AmbitXT v2.1.0 Manual

Transcription

1 AmbitXT v2.1.0 Manual June 2009

2 1 Table of Contents Introduction... 2 Functions of AMBIT XT v Workflow of AMBIT XT v Using Database Utilities... 4 General Information... 4 Prerequisite for using Database Utilities... 4 Getting connected... 4 Importing structures... 5 Importing properties... 5 Calculating fingerprints and descriptors... 8 Using REACH PBT & vpvb Assessment... 9 Using Profile & Category General Information Prerequisite for using Profile & Category Building a category Exporting results Using Simple Search General Information Prerequisite of Simple Search Using search Using Advanced search Refine search results Browse previous search results Displaying Properties Exporting search results... 18

3 2 Introduction AMBIT XT v2.1.0 consists of a database and five functional modules that not only allow a variety of flexible searches and mining of the data stored in the database but also capable of performing PBT Assessment if needed. Interface of AMBIT XT v2.1.0 is shown as follows: Modules choose & press to open Workflow steps Main Window Workflow options Progress bar indicates processing status Functions of AMBIT XT v2.1.0 AMBIT XT v2.1.0 consists of five functional modules, which are: - Simple Search - Profile & Category - REACH PBT Assessment - Database Utilities

4 3 - Admin Each module performs individually without influencing other modules. Workflow of AMBIT XT v2.1.0 AMBIT XT v2.1.0 communicates with the users via the workflow window. Each workflow step will be indicated by one of the following symbols: = This step has been successfully done and the answer of the question/condition is YES. = This step has been successfully done and the answer of the question/condition is NO. = Pending till all the conditions are fulfilled. = This step is successfully done. When an error occurs, it is recommended to always check with the last workflow step performed and restart accordingly.

5 4 Using Database Utilities General Information Database Utilities controls and manages the AMBIT databases. Its main functions include: - Importing structure / properties into the database; Calculating fingerprints and descriptors for structures in the database; Control MySQL server; Generates database statistics, and Manage templates and properties. Prerequisite for using Database Utilities - Stable Internet connection Getting connected You must log into the database in order to perform all the functions in this module. Double click Database tools > MySQL start AMBIT XT v2.1.0 comes with a default user guest with password guest in the default database ambit2. You can check your connection status in the status window:

6 5 Importing structures You can update the database with importing chemical structures (e.g. SDF file) to the database. 1. Double click Database tools > Import structures; 2. Choose the file (e.g. SDF file) that needs to be imported, then click Next. The importing process might take few minutes or longer depending on the size of imported file, pay attention to the process indicator bar at the right corner: DO NOT log out while it is still moving! The completion of importing process is indicated in the Database tools window as below: Importing properties You can also update the database with importing chemical properties (e.g. SDF file) to the database. 1. Double click Database tools > Import properties; 2. Choose the file (e.g. SDF file) that needs to be imported, then Next;

7 6 3. Click to select your matching criteria (e.g. to match by CAS registry number; EINECS registry number, PubChem Compound ID, InChi or SMILES), then click Next; 4. Configure the dataset i.e. name, reference etc. in the prompted window, then click Next. The importing process might take few minutes or longer depending on the size of imported file, pay attention to the process indicator bar at the right corner: DO NOT log out while it is still moving! The completion of importing process is indicated in the Database tools window as below:

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9 8 Calculating fingerprints and descriptors To calculate fingerprints and descriptors for the chemical structures in the database: 1. Double click Database tools > Calculate; 2. Configure your dataset i.e. name, reference etc. in the prompted window, then click Next; 3. Click to select the type of descriptors that need to be calculated in the prompted window, then click Next. Use and to select and remove single descriptor; To select all the available descriptors, press To remove all the selected descriptors, press button in the prompted window; button in the prompted window. The calculation process might take few minutes or longer, pay attention to the process indicator bar at the right corner: DO NOT log out while it is still moving!

10 9 Using REACH PBT & vpvb Assessment Please download the independent user manual for REACH PBT & vpvb Assessment from AMBIT XT v2.1.0 website.

11 10 Using Profile & Category General Information Profile & Category allows the users to build the category with individual profile e.g. properties, endpoints or descriptors and comparing the similarities among selected substances under different criteria. This module is still under development in AMBIT XT v Prerequisite for using Profile & Category - AMBIT database is connected Building a category 1. Double click Workflows > Category building; 2. Click to define the structure(s) in the prompted window; 3. Follow the instructions in the prompted windows accordingly; 4. To complete structure definition, click to select No, the set of target structure is complete, then Next; 5. To complete profile definition, click to select Quit profile definition, it is complete, then Next. The results will be shown in the Profile & Category main window as two pages: Target chemical(s) and Source chemical(s). You can sort out the result in different ways, such as ascending by metric. Press the buttons accordingly and click to select from the drop-down selections:

12 You can also select or unselect all the results by pressing the select button and click to select from drop-down selections shown as below: 11

13 12 Exporting results To save the result as a file: 1. Double click Workflows > Export results; 2. Click < > to choose file location, type file name and select the file type as PDF/RTF/HTML/SDF in the prompted window, then click Next.

14 13 Using Simple Search General Information Simple Search provides a comprehensive yet efficient searching function throughout the AMBIT database. Various search criteria can be defined and different display options for search results can be selected and exported e.g. as PDF file. Prerequisite of Simple Search - AMBIT database is connected Using search Simple search is suitable when a fast and general search in the database is needed. To use simple search: 1. Double click Workflows > Search; 2. Select Field name and Condition from the drop-down selections and type the value (i.e. substance name) accordingly in the prompted window, then click Next; 3. Click to select the search scope in the prompted window (Entire database; Last results; Previous search results or Datasets), then Next. The completion of searching process is indicated in the Simple Search window as below: The search results will be shown in the simple search main window, for example:

15 14 You can have Table, Matrix or Columns view of the search results: Table view Matrix view Column view Zoom in Zoom out

16 15 Using Advanced search Advanced search provides more specific digging in the database that requires definitions on various searching criteria and longer time. To use advanced search: 1. Double click Workflows > Advanced Search; 2. Click to select the type of query in the prompted window, then click Next; 3. Select Field name and Condition from the drop-down selections and type the value accordingly in the prompted window, then click Next. The completion of searching process is indicated in the Simple Search window as below:

17 16 Refine search results This workflow allows a refined search within the last search results. To start, double click Workflows > Refine search results; then follow the same procedure as in the advanced search to define the search criteria. Browse previous search results You can have a look at the previous search results by double click Workflows > Browse previous search results. Click to select from the previous search results list:

18 17 Displaying Properties 1. Double click Workflows > Properties; 2. Click to add properties, endpoint(s) or descriptor(s) in the prompted window; Click to choose from the listed available elements in the prompted window: 3. Choose Clear the profile and start again if you need to redefine profiles; 4. Choose Quit profile definition, it is complete when you finished with profile definition, and then Next.

19 18 Exporting search results 1. Double click Workflows > Export results; 2. Click < > to choose file location, type file name and select the file type as PDF/RTF/HTML/SDF in the prompted window, then click Next. The completion of searching process is indicated in the Simple Search window as below: