Beilstein and Gmelin Databases

Introduction

CrossFire Beilstein and Gmelin Workshop handout (PDF)

The Chemistry Library offers free drop-in CrossFire Beilstein and Gmelin workshops in January and July. We also offer customized sessions for individuals, groups or courses. Check UW-Madison Libraries Workshops, Classes, and Tours site for these and other free drop-in workshops. Contact Emily Wixson (email) to schedule a customized session.

BEILSTEIN covers properties and preparations of organic compounds. It contains physical and chemical substance properties as well as pharmacological, ecological and toxicological outcomes. It is searchable in multiple ways, including chemical structure, reaction, formula, and physical property parameters. It is worldwide in scope and indexes periodicals (currently 174 journal titles - see extracted journals list), books, dissertations, patents (1869 - 1980), and the sources reviewed for inclusion in the Beilstein Handbook of Organic Chemistry.

  • Over 10 million compounds;
  • Over 10 million chemical reactions;
  • Over 320 million experimental property data
  • Over 960,000 abstracts and titles indexed from the primary organic chemical literature since 1980;
  • Over 500,000 bioactive compounds.
    http://www.beilstein.com/features.shtml (Accessed 9/29/08)

GMELIN covers preparations, properties, and reactions in inorganic and organometallic chemistry and materials science. It is the only searchable source of reactions and properties from inorganic and organometallic chemistry journals. It is searchable in multiple ways, including chemical structure, formula, and physical property parameters. This index is based on the Gmelin Handbook of Inorganic and Organometallic Chemistry (1772-1975) and a core selection of journals.

  • 2.5 million compounds - coordination compounds, alloys, solid solutions, glasses and ceramics, polymers and minerals;
  • 1.9 million reactions;
  • 1.3 million citations, including titles and abstracts from 1995.
    http://www.info.crossfiregmelin.com/features.shtml (Accessed 9/29/08)

AutoNom (AUTOmatic NOMenclature) is a program that generates IUPAC names directly from a structure. Clicking on the AutoNom icon button on the Beilstein commander window launches the application. Structures are input using the Beilstein Structure Editor or ISISDraw.

CrossFire is the search engine that ties all of this together.

Initial Set-up

  1. Select preferred STRUCTURE EDITOR. CrossFire may be set to use two different structure editors: CrossFire Structure Editor and ISISDraw. All UW-Madison Libraries Beilstein Help pages use CrossFire Structure Editor.
    Structure Editor Options

Database Organization

CrossFire Commander window

Three types of data (or "domains"):

  1. Substance: contains structural information with all associated facts and literature references, including chemical and physical properties and bioactivity data.
  2. Reaction: details the preparation of substances.
  3. Literature citations: author, title, and abstract (1980 - present), which are hyperlinked to substance and reaction records.

Fact Editor is often the best way to search GMELIN database.

Structure Editor is the best way to search BEILSTEIN database.
Note: Compounds of the type "biomolecule" (ctype=biomolecule), mixtures, and polymers do not have structure diagrams.

Sample Gmelin record: Water GRN 117
Sample Beilstein record: Acetic Acid BRN 506007

For comprehensive retrieval, conduct both structure and property searches.

Note: It is possible to search Beilstein and Gmelin simultaneously. If both databases are selected, only structure, text, and fields common to both databases may be searched.

Structure/Substructure Searching

See Structure/Substructure Search - v. 7 and Structure/Substructure Tutorial video for additional help.

Basic Procedure

corssFire 7 Structure window

Toolbox:
CorssFire 7 structure toolbox

  1. Double-click in the STRUCTURE window to switch to Structure mode.
  2. Click on EDIT in the Toolbox.
  3. Draw the structure with the currently active atom (default is C) and bond (default is single), or select one of the ring templates.
  4. Click on an existing atom to open the atom dialog box to modify it.
  5. Set the number of free sites (default is none) and other specifications.
  6. To merge individual structures, select the structure with LASSO or SELECT. Drag the square in the middle of the bond to the target bond or drag the square at the atom node to the target atom. Drag the square at the atom to merge it with another atom.
  7. Click on Return to Commander to return to COMMANDER.
  8. (Optional) Select STRUCTURE QUERY OPTIONS.
  9. Click on START SEARCH.

Search Examples

1. Spiro[cyclopropane-1,9'-fluorene]spiro(1,9')-fluorenyl-cyclopropane
Structure example

2. Substructure Search with specified Free Sites:
Substructure Free Sites example

3. Substructure Search using predefined Atom Lists and Generic Groups
Substructure-predefined-generics-example

  • All symbols ending with an "H" allow for hydrogen instead of the defined list or group.
  • Atom Lists: A = any atom; Q = any atom except carbon or hydrogen; QH = any atom except carbon; M = any metal; X = any halogen.
  • Predefined generic groups can only have one bond to the parent structure and setting explicit free sites is not allowed.
  • Predefined atom lists and generic groups are entered into the structure like ordinary atom symbols.
  • G or GH = Any arbitrary structure.
  • G* or GH* = Any arbitrary structure which can have any number of ring closures to any other G* or GH* group or free site.

4. User defined Atom Lists (A1, etc.) and Markush Groups (G1, etc.)
Substructure user-defined Atom List

  1. Select A1 in Generics Window.
  2. Assign A1 to atom nodes.
  3. Click on An in the Toolbox.
  4. Select the correct Atom List Number.
  5. Click OK to open a periodic table.
  6. Select the desired elements.
  7. Click on OK to accept the chosen elements.

Reaction Searching

See Reaction Search - v.7 for additional help.

Note: Multi-step reaction searching now available.
Prior to the database update 2. quarter 2008 (BS0802), you had to search one step at a time: A->B, B->C, C->D. Beginning with update 2. quarter 2008 (BS0802), you can now search A->D, A->C, B->D, etc. Only reactions which comply with the following rules may be searched in multi-steps:

  • a   multi-step sequence is limited to a given article or patent.
  • all steps of a multi-step reactions must be mapped
  • no loops are allowed
  • the starting material must have 5 carbon atoms at least
  • 20% of the carbon atoms of the starting material must be present in the final product at least
  • System requirements:CrossFire Commander 7.1 or higher

Basic Procedure

  1. Draw structure(s) and/or substructure(s)
  2. Click on REACTION ATTR. Reaction Attributes icon
  3. Use SELECT or LASSO to select each substituent.
  4. Define substituents as reactants and products.
  5. Define Atom Attributes, Atom-Atom Mapping, and Query Options if necessary.
  6. Click on Return to Commander window to return to COMMANDER.
  7. Click on START SEARCH.

Half-reaction example
Half-reaction example

Property Searching

See Property Search - v.7 for more help.

Basic procedure

If a previous search is present in the STRUCTURE window or FIELD TABLE, click on CLEAR.

Enter a fact query in one of two ways:

I. For simple searches, use Predefined Search forms:

  1. Click on PREDEFINED SEARCH FORMS.
  2. Double-click on the appropriate form.
  3. Enter search criteria.
    Note: Always click on LIST to preview field data format.
  4. Click on OK.

Fact Editor search built from Beilstein Predefined Search Forms
Fact Editor pre-defined Search Forms

II. For complex searches involving many less common data fields, use the SEARCH FIELDS tab to identify appropriate fields or enter criteria directly in the SEARCH FIELDS TABLE.

  1. Click on the SEARCH FIELDS tab.
  2. Click on FIND FIELD OR FORM.
  3. Type a property name in the SEARCH FIELD NAME IN HIERARCHY search box.
  4. Click on OK.
  5. Click on FIND NEXT to view additional entries in the hierarchy.
  6. Double-click on the desired field code to copy the code name to the SEARCH FIELDS TABLE.
  7. Select appropriate operator from the RELATION drop-down menu.
  8. Enter data value in FIELD CONTENT cell.
  9. Click on START SEARCH.

Fact Editor value range search combining field code and controlled term
Fact Editor value range and controlled vocabulary search

Displaying Records and Data

CrossFire retains the VIEW defined by the previous user. Therefore, you should set the initial display VIEW to the following settings:

  • "ALL FIELDS"
  • "ALL REACTIONS" or make the appropriate selection
  • "HIGHLIGHT HITS" for ease of viewing substructure
  • Use "INCLUDE FIELD AVAILABILITY" for quick display of record fields and to "jump" to specific fields in the record
  • Click on Field Availability in separate window... (F5) to define custom user views.

Basic procedure

  1. Click on VIEW in the SEARCH STATUS REPORT window.
  2. Click on VIEW in the top menu to customize the display.
  3. Click on GO TO NEXT HIT or GO TO PREVIOUS HIT to move to the next or previous record.
  4. Use BACK and FORWARD hyperlinks to move between links to substances, reactions and citations within the record.
  5. Click on GET to get related substances, reactions or citations.
  6. Click on SORT BY to sort or group the hitset by specified criteria.

Printing Records and Data

The FILE menu always applies to the task that is currently active. This includes PRINT and SAVE.

Printing all or selected records in a hitset

  1. Display the hitset and note the desired record numbers. (Caution: Some records are quite lengthy. Use VIEW to customize the display.)
  2. Click on PRINT HITS.
  3. Select Range choice.
  4. Select Options choices.
  5. Click on OK.

Printing selected property data from all records

  1. Display the hitset.
  2. Check specific property selection box.
  3. Click on PRINT HITS.
  4. Select Range choice: SELECTED FACTS.
  5. Select Options choices.
  6. Click on OK.

Saving Records and Data

Hitsets can be temporarily saved on the GLS server and opened for viewing later that day at a Library public workstation or a personal workstation configured with the CrossFire client. Structures can be saved locally. Saved hitsets and structures drawn with the CrossFire Structure Editor can only be viewed within Beilstein. The FILE menu always applies to the task that is currently active. This includes SAVE.

  1. Click on DISPLAY HITS.
  2. Click on FILE.
  3. Click on SAVE HITSET AS.
  4. Type filename. (Hitset is temporarily saved on the Library's server)

Saving a structure

  1. Draw the structure in the Structure Editor.
  2. Click on FILE.
  3. Click on SAVE COPY AS.
  4. [For library workstation] Change the drive to E: to save and email as an attachment.
  5. Type filename. CrossFire automatically assigns the extension .bsd for CrossFire Structure Editor or .skc for ISISDraw.

Exporting Records and Data

See Export Results - v. 7 for additional help.

EXPORT permits export of structure, reaction and citation data in HTML, Excel or WORD formats. The available pre-defined export settings depend on the record "context". - substance, reaction, or citation. It is possible to create individual export settings for local installations.

  1. Click on EXPORT.
  2. Select type of information and file format to export.
  3. Click on START.
  4. Specify file location.
  5. Click on SAVE.

Client Distribution and Online Help

UW-Madison Beilstein web site: http://chemistry.library.wisc.edu/beilstein/
Search Help: http://chemistry.library.wisc.edu/beilstein/search.html
Client Distribution Page: http://minerva.library.wisc.edu/

Obtain the following information from Emily Wixson, Sharon Mulvey, or http://chemistry.library.wisc.edu/askchem.html:

User ID: 
Password:
Group name: 

Host IP Address: crossfire-acad.elsevier.com
v. 7.1  Article Resolver: http://sfx.wisconsin.edu/wisc/