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About the Beilstein Database and
CrossFire
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The Beilstein CrossFire search system is a client interface that
provides access to the CrossFire search and retrieval software and
links structure, reaction, text and numeric data in the Beilstein
and Gmelin databases. The Beilstein database contains information
on more than 8 million organic compounds and associated chemical
and physical properties and 5 million chemical reactions. There are
more than 30 million numeric and text reports arranged in some 300
fields, all of which are searchable. The Gmelin database covers
more than 1.4 million organometallic and inorganic compounds
(including coordination compounds, alloys, glasses, ceramics,
polymers and minerals), with more than 800 property fields defined.
Searchable data fields include Chemical Abstracts Service (CAS)
Registry Numbers, chemical names, molecular formulae, boiling
point, spectral parameters, solubility, dissociation constants,
thermodynamic data, dipole moments, and reaction conditions.
Historical coverage in both Beilstein and Gmelin are particular
strengths of the databases, with references to the chemical
literature back to the 1770's. Print predecessors to these
databases are Beilstein Handbuch der Organischen Chemie
and Gmelin Handbuch der Anorganischen Chemie.
This document is intended to introduce new users of the database
to some basic search techniques; those who have complex search
needs will find additional documentation in manuals provided by
Beilstein Information Systems (copies available in the Chemistry
Library Office), in more advanced guides on the Beilstein
information page or from the Help feature in the
CrossFire/Commander menu. Users at the University of Chicago may
use CrossFire at library public workstations in the Chemistry and
Crerar Libraries, or may download the software client for use on
their own networked machines. At this time, there is no option for
off-campus remote access. For more information on downloading the
client, point your browser to the Beilstein
information page on the Chemistry Library web site, or contact
the Chemistry
Librarian.
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Getting Started on a Windows Workstation
On a machine where CrossFire/Commander has been installed you
should see a Beilstein 2K icon. Double click on
the Beilstein 2K icon on the
computer desktop to start CrossFire: |
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The main Beilstein Commander window will appear.
Click on the crossed red arrow icon to login (see
Figure 1). If the workstation has been properly
configured, login should proceed automatically with no need to
enter a loginid or password. If you are prompted for a loginid and
password, contact the Chemistry Librarian for
instructions. Note that the top of the screen displays a menu bar
and a function button bar. The function button bar are shortcuts;
all functions are also available from the drop down menu bar. |
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Figure 1.
Logging into CrossFire from the Beilstein Commander
window
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Easy Data Search (EDS) Options
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Verify that the Beilstein database is selected for organic compound
searching by clicking the radio button to the left of the box with
the prefix BS (the GM prefix is
for Gmelin, which covers inorganic/organometallic compounds).
Simple searches for registry numbers, chemical names or name
segments, molecular formula, and several common property data
fields (solubility, boiling point, etc.) are available using the
Easy Data Search (EDS) forms. Select the desired
category and click the Open button to bring up the
form (see Figure 2).
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Figure 2. Selecting the
Beilstein Database and EDS Category from the Commander
Window
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Once a category is selected, values can be entered into the search
form (see Figure 3). Query terms may be typed
directly into the boxes on the form. Best results are obtained if
the magnifier tool  is used to
check the database index for spelling variations, punctuation and
other syntax requirements. Entering values in more than one box
creates a search with a Boolean "AND" (all terms must appear in the
same compound record to be retrieved as a hit). Click the
OK button to transfer to Commander
screen. At the Commander Screen, click
the Start Search button (see Figure
4).
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Figure 3.
Using an EDS Form to Create a Simple Search Query
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Figure 4.
Start Search Button on Commander Screen
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Some hints for EDS Ident. Data queries:
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| CAS Registry Number |
Enter known CAS Registry Number
including hyphens! NOTE: CAS RN's are not
included for all the compounds in the database; always try
alternate searches (name, molecular formula, structure) if desired
compound is not retrieved. |
| Molecular Formula |
Molecular formula searches are entered
in Hill order (i.e., carbon, hydrogen, followed by all other
elements in alphabetically order). For example, 1,3-dichlorobenzene
is entered "c6h4cl2". |
| Chemical Name (segments) |
Always use the magnifier
tool (see
Figure 5 for more detail) to look for alternate
spellings, punctuation, etc. Right and left truncation using the *
is allowed. (e.g., *succinamid* will retrieve
3-hydroxy-2-(4-phenylpiperidino)-5-succinamidotetralin,
among others). Consider molecular formula or structure search as an
alternative strategy if desired compound is not found. |
| Chemical name (complete) |
IUPAC systematic names or common names may be
searched. Always use the magnifier tool (see Figure 5 for more detail) to look for
alternate spellings, punctuation, etc. Right and left truncation
using the * is allowed. (E.g., *succinamid* will retrieve
3-hydroxy-2-(4-phenylpiperidino)-5-succinamidotetralin,
among others); be cautioned that this type of search can take
several minutes to complete. Most entries have only one or two
synonyms listed, so consider a molecular formula search or
structure search if desired compound is not found. Typically,
common or trivial names in English and German may be successful;
trade names less so. |
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Figure 5.
Using the Magnifier Tool to Check Spelling, Punctuation and Other
Syntax for Search Terms
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Fact Editor (Tabular
Query) Searching |
More complex searches, including those that combine identification
fields with property data fields, searching ranges of values, and
searching fields not included on one of the EDS forms require the
use of the tabular query based Fact Editor. Select
the Fact Editor from the Beilstein
Commander screen (see Figure 6).
This is an extremely powerful, but complex search interface, so be
prepared to spend some time in developing effective search
strategies to retrieve the desired results.
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Figure 6.
Starting the Fact Editor (Tabular Query) Function
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In the Fact Editor, all data fields are
searchable. The form has three columns, labeled
Operator, Field Name and
Field Value. Each term in the search query will be
entered on a line, with the Field Name and
Field Value being specified for each desired
property, name or other term. In order to achieve good
search results, use the List Values button to find the desired data
Field Name and then Field Value terms! Precision in
entering search terms is extremely important -- the List
Values function is an invaluable tool in insuring good
search results. An example of a search for 13C NMR spectra of
quinones is shown in Figure 7 and Figure
8.
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Figure 7. Using List Values Function to Select Desired
Field Name
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Figure 8. Using List Values Function to Select Desired Field
Value(s) |
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Tips for Fact Editor searching:
- Use the List Values button with the cursor in
the Operator column to select among
Boolean/adjacency operators (AND, OR, NOT, NEAR, NEXT, PROXIMITY).
Look at Help to determine which operator is appropriate for the
desired search results (AND, NOT, OR usually sufficient for most
searches)
- Be sure to expand folders (click on + sign on folder) to see
the individual searchable fields in a data category (e.g., in
Figure 7, the folder is Nuclear Magnetic Resonance
(NMR) with searchable fields of Description, Nucleus, Coupling
Nuclei, Solvent, etc.)
- The Tab key is used to move from box to box in the Fact
Editor form
- To delete an entire line from the Fact Editor
query, put the cursor in one box on that line and click the
Delete Line button
- Numeric Field Values may include
ranges and > or <
indicators.
- Field Values may be truncated using *
wildcard character (good for alternate spellings and
variant endings)
- Nested search statements may be constructed using the
parentheses buttons
- Entering only a category level (marked with
"folder"
 ) Field
Name, without a corresponding Field
Value, will limit retrieve only those records which
include that category of data (e.g., "mf=c12h20" will retrieve 893
hits, but "mf=c12h20 AND raman" will retrieve only 11 records,
those compounds which have a molecular formula C12H20 and have a
Raman spectrum). This technique will not work at
the individual data field level (marked with
"page" ).
Once the search is constructed, transfer the search query to the
Commander screen by clicking OK
button on the Fact Editor screen. Be sure that
desired Display As mode is selected in the drop
down box. (Hint: In general, when looking for properties, select
Display As: Substances; if looking for compound
preparations, select Display As: Reactions).
Perform the search by clicking the Start Search
button (see Figure 9). The Start
Search button will change to red color and text will
change to Stop Search. If a search takes too long,
just click this button to stop the search. A partial set of results
will be available for viewing -- go back to the Fact
Editor form and edit the search. Searches may be edited
and repeated as necessary until the desired search results are
obtained.
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Figure 9.
Running a Fact Editor Search from the Commander
Window
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Displaying Results
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Once the search has completed, a Query Result
window will pop up. The number of substances matching the
query will be displayed (e.g., 138 substances matched the
quinone/nmr query as shown in Figure
10).
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Figure 10.
Query Result Window Showing Number of Substances Matching the
Search Query
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There are a number of predefined display options available, in
addition to the ability to create individual customized displays.
Full database records may be extremely long, slow to load for
viewing, and even slower to print out (some records are more than
100 printed pages). Use of predefined or customized (User
View) displays results in much shorter records for viewing
and printing. If the predefined options are not sufficient, it will
be necessary to create customized displays.
 Predefined Display Options:
Click on Display Hits button in the
Query Result window to look at the substance
records. Select View from the menu bar in the
resulting Display Hits window to switch to a
different display option. There are four main predefined displays
that are available (Short Display,
Identification, Hit Only and
All Fields) as shown in Figure
11.
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| Short Display |
Displays hits as structures in a grid. Number of
rows and columns displayed can be changed under
Options (on menu bar), then Select Short
Rows and Columns. Useful for scanning quickly through a
set of compounds. |
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| Identification and Include Field
Availability |
Recommended display (see Figure
11) for quickly browsing through a result set to see the
types of data available for each compound. Once the fields of
interest are determined, select All Fields from
the View menu or create a customized User
View including those fields to see the data. |
| Hit Only |
Identification fields (name, formula,
registry numbers), references and specific data fields that matched
the query entered (e.g., only 13C NMR data displayed for the query
shown in Figure 8). Select Highlight
Hits to see matches of search terms in the display. |
| All Fields |
Full record display. Select Include Field
Availability and use underlined codes (hyperlinks)
to jump to desired sections of the record. This format
NOT recommended for printing and/or exporting
records! |
Figure 11.
View Menu Options and Predefined Views
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Customized User View Display
Options:
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If predefined formats are
not appropriate for specific display, printing and/or saving
requirements, create a customized User View. There
are two menu/function steps: Options/Define User
View and View/User View. To
Define User View follow the steps outlined in
Figure 12. After finding and copying fields of
interest, click OK to return to the
Display Hits window. The new customized view will
not be displayed yet -- to activate the customized view, be sure to
select User View from the View
drop down menu (Figure 11).
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Figure 12. Define a User View |
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Once a view (predefined or user defined) has been selected, use the
buttons at the top of the Display Hits window to
navigate through the compound hit set and to navigate back and
forth from reaction and reference displays. The most useful buttons
are explained in Figure 13.
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Figure 13. Navigation Buttons for Display Hits Window |
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Tips for navigating hit sets:
- Underlined
numbers in various colors are hyperlinks to other compounds,
literature citations or reactions. To navigate back from a
hyperlink, use the special previous and next (white) arrows.
- Jump back to the top of a record using the Top hyperlinks in the compound
records.
- Switch structure display on or off using the Structure
On/Off button. The structure window may also be resized to
make it smaller for easier viewing of the record, or larger to see
structural details.
- If viewing hit set for preparations (remember to choose
Display As: Reactions on the Commander screen
before starting the search), be sure to Structure
On to see a graphical display of the reaction.
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Printing and Exporting/Saving
Results
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When printing or saving records from hit sets, the current display
setting is the default setting for the printed or saved records.
Therefore, if All Fields is selected, the entire
record will be printed or saved, often resulting in dozens of pages
of unwanted information and/or extremely large saved files. Use a
shorter predefined or customized display to create smaller print
jobs and files.
If printing, verify that the desired display is active, and
choose File/Print to further customize the print
job output. A Print window (Figure
14) will pop up; modify the settings as desired for the
print job using the radio buttons on the left side and the bar
buttons on the right side. If a range of hits is desired, be sure
to select the range; the default is only to print the record
currently showing in the Display Hits
window.
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Figure 14.
Print Options Window |
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Exporting records for use in other applications is not a trivial
matter. Specific export parameters must be defined by the user, and
novice users with little knowledge of data export/import procedures
may encounter difficulties. Beilstein CrossFire
2000 does provide some guidance, in the form of an
Export Wizard (Figure 15).
Delimited files created using this wizard may be imported into a
variety of software, including non-chemical applications like
Excel. In general, most occasional users will find it more
convenient to print out desired data than to spend time figuring
out the export process. Regular users may find that the ability to
save and reuse export settings will be worth the effort. Consult
the online help or contact the Chemistry Librarian for
assistance if the Export Wizard does not provide
enough guidance.
Alternatively, it is possible to copy and paste fields from the
Display Hits window into any text editor. Use the
mouse to highlight the desired text, select
Edit/Copy. Paste the selection into the text
editor and save the text file. The resulting text will be encoded
as HTML; change the .txt in the filename to .htm and use a browser
to view the results. This method will be time consuming for large
hitsets, but for a few compounds provides perfectly acceptable
results.
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Figure 15.
The Export Wizard Introductory Screen for Creating Reusable Export
Settings
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Logging Off |
Exit the Beilstein system by choosing
File/Exit from the menu bar in the
Commander window. When using any library
workstations, answer No when asked if the search
and results are to be saved. (Users may choose to save searches on
their own machines; these searches and hitsets can be rerun and
redisplayed in future sessions). If the Structure
Editor window was opened, it will need to be closed
manually; all other Beilstein windows should close
automatically.
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Advanced CrossFire Searching |
The Beilstein and Gmelin databases are large and
complex; the Commander/CrossFire search system is
extremely powerful and flexible. These instructions cover only the
most basic introduction to a few of the search features available.
Additional guides for structure searching, reaction searching, and
advanced searching tips and tricks are available at the Chemistry
Library Beilstein information page. More information may be
found in a set of manuals produced by Beilstein Information
Systems, Inc. (located in the Chemistry Library office), as well as
in the Help menus in CrossFire itself. If further assistance is
needed, contact the Chemistry Librarian for
assistance or to arrange a workshop/training session (any level,
beginner through advanced, individuals or groups). |
About the Authors |
This guide was created by Andrea Twiss-Brooks (Bibliographer for
Chemical and Geophysical Sciences) and Barbara Kern (Physical
Sciences/Reference Librarian) at the University of Chicago's John
Crerar Library. Any comments, suggestions, or corrections should be
sent to Andrea Twiss-Brooks (atbrooks@midway.uchicago.edu)
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