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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"
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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"
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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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