Lecture 6: CrossFire Beilstein and Gmelin

CrossFire History

The CrossFire interface for the Beilstein database was released in 1995 by Beilstein Information Systems. It quickly gained popularity as a relatively economical alternative to the printed edition of Beilstein. A consortium of Midwestern universities struck a deal to mount the database on their server. This deal was later expanded to cover all interested North American universities under the name Minerva.
In 1998, Beilstein Information Systems was purchased by publishing giant, Reed-Elsevier, and merged into their MDL, Inc. division, long-time providers of chemical data manipulation software.
Shortly thereafter, Reed-Elsevier also acquired the rights to the then-moribund Gmelin database and made it available through the CrossFire interface.
Several UC campuses purchased subscriptions to one or more of the CrossFire databases, but negotiations for a systemwide licence were finally concluded at the end of 2003. The UC's access is not through the Minerva consortium server (at the University of Wisconsin) but through a new server located at MDL itself.
In 2007, Elsevier sold MDL to Symyx Technologies. In the sale, Elsevier retained the Beilstein and Gmelin databases and the CrossFire platform Symyx/MDL retained the DiscoveryGate platform. For now, the databases are stlll hosted on MDL servers.

CrossFire Content

The Beilstein database contains records from the mid 1800's to the present, for over 10 million substances, over 10 million reactions, and titles and abstracts for about 2 million documents (since 1980), in organic chemistry. Current data is indexed from over 175 journals and is updated quarterly.
The Gmelin database contains 2.2 million compounds and 1.6 million reactions from 1772 to the present, and 1.1 million citations, including titles and abstracts from 1995. Current data comes from 62 journals in inorganic and organometallic chemistry.
Each database is text searchable, structure searchable, and data searchable, and in any combination of the above.
Elsevier also makes a Patent Chemistry Database available through the CrossFire platform. It contains substance, reaction and property data from the European and WIPO patent offices from 1978 to present and the U.S. patent office from 1976 to present, amounting to over 3.7 million reactions and 4.3 million compounds as of Ded. 1, 2007. This complements the Beilstein and Gmelin databases, as they currently do not index the patent literature. The University of California does not currently subscribe to the Patent Chemistry Database.

CrossFire Commander

Like SciFinder Scholar, CrossFire is a client-server system, not a Web interface. The client software for CrossFire is CrossFire Commander. It is currently available in Version 6 for Macintosh computers and Version 7.1 for Windows.
The CrossFire client uses a combination of passwords and IP authentication to recognize licensed users. Since it is not a Web application, the UCSB proxy server will not enable off-campus use of the UC CrossFire licence. UCSB students and faculty can, however, use CrossFire off-campus with the campus VPN (Virtual Private Network) client.

Accessing CrossFire Commander

The CrossFire Commander client is currently installed on five workstations in the UCSB Library (the same workstations on which the SciFinder Scholar client is available.)
The software may be downloaded for installation elsewhere on campus from the UC CrossFire website at http://software.chem.ucla.edu/crossfire/ These pages contain links to the software and associated password files for both Windows and Mac operating systems, as well as the instructions for installation and set-up for each UC campus.

Using CrossFire Commander

When you open CrossFire (after installing the software and entering the username and password), you must first select the database to search (Beilstein, Gmelin or both). A message log may appear. When it is finished loading, click the "Close" button. You then go to the basic CrossFire search screen.

Above is the opening screen for CrossFire Commander, version 7.1 for Windows. The search screen is complex, but makes more sense if you look at the various regions of the screen.
The top of the screen contains the familiar Windows-style menu bar. Its functions include:
- File -- From here you can Select Database, Clear Query, Open Query or Execute Query, and Exit.
- Edit -- Contains the Undo function, and Cut, Copy and Paste functions.
- Task -- Lets you enter Structure Building, or create and modify Alert searches.
- View -- Lets you modify the way the screens display.
- Options -- Allows further setting of preferences. The most immediately important here is "Select Structure Editor". CrossFire can use any of three structure drawing programs: MDL ISIS/Draw, MDL Draw, or the basic CrossFire Structure Editor. We will be using the CrossFire Structure Editor for this course.
- Query -- Lets you set some search parameters. The most important here is AutoSearch. With AutoSearch on, CrossFire will automatically broaden a structure search to do substructure searching after searching for the original exact query.
- Help -- Takes you to the HTML guides for CrossFire Commander, and the Beilstein and Gmelin databses.
The Button Bar (below the Menu) gives quick access to important functions also found in the Menus: Query History, Open Query, Save Query, Print Query, Clear Query, Select Database, Draw Structure, Modify Alert, Create Alert and Start Search are also available.
Below that is the Query Builder area.
Note that there are two basic methods of searching the database:
- Search Text/Field Contents -- lower right hand side of screen
- Structure Search -- the large window in the middle right. Double click in the window, or click "Create Structure" on the Button Bar to activate the structure editor.
- Each of these search methods will be detailed below.
The window on the left hand side, referred to in the CrossFire Help as the Tree Pane is a tool to help guide you through creating fact searches.
- The Find Field or Form button allows you to search for keywords in the field hierarchy if you are not sure in which group a particular property falls.
- The Search Fields tree lets you browse through the different searchable fields in a hierarchical fashion, working from broad categories of data down to specific ones.
- Predefined Search Forms gives you a menu of search options for each of the categories of properties. See below for an example.
- The Queries tab lets you reuse previous queries from the current session, or saved queries from previous sessions.
- Hitsets lets you reuse previously created answer sets.

Text Searching

To search for keywords anywhere in the text of the records, double click the "Field Content" window to the right of the "All Text" listing and enter the desired terms. For example, putting the terms diels alder in the window window, and clicking on the blue Start Search button in the lower right hand corner of the screen, generates the following display.

You then select which type of answer set you wish to see (substances, reactions or citations) and click the View button. Answer sets are displayed in a Results window. (To return to the Query, just click on the Query tab above the Button Bar.) A sample set of reactions from the Diels-Alder query is below.

An answer set for citations is below:

And for substances:

To see the full record for any individual item, doubleclick the desired entry. A portion of a sample substance record is below:

Note that in each category, references, and (in most cases), the actual numeric data is given. Note also that in most cases a given data field will have a link to the full text (where available) of the reference from which the data is taken.

Fact Searching

CrossFire allows muliple approaches to fact searching. You can directly enter field codes and numeric values in the Search Fields window, or select fields from Predefined Search Forms or the Search Fields Menu tree. Note that the commands generated from the menus appear in the command window. This helps the user to learn the command structure, and allows the user to modify the commands before searching. For users who are extremely familiar with the field names and command language, clicking the Advanced Mode box allows one to type in command language queries directly.

Predefined Search Forms

To search data in a particular category, click the Predefined Search Forms tab, then doubleclick the name of the category in the Predefined Search Forms window. For example, to search for melting and/or boiling points, doubleclick on Physical Data.

You may either specify a particular value or range of values, or you can click the appropriate checkbox to require the presence of a particular data type without specifying a value. Notice that next to each window where you could enter a value (e.g. for a melting point), there is a list link which you can click on to browse a list of the values which actually exist in the database. When you have entered all the values you want on that table, click "OK", the values are entered for you into the Search Fields table. You may then go back and add more parameters in the same way.

Search Fields Menu Tree

Alternatively, you may expand a broad category in the Search Fields Menu Tree to see what data types are contained in that category. You can single click on any item in the tree to see a definition of the property. Doubleclick on the property to enter it into the Field Name portion of the Search Fields window. In the case shown below, I clicked on Physical Properties, then Single-Component Systems, then Spectroscopic Information, then NMR Spectroscopy to get a description of the searchable data for NMR spectroscopy in the Beilstein database.

Direct Entry into the Search Fields Window

If you know the relevant field codes, you can enter field names, relations and operators directly into the Search Fields Window. If you aren't sure of the operators, relations or ranges of values available, tab to the appropriate box, then click the List icon next to the field content window for the desired property, and you'll get a list of the possible choices. If you aren't certain of the field codes, use one of the methods above. In the example below, I selected Purification as a field by searching for it with "Find a Field or Form", then clicked the list icon in the table for it. I then searched for "recrystal" to find all the variant forms of "recrystallization", selected them, and moved them into the right-hand box. Clicking on "OK" then loads all those terms as synonyms into the "Field Content" box for Purification for searching.

When you have assembled the search terms you want, click the Search button.

Structure Searching

CrossFire gives the option of using three different structure building programs, either the built-in CrossFire structure editor, or MDL's ISIS/Draw or MDL Draw, both of which are available as free downloads from MDL. You may also copy structures from other structure editors if they have the capability to export structures in the CrossFire or ISIS formats. The UCSB Library's CrossFire terminals are set to use the native CrossFire structure editor.

To access the structure editor, click on "Draw Structure" on the Button Bar, or doubleclick in the Structure window. A separate window will open for structure drawing. As you draw the structure, it will appear in the search window as well.

Note the menu bar at top, and the toolbars along the top and left edges of the structure drawing window. To learn the function of any tool, hold the cursor over the button to see a brief description.

Rings and chains may be drawn with the Pencil tool, or standard rings may be selected from the templates at the upper right. You can change atoms from one element to another, or bond types from one to another by selecting the atom or bond to be changed with the Select tool, then clicking on the desired atom or bond from the buttons along the top of the window.

When you have finished drawing the structure, click the CrossFire icon (crossed arrows) to transfer the structure to the Structure Search window. You can set search options in the boxes at the right of the Structure Search window.

To carry out the search, click the Search button.

Many of the drawing tools are similar to those in the SciFinder Scholar structure editor, which we will explore in greater detail later. But there are enought differences that a user familiar with one who comes to the other for the first time can be confused. For example, in SFS to change an atom from C to N, you click on N as the pencil atom, then click on the target atom. In CrossFire, you must use the Select tool to select the atom to be changed, then click on the new element. Similarly, in CrossFire, to change a single bond to a double bond, you must select the bond, then click on the new bond type. In SFS, you can trace over a single bond a second time and change it to a double bond, or a double to a triple bond.

Besides the differences in drawing, there are significant differences in searching. When you search a substructure in SciFinder, the system assumes that substitution is allowed at any site unless you lock out substitution. In CrossFire, you must specify which sites are "free sites". CrossFire also allows more flexibility in creating generic groups.

For more information on CrossFire structure searching, see CrossFire Structure Searching and CrossFire Reaction Searching from the University of Wisconsin at Madison (http://chemistry.library.wisc.edu/beilstein/search.html)

This page created by Chuck Huber (huber@library.ucsb.edu).
Updated: 01/03/08 03:42:22