Searching CrossFire Beilstein Using CrossFire Commander 7.1 Quick User Guide
CrossFire Software: Copyright 1995-2008, Elsevier Information Systems GmbH. CrossFire Beilstein Database: Copyright 2008, Elsevier Information Systems GmbH. Patent Chemistry Database: Copyright 2008, Elsevier Inc., licensed to Elsevier Information Systems GmbH. Gmelin Database: Copyright 2000-2008, Gesellschaft Deutscher Chemiker, licensed to Elsevier Information Systems GmbH; 1988-1999, Gmelin Institut fuer Anorganische Chemie und Grenzgebiete der Max-Planck-Gesellschaft zur Foerderung der Wissenschaften. All rights reserved. 02/2008
Table of Content 4. RESULTS... 34 1. GENERAL... 1 4.1 OVERVIEW... 34 4.2 GRID VIEW... 35 1.1 STARTING CROSSFIRE COMMANDER 7.1... 1 4.3 GROUPING AND SORTING... 36 1.2 OVERVIEW... 2 4.3.1 Working with a grouped hitset... 39 1.3 CONNECTION... 3 4.4 TREE VIEW... 40 2. QUERY... 9 4.5 DETAILS VIEW... 41 2.1 SELECT THE DATABASE... 9 5. REPORTING AND EXPORTING... 46 2.2 WORKING WITH THE QUERY PANE... 11 5.1 REPORTS... 46 2.2.1 The structure query formulation... 12 5.2 EXPORTS... 48 2.2.2 Text Search... 15 5.2.1 Creating/changing export settings... 49 2.2.3 Fact Search (using the Drop-down menu)... 16 5.2.2 Prepare an export setting... 50 2.2.4 Using the tree... 20 5.2.3 Selecting a View... 52 3. SEARCH... 29 5.3 THE REPORT PANE... 54 3.1 START A SEARCH... 29 6. ALERTS... 56 3.2 SEARCH PROGRESS... 31
1. General 1.1 Starting CrossFire Commander 7.1 To start Commander from whichever platform you are using: double click the icon on your desktop or, from the Windows start menu, select Programs> CrossFire Commander 7.1 Desktop icon Page 1 of 58
1.2 Overview The Tree Pane - Find the building blocks to create a query, including: fields, forms, previous queries, and previous hitsets. The Structure Query Area - Define graphical structure and reaction queries using various structure editors. Fact/Text Search Area- Assemble your query using fact fields, data operators, and text. Page 2 of 58
1.3 Connection Information about corporate-wide IP access can be found on page 7. Access to the CrossFire Server requires the creation of a server profile. Please Note: These settings may have already been done by your administrator. To create a profile select Options> Connection Settings Create a new profile or edit an existing profile Page 3 of 58
Enter the server information (ask your administrator for details if needed). Available ports are: 8001 8010 210 Server information Page 4 of 58
There are two ways to connect to the CrossFire Server: 1. Options> Connect to server <name of your profile> 2. You can also use the Connect button On first logon you will be prompted for your user ID and password Check here to save your User ID / Password for automatic logon Page 5 of 58
If you checked save user ID and password and then want to be prompted for user ID and password, select Options> Connection Settings and select the appropriate profile. Check here to get prompted for User ID and Password Page 6 of 58
Corporate Wide Access / IP licensing If your company has a license for IP access, you will be logged in as an anonymous user by default once you click the Connect button. In order to perform certain functions, such as saving hitsets and defining Alerts, you must register with a User name and Password. As an anonymous user, these features are not available. However, you can log in with a user name and password after you have connected anonymously. 1. Follow the Server Profile steps on pages 3 and 4. 2. Click the Connect button on the Button Bar, (alternatively, you can select Options>Connect) 3. Click the login button on the Button Bar, (alternatively, you can select Options>Connect) When the login box appears, you can login (or click Register if you do not have a UN/PW) Click here to register for a User ID and Password. It will be sent to you through email. Page 7 of 58
When the Commander is closed it will offer to save the parameters of your current session. Check here to automatically get connected the next time you start the Commander (you won t need to click the Connect button the next time you start the Commander). Click here to close Page 8 of 58
2. Query 2.1 Select the Database Click this button to select one or more databases for your search. If you are not connected you will see the Connect button in place of the Select Database button. Clicking this button will connect you and open the Select Databases box. Page 9 of 58
The Database Selection Window allows you to select one or more databases for your search. Available Databases: Check the box(es) to select database(s). Please Note: All databases may not be available, depending on the licensing at your site. Information about the highlighted Database Page 10 of 58
2.2 Working with the Query Pane Structure Search The Commander comes with 3 structure editors that can be used to draw a structural query for use in CrossFire Commander 7.1: The CrossFire Structure Editor, ISIS/Draw 2.5, and MDL Draw. You can use other structure editors by including a DLL file for the editor in the Commander program folder. Please consult the CrossFire API for Structure Editors guide within the documents section of the CrossFire Commander installer for details. To select the Editor of your choice please use the menu Options> Select Structure Editor Page 11 of 58
2.2.1 The structure query formulation Double-click to open the structure editor and draw a structure or a reaction and return to Commander or paste a structure from the clipboard (note: not all information can be pasted) Options for structure queries Page 12 of 58
A chemical structure can be searched with the following options: Use these options to set free sites on hetero atoms or on all atoms for the entire molecule Please Note: Free sites on individual atoms must be set in the structure editor. When all atoms is checked in the Free Sites box, it is interpreted as a substructure search. To allow this, the options Allow: salts, additional rings, isotopes, charges and radicals are set automatically. Each of them can be unchecked if not wanted: If Autosearch is enabled these options will be set automatically during the search (see page 33) Page 13 of 58
Search the drawn structure as such (recommended context: Substances) Search the drawn structure as reactant, explore it s chemical reactivity (recommended context: Reactions) Search the drawn structure as product, explore the preparations (recommended context: Reactions) Search the drawn structure as auxiliary in a reaction (recommended context: Reactions) Off: Any stereochemical information in the drawn structure will be ignored Please Note: The option search as reagent/as catalyst/as solvent is not available for all databases. Absolute: Any stereochemical information in the drawn structure will be searched exactly as drawn Relative: Any stereochemical information in the drawn structure will be searched as relative stereochemical information Racemic: The racemic mixture is searched Page 14 of 58
2.2.2 Text Search You can search for keywords alone or in combination with structure or reaction queries. CrossFire Commander provides a default field for simple text searching called All Text, which is always visible in the fact search table. Just leave the item unchanged, enter a keyword or expression into the Field content area and click the Search button to get the corresponding results. Note: If the Field content area is empty, All Text will be ignored for searching. 1. Select operator to connect a structure search with a text search 2. Type in your query. Select the dropdown menu to select related words to add to your query. malaria 3. Choose the relation: is, starts with, ends with, contains, <, <=, >, >= Please Note: Exists cannot be used with All Text. Page 15 of 58
2.2.3 Fact Search (using the Drop-down menu) You can search for keywords alone or in combination with structure or reaction queries. Fact query: You must select a field to search before doing a Fact query. There are 2 ways to select a field: 1. use the Dropdown menu shown below (menu will contain previously used field names), or, 2. use the Search Fields Tree (shown on the next page). 1. Select operator to connect a structure search with a fact or text search 2. Use the dropdown menu under the Field Name column to select the appropriate field. Example: Pharmacological data 4. Type in your query. Select the dropdown menu to select related words to add to your query. 3. Choose the relation: is, starts with, ends with, contains, <, <=, >, >=, exists Page 16 of 58
Fact Search continued (using the Search Fields Tree)* *See Pg 19 for additional info on the Search Fields Tree. 1. Select operator to connect a structure search with a fact or text search 4. Type in your query. Select the dropdown menu to select related words to add to your query. 2. Double click a field in the Datastructure tree. The Field name will be copied to the grid. 3. Choose the relation: is, starts with, ends with, contains, <, <=, >, >=, exists Page 17 of 58
Fact Search continued (Advanced Mode) Advanced Mode: Provides a text field where a query in command language can be entered. For experienced users. Syntax: <field code>=<value> and/or/next/proximity <field code>=<value> Example: (CNS="taxol" or CNS="paclitaxel") and PHARM.E="cardio*" Check this box to change the Search Text/Field Contents box to the Advanced Mode. Type your query into the Advanced Mode box. Page 18 of 58
Fact Search continued (Enlarge) Enlarge the Field Table: The Enlarge feature enables complex queries using multiple fields from the Database. To enlarge, use the View menu or simply drag the blue line separating the structure box from the Search Text/Field area. Set brackets Operator to connect the definitions with and or proximity not near next Type the value or word you are looking for in the specified field. To view and select the content of the field use Type the field code (e.g. RX.ID, PHARM.E) Click the down-arrow to select additional search fields. Choose the relation: is, starts with, ends with, contains, <, <=, >, >=, exists Page 19 of 58
2.2.4 Using the tree The tree on the left side of this Window has multiple functions and offers various options to work with Commander Browse and use the Database s Datafields to formulate your query Use the Predefined Search Forms (PSF) to formulate your query Browse and use saved or recently used queries. Browse and use Hitsets from the current session or saved Hitsets Page 20 of 58
The Search Fields The datastructure of the selected database can be browsed in this tree. To set up a query on a particular field, double-click on the field name and it will be copied to the Fact/Text Search Area grid. A singleclick on the field name will bring up the Help entry for that field. A right mouse click offers to copy the field to the grid or to collapse the tree. Double click Single click Turn Help on or off. Page 21 of 58
The Find function If you cannot find the field you need, click the Find Field or Form button, type in a word to describe the type of fact you need, and click OK. The first field containing the text that you entered will be highlighted. If this is not the field you need, click the Find Next button to see the next field that contains your text. Click to type in a field. Click to find the next occurrence of the text that you typed in. Page 22 of 58
Predefined Search Forms (PSF) The Predefined Search Forms summarize the fields of a specific area of interest in an easy to use form. You can use more than one form to build your query. Use the Find features to locate a specific topic in the forms Double click an entry to open the form Sort the Search Forms in alphabetical order or by default Page 23 of 58
If more than one database is selected the search forms are replaced by the Predefined Search Forms for Cross Searches. These summarize the fields that are available for simultaneous searching over multiple CrossFire databases in easy-to-use forms. Double-click on a form name to select the form Page 24 of 58
Query History Double-click a query to see the query properties (see next page). Find feature: Find Query by name, date etc. (see next page) Saved Queries Queries from past sessions Queries from last session (either Date or Yesterday s queries ) Queries of the current day Page 25 of 58
Query properties: Double-click a query to see the query properties (see previous page). Query Information (Find feature searches here) Query Definition and Conditions Click here to copy this query into the query builder Click here to use this query s hitset as the search domain (refine results). Hyperlink is visible for current session query properties. Page 26 of 58
Hitset History Right-click to: -view the properties (see next page) -open the hitset in the results window -collapse the tree (if there are hitsets from more than one database present) Double-click a hitset to use as search domain (refine results, subset search) Select the operator, e.g. not Select 2 or more Hitsets to perform ListLogic operations, e.g. build the difference between the content of 2 hitsets Page 27 of 58
Hitset Properties: Information about the hitset s corresponding query Click here to open the hitset in the results window Click here to copy this query to the query builder Page 28 of 58
3. Search Process 3.1 Start a search Your results will be displayed as substances, reactions, or citations. You can choose any of these 3 result contexts regardless of the context of your query. For example, you can enter a structure query and select reactions as your results. However, it is recommended that you do the following: Substance Reactions Citations Choose this context if you have drawn a structure or if you are looking for data or properties of a compound Choose this context if you have drawn a structure and selected as product or as reactant, if you have drawn a reaction or if you are looking for data and properties of a reaction Choose this context if you are looking for an Author, a publication or any other publication related topic Please Note: You can also start a search using the Return/Enter Key Select your search context before clicking the Start Search button Page 29 of 58
At the start of each search, CrossFire Commander 7.1 compares the query with the selected context. If the query is unusual for the chosen context Commander will prompt you to verify or change the context: Click here to search in the recommended context, or simply click the Return/Enter key or press the F7 key. Click here to search in a different context of your choice Page 30 of 58
3.2 Search Progress The search progress is displayed in a new window: Structure Search Status Report Click Cancel to stop a search. Hitsets finished before canceling are available for viewing. Currently running Search is highlighted Definition of the Query View the selected hitsets Copy this Window to a report Page 31 of 58
Text Search Status Report (See page 15 to view the query) Use checkboxes to select a hitset for view View the number of hits in each context. The Commander searches the Basic Indices for Substances, Reactions, and Citations whenever a Text search is performed. When a search is finished, the top of the Search Progress Window changes to allow browsing of the sessions s searches: Use these buttons to browse searches from the current i Page 32 of 58
AutoSearch If AutoSearch is enabled Commander will refine a structure step by step to find the closest hit; first by performing an Exact search, then a search for substitution on heteroatoms, then a search for substitution on all atoms. AutoSearch can be enabled/disabled in the Menu Query. Switch on/off AutoSearch Sets AutoSearch to stop when a first hit is found (equals find closest hit) Page 33 of 58
4. Results 4.1 Overview Example: The results of a structure query. Result Tree Grid View Details View Page 34 of 58
4.2 Grid View The Grid View provides an overview of the structures, reactions, or citations of a hitset. To see the hit details, use the buttons Grid and Details or double click an Item in the Grid. Grid View of a Substance Hitset Grid View of a Reaction Hitset Click to view Citation Details or Full text (access to full-text depends on which sources you are licensing). Sort by Source or Year by clicking here. Grid View of a Citation Hitset Page 35 of 58
4.3 Grouping and Sorting A Hitset can be sorted and grouped by the values of selected fields. Sort or Group the current Hitset by clicking the Sort/Group Button. To select another hitset, rightclick a hitset in the Tree and select Sort/Group. Page 36 of 58
Sorting Select Sort View Hitset, Database and current status: Unsorted, sorted, sorted,grouped Choose criterion for sorting. Sorting is available on several levels. View Sorted Hitset: Sorting Criterion Page 37 of 58
Grouping Select Group Choose criterion for grouping. (The hitset is pre-grouped by all available criteria. You just need to choose one.) The groups for the chosen criterion are displayed along with the number of members in each group. Create subsets by checking the groups you want to include or exclude. View Grouped Hitset: Grouping Criterion Page 38 of 58
4.3.1 Working with a grouped hitset In the tree: Click the Hitset top level to see an overview of all groups within the Hitset. Click a Group to see an overview of a group (group members) Group Number 2 (Number of group members): (3) Value of grouping criterion for this group Acetone (Solvent) In the grid view: Please Note: The image in the grid shows the first member of the group. Page 39 of 58
4.4 Tree View On the left side of the screen the tree view provides fast navigation through saved Hitsets and Session Hitsets. Select the Hitset you want to see. The main screen will switch to Grid View. Click on in the tree to drill down to details (ultimately to the field level). Double-click on these details to display them in the main screen Move the mouse over a chemical name to view it s structure. Page 40 of 58
4.5 Details View The Details view contains all data about a compound, citation, or reaction that are available in the database. Structures: The structures contained in a Substance or Reaction hitset can be embedded within the Results screen and/or displayed in a separate window: The structure display in a separate window can be toggled on/off 3 different ways: 1. Press the function key F2 on the keyboard. 2. Use the menu item View>Structure in separate Window 3. Press the Show() button in the button bar. Structure displayed in a separate window.. To include structures in the display within the results, use the menu item View>Structures included. This option not only displays embedded structures in Substance and Reaction records, but also displays all of the substances and reactions described in a Citation record. Structure embedded within Results. Page 41 of 58
The Field Availability List The Field Availability List provides: a listing of the Fields containing data within a record the number of data points per field (occurance) links to get directly to these data Use the View menu to control your display of The Field Availability List. It can be viewed embedded in the results or in a separate window. Press the function key F5 on the keyboard to quickly display The Field Availability List in a separate window. Page 42 of 58
Highlight Hits The results for the search term and/or substructure can be displayed highlighted for easy viewing. Example: Search for Ibuprofen as structure with the data constraint pharmacological Effect=anti-inflammatory View>Highlight Hit terms Search Term highlighted in text Options> Define Colors Substructure highlighted in red Click here to change structure highlight color Page 43 of 58
View Hit Only The display can be reduced to show only the substance or reaction Identification Data and the Fact that includes the search term. Focus on relevant data by selecting View> Hit Only This View can be achieved as well using the View button in the button bar: Page 44 of 58
Get The Get Feature is designed to easily retrieve information related to the current hitset: Not available in a Reaction Hitset Jump directly to a Registry Number mentioned in the text Not available in a Citation Hitset Example: Get All Related Reactions from a Substance Hitset Narrow your results to reactions in which your substance of interest plays the role of reactant, product, or either. Page 45 of 58
5. Reporting and Exporting 5.1 Reports The reporting of selected information into a simple web-like form has been extended in CrossFire Commander 7.1. The items that can be reported are selected information from a hit display, Queries and Information about search results and progress. Reporting selected Facts In the Details view, each field is equipped with a Title Bar on top that is used to select factual data Select Data for reporting by checking this box Several facts can be selected separately and reported in one step; additional facts can be appended to an existing report as well. Page 46 of 58
Clicking on the button or a right mouse click anywhere inside the fact opens a menu: Add the selected facts to Word or to an existing report Choose whether to include structures or not. Select structure format. Define report name The reports are available inside the Commander. Click the Reports tab to view the reports. Please Note: Queries, Search Status Information and other information can be copied to a report. Look for the To Report button: Page 47 of 58
5.2 Exports Results can be exported to various targets. Clicking Export Hits in the button bar opens a menu with different export settings depending on the context of the hitset. You can also create your own export setting or change an existing export setting (see next page). Export Settings in a Substance Context Export Settings in a Citation Context Export Settings in a Reaction Context Compound Report Examples: Bibliographic management file SAR Table Page 48 of 58
5.2.1 Creating/changing export settings Click Export Hits to open the Export Settings box Select and start an export Create a new export setting Modify an existing export setting Delete an export setting Create an identical copy of an existing export setting User-created Export setting Page 49 of 58
5.2.2 Prepare an export setting Selecting New or Edit from the previous dialog box will start the Export wizard so that you can define the format and content of your new export file. Select the desired file type. HTML files can contain structures and facts. ASCII and Literature Management files contain no structures. Set delimiters (Tabs, Blanks, Commas etc.) for an export to ASCII or to an import file for a reference manager using the select box: Define behaviour of the target application: starts automatically when exporting, does not start, or starts in a different application Define handling of the exported data: hand over to application via Clipboard (no file is created) or store in a file (name conventions can be defined using the Change Settings button) BSD: The structures of your hits will be exported to a BSD-File (Beilstein Structure and Data Format) which can later be loaded into the Commander to perform searches. SD: The export is saved as SD-File (MDL Structure Data Format) which can be used with other databases. RD: The export is saved as RD-File (MDL Reaction Data Format) which can be used with other databases. Page 50 of 58
Define Content Please Note: The options in the Define Content screen change with the selections of the previous screen. Include image of the title compound or reaction. This is the one shown in the separate structure window of the Details view. Include images of the compounds or reactions that are referenced within the data of the hit. Select the facts to be exported. Please see next page Export only data requested in the query (highlighted data in Display, see page 44) Please check if you want to include the Field Availability List and/or the List of References in the export Page 51 of 58
5.2.3 Selecting a View It is important to define which data fields shall appear in an export. In the Define Content window of the Export wizard, click Then click New to define the fields for your export. Select the desired fields from the datastructure. Example: molecular weight and boiling points: Double click the field or select the field and use the >> button to add it to the view layout. Optional: Enter a short descriptive text in case you want to remember this view for future exports. After clicking OK, a Save dialog box will appear so that you can save your new user view. This will save just the view not the whole export setting. Page 52 of 58
After saving the user view it appears in the list of User views. It is important to click Apply to assign the highlighted view to the export setting! Click Apply to assign the highlighted view to the export setting The wizard will re-open. Click Next to continue. Click Start Export Click the Start Export button Type in a description of the export setting Save the export setting Page 53 of 58
5.3 The Report Pane All reports are available from within CrossFire Commander when they are saved to the default Commander> Reports folder (reports can be saved to other folders, as well). In addition, all exports in.html and.txt format are available in the Reports pane. To access the report pane click the Reports Tab: Report Title Tree: Select Report or Export to be displayed in the main display. Main Display: Content of the selected Report or Export. All Hyperlinks are active The currently active Report is displayed in bold Right mouse click offers Settings and Delete. Page 54 of 58
Reports can also be viewed in other applications from the Reports pane. Click Open Document and select the target of your choice. Click Print to print a report. Page 55 of 58
6. Alerts CrossFire Commander 7.1 offers an Alert feature. It is designed to retrieve results from a query that is run against the new data of an update at no additional cost. To create an Alert you must first create a Query in the Query Builder. Then click Create Alert in the Button bar. Page 56 of 58
The query is then transferred into the Alert Window, where the alert options must be set. The number of alerts that can be defined by the user is between 5 and 10. The administrator of the application sets the exact number. Profile Name, will appear in the Alert Tree Alert Query Definition Alert Options Page 57 of 58
Alert Options: Define the frequency of the alert run Enter the date on which you wish the first run of the alert Define the Database on which the Alert shall run (no multiple Databases) Date and time of the last run of the alert Enter e-mail-addresses of the people who should get informed about the result of a run of this alert. Note: Only the owner of the alert can view the results Enter Comments. The Alert-Find feature will browse these comments. Last run with hit will be mentioned here (click show to view) Save the profile Page 58 of 58
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