Beilstein (Elsevier/MDL CrossFire Commander 7.1)

Transcription

1 Introduction Beilstein (Elsevier/MDL CrossFire Commander 7.1) Beilstein vs. SciFinder Scholar As two of the most important databases in chemistry, Beilstein and SciFinder Scholar serve different needs. Usually, Beilstein is used to find properties, preparations, and reactions for organic compounds. The database goes back to the 1770's and therefore covers a much larger time span than SciFinder Scholar. It is much easier to find a melting point or pharmacological data in Beilstein than in Scholar, even with the latter's recent addition of many basic properties and actual spectra from Wiley. However, SciFinder Scholar covers a much broader range of the 'chemical' literature than Beilstein does and allows efficient keyword searching. Additionally, SFS also covers patent literature which Beilstein dropped after It is strongly suggested that compound searches be performed in both databases because they are actually complementary. The figure above shows the interface of Beilstein/Crossfire Commander. Part I. Structure search 1. Substructure search Substructure searching allows user to retrieve compounds containing a structure drawn in structure query window as the core structure. One way to select a substructure search is to check to all atoms box under Free Sites. When you check the all atoms box, it automatically allows for salts, additional rings, isotopes, charged compounds, radicals, and mixtures. If you don t want certain options included, just uncheck the check boxes next to these options. You can also set Free sites for certain atoms in your structure query.

2 Another way to do a substructure search is to generalize your query using predefined generic groups. The way to specify predefined generic groups is similar to specifying various atoms. 2. User-defined and nested generic group search In some cases, the above mentioned general substructure search doesn t provide satisfactory search results for users. In these cases, user defined generic groups and atom lists should be used. User defined generic groups allow substituents to be described precisely. User defined generic groups There are two steps involved in creating a user defined generic groups. i. Create a user defined generic group. Follow the steps shown below. Note: More than one generic group can be defined in one query. ii. Define attachment points For fragments containing more than one atom, attachment points must be defined. Attachments points define the position where the fragments will attach to the core structure.

3 User defined generic groups can also be used for allowing ring expansion. Create a user defined generic group containing fragments having one or more carbon atoms, and define attachment points at each end of each fragment. Atom list To create an atom list, open the Edit Atom dialog box. Choose List from the drop-down menu under Symbol. Click the atoms on the periodic table and click OK. Nested generic groups By definition, a nested generic group is a query where a user defined generic group appears within another user defined generic group. For nested structure search, you can use any of the three drawing tools provided. For nested structure in a reaction query, only the Crossfire Structure Editor should be used.

4 Define frequency for generic groups In some cases, we would like to retrieve compounds containing certain number of substituents. Structure queries where a specific number of substituents that can be present at different position are used to perform this task; and this is done by defining frequencies for the generic group. Set group logic If there is more than one generic groups present, group logic can be defined for each generic group in the query. Sometimes we may want to set the occurrence range of one generic group to be between two numbers (For instance, 2 and 5). For example, we want to retrieve di-, tri-, and tetrasubstituted quinolines not mono-substituted quinolines. In such cases, several steps are needed. First, we need to conduct two queries where the group logics are set to be < 5 and <2. Then we need to use field search to retrieve the results contained in one query (group logic <5) but not the other (group logic <2).

5 3. Stereochemistry Beilstein allows user to set the stereochemistry of structures in queries. To perform a stereo search, users need to activate the appropriate selection. The choices are: Off, the stereo search option is not in use. Absolute, retrieves compounds having the identical absolute configuration as the query structure. Relative, retrieves compounds and their enantiomers. Racemic, retrieves only the racemate of the query structure. Part II. Factual Search 1. Predefined Search Forms Crossfire provides predefined search forms for users to search the Beilstein database using Bibliographic data, substance identification data, molecular formula, reaction data, physical data, spectroscopic data, pharmacological data, ecotoxicological data, and solubility data. The above image shows the predefined form for searching by substance identification data. To use this function, simple input information you have for your query, and click OK. 2. Search Fields Search The Operator top left will combine your fact query with an existing overlaying structure or text search query. The Input mask contains rows covering several columns. The first column is the operator column, the second and the last columns allow setting parentheses.

6 Field name: Double click a field from the tree pane will transfer the search field (or a query or a hitset) into the query builder row. Alternatively you can enter a field name manually, if you know the field code which is valid for a selected database. Some examples are CN for chemical name, BP for boiling point, MP for melting point, and IR for infrared resonance. Field content: Please enter a value for the selected search field unless you just want to know if a structure contains information on a particular property such as IR. In this case no value is needed only the field name. The List function will display all available index values of a selected search field together with the frequency. If nothing has been entered in the edit field the list starts with the first database index entry. It is possible to browse through the index using the sliders. Paste Query: This function will paste selected lines from the result window as formulated query into the grid. Example: Mark two lines in result window and copy to clipboard (Ctrl+C or via Edit Copy File Menu). Parentheses: The List box allows selecting up to 8 parentheses. This is useful when using the OR operator. Part III. Set up alerts Beilstein/Gmelin allows users to setup alerts on their queries. Each user is permitted to setup 5-10 alerts. These alerts are stored under specific names on the Crossfire servers. Users will receive an notification when updated search results become available. Following section will take you through steps needed to create or modify an alert. 1. Create New Alert: 1) Conduct a query as usual if you want to save a query as alert. After the search is done, push the button Create Alert from the tool bar in the query tab. The Commander will change automatically to the alert tab. The query will be shown in the query window of the alert profile window. The database name, which has been selected in the query tab, will be displayed. Note: An alert can run only in one database. When the same alert query should run in different databases, one alert must be created for each database. 2) Define the alert conditions: Name the alert profile: The alert profile name can be any text string of maximum 14 characters consisting of only letters, numbers and underscores ( _ ). Blanks and other special characters are not allowed. Set the First run date : The default date is today. The date can be entered with a calendar or can be manually typed in the text box. First run date can be a date in the past or in the future. If you choose a date in past, then one alert run will be initiated immediately for the complete past time phase regardless of the frequency chosen.

7 Define Frequency: The default option is after each update. You may choose from entries including deactivated, weekly, biweekly, monthly, after each update. If you choose the Deactivate Alert option, Commander will automatically set frequency to deactivated. To reactivate a deactivated alert, a frequency has to be selected again. Note: The First run date should not be changed! Then the first run of the new alert covers the time period from the last run date and the day the alert was reactivated. Send results to : Enter your address when you want to get a message about the number of hits after each alert run. This includes a direct link ( Please click here to view hit set ), which opens CrossFire in the Results Window. The cursor is positioned on the corresponding alert hit set, which is listed in the left tree box below a sub-header Saved Hitsets/Alert Hitsets. Send copy to : You can enter addresses of colleagues here. These colleagues should also have a CrossFire account to be able to view the search results. All entries have to be separated by semicolon ;. The fields Database, Last run and Hits are read only. If an alert has already been executed, the information about the date of the last run and the result is displayed. 3) Save your Alert Profile by clicking on the Save Alert button. The complete Alert Profile will be saved on the Crossfire server. 2. Modify an existing alert Just hit the "Edit/Modify Alert" button on the tool bar. Your query will be transferred to the Query Tab where it can be changed. To go back and finish your alert you have to hit the "Modify Alert" button on the toolbar in the query tab. Part IV. Download to EndNote See Chemistry library Guides and Handouts section for details. Part V. Manipulating Your Results 1. Save your query After conduct a query, click the Save query button. A dialog window will appear and prompt you to enter a name for that query. Note: 1) Queries are saved locally on your desktop. Saved queries can be opened at any time to use or to modify. 2) Generally, it is better to save a query rather than a hitset. 3) You can save a query in XFQUE or BCCOM format. 2. Copy to Word/Excel To copy your desired facts to Word, press and drag to select the lines you wish to copy, and click the copy button ( ), choose Copy selection to Word. To copy facts to other

8 applications, select those facts, copy them to clipboard, then open other applications, paste them. To select a desired field, check the box next to the copy button ( ). 3. Create a report Similar to making a copy in Word, select the fact you want to copy to a report, and click the copy button ( mode. 4. Export Wizard ), choose Copy selection to Report report.html. Then view it in the report Another option of viewing your search results is to export results to an external application, including MS Word, Excel, and citation management programs. You can choose to use either predefined export settings or Export Wizard to define your own preferences. 1. Predefined export process After you click on the Export Hits button, a list of predefined exporting settings will become available. Select a setting that meets your needs, and click on the Start Export button on the up left corner. A window will show up and ask you to select the range of hits that you would like to export, make a selection and click Start. You will be prompted to choose where you would like to save the file. Follow the instructions, and your results will be exported. 2. Export Wizard If none of the predefined export settings meets your needs, you can use the Export Wizard to define your own settings. Export Wizard consists of four main steps: Start, Define Format, Define Content, and Finish. You can see which step you are working at through the interface window of Export Wizard. Below is a figure of the interface of Export Wizard.

9 Start When you choose Export hits New, we will automatically be at the first step. The interface shows you the default export settings. To start creating your own settings, click Next. Define Format This step allows you to choose the format. Available formats including MS Word, Excel, HTML, reference management system, etc. After you select the format, the Program Starting Options step allows you to choose whether or not to start an application program after the export is complete. Define Contents In the step, you can choose to include or not include structures, facts, and additional data in your export. The most important part in this step is to define User View. The User view is the data you want to export from the Results tab.

10 To include structures in your export, check the appropriate structure box to export the structures in the desired format. If the chosen format does not allow storing structures, such as an ACSII file, then this check box will be grayed out. The Facts check box is used to export data. Before data can be exported, you need to define the fields from which the data should be taken. The list of fields to be exported is called the User View. Set User View To set you own User View, click the Select Facts to View button to define the fields you want to export. User Views depend on the context and the database for which the view will be defined. To include a field in the user view, highlight the field and click the Copy (>>) button. The selected fields will be displayed in the right window.

11 After you set your User View, you will be prompted to save it. Enter a file name and click Save. Once the user view has been saved, you can select and apply it for your current session or for future use. Note: In Substance and Reaction context, you must NOT select any Bibliographic Data fields; the data will not export correctly. Instead, you should select the check box for incl. References. Finish The last step gives you a summary of your settings, and allows you to select the range of hits you want to export.