to display
only the desired fields in the records, as described in the previous section.
While viewing in this customized User View mode, choose
Print from the File menu. The Print screen will
appear (Figure 7).
Do not choose the to File option -- the format is only
readable using the CrossFire software. Use the other boxes and
buttons on the screen to customize the printout further if desired.
Figure 7. Print Screen
Logging Off
Exit the Beilstein database by choosing File, then Exit
from the top menu bar of the Commander screen. When prompted to save the
session and results, answer "No" when using the Library public
workstations. This will help to prevent problems with the public
terminals.
The Beilstein database is large and complex, and the Commander/CrossFire
software is an extremely powerful and flexible interface. These
instructions have covered only the most basic search features. More
information may be found in the set of several manuals produced by Beilstein (copies are available in Chemistry and in the
John Crerar Library; ask at the reference desks in either location),
as well as in the online Help menus in Commander and CrossFire. If you
do not find the information in either of these sources, or you would
like to have a personal consultation or training (at any level,
beginner through advanced), please contact the Chemistry
Librarian or email the Chemistry Library at
ChemistryLibrary@lib.uchicago.edu.
Adapted from
a guide developed by Julie Hurd at the University of Illinois at
Chicago.
by
Andrea Twiss-Brooks
Chemistry
Librarian/Chemical Information Specialist
The University of Chicago
Library
atbrooks@midway.uchicago.edu
312-702-8777
April 19, 1996
The
Beilstein Database