Entities overview

    In IJC, data from database tables are represented by entities. Please look at the documentation pages for more information about IJC’s architecture and terminology. IJC currently supports four types of entities: standard entity, structure entity, SQL entity and pivot entity.


    An overview of all types of entities and their characteristic features are included in the following table:

    images/download/attachments/5316554/entity-standard.png Standard entity There are three subtypes of standard entities. The first subtype, a normal database table, can be used to store numeric and textual data in a standard entity. Only basic query functionality is offered by this standard entity. The second subtype is an entity using a standard table with JChem Oracle Cartridge, the third subtype is an entity using a standard table with JChem PostgreSQL Cartridge.
    images/download/attachments/5316554/entity-jchembase.png Structure entity A structure entity uses JChem structure tables (JChemBase or JChemBase with cartridge index) to allow chemical structures to be stored and offers a variety of structure search features. Documentation page about the JChem cartridge table types in IJC can be found here.
    images/download/attachments/5316554/entity-standard.png SQL entity A SQL entity is created using an SQL SELECT statement.
    images/download/attachments/5316554/entity-standard.png Pivot entity Since Instant JChem version, it is possible to create a virtual data view containing pivoted data from another entity. It is not possible to query this entity directly and it is by default linked to the original entity by 1:N relationship.

    It is also possible to add existing tables which are already present in your database to IJC by promoting them to entities.

    If you are using an Oracle database and the Oracle schema which you are connected to has the JChem Oracle Cartridge enabled, or if you are using a PostgreSQL database and the PostgreSQL schema which you are connected to has the JChem PostgreSQL Cartridge enabled, then you can choose between four different types of structure entities:

    images/download/attachments/5316554/entity-jchembase.png Structure entity (using JChem base table) These are the normal JChem tables that are also present in the non-Oracle databases. When using this table type all processing (including searching) takes place inside IJC and uses IJC memory. For large structure tables (100,000 structures or more) you may need to ensure that you have additional memory allocated to IJC.
    images/download/attachments/5316554/entity-jcc-std.png Structure entity (using standard table) These are standard (non-JChem) database tables which have had a JChem cartridge index applied to their structure column. This allows the table to be searched in a chemically intelligent manner. All operations are performed using SQL operations in the Oracle database and there is very little processing or memory required from IJC. For this reason, very large tables (multi-millions of structures) can be searched in IJC with normal memory requirements.
    images/download/attachments/5316554/entity-jcc-jcb.png Structure entity (using JChemBase table) These are JChem database tables that have had a JChem cartridge index applied to the cd_structure column to allow it to be searched using Oracle SQL operations. This type of entity is a hybrid of the first 2 types. Whilst searching is performed in Oracle, many other operations such as addition of chemical terms fields are performed using the JChemBase API. Because of this the JChem (running in the Oracle cartridge) and IJC version must be the same. If the JChem and IJC versions are different, some features of this table type will be disabled. For this reason, the cartridge entity using standard tables is preferred.
    images/download/attachments/5316554/entity-jcc-std.png Structure entity (using PostgreSQL Cartridge table) These are special PostgreSQL cartridge tables with the structure column type MOLECULE('sample') which is searched in a chemically intelligent manner. All operations are performed using SQL operations in the PostgreSQL database which places very little processing or memory requirements on IJC. For this reason, very large tables (multi-millions of structures) can be searched in IJC with normal memory requirements.

    When the conditions listed above are not met, you will only see the first of these four types. Details of how to administer the JChem Cartridge for IJC can be found in the administration guide.

    Entity creation

    Creating an entity with Data Tree

    When creating an entity, it is often useful to also create a data tree along with its views (grid view or form view). An entity can either be created on its own or it can be created with its new Data Tree.

    To create an entity with a new table along with a new Data Tree there are three options:

    • In the Projects window, right-click the Schema node (images/download/thumbnails/5316554/Connection16.gif) and choose 'New Data Tree and structure entity (table)', 'New Data Tree and standard entity (table)', 'New Data Tree and SQL entity (virtual view)' or 'New Data Tree and Pivot entity (virtual view)' from the popup menu .

    • Open the Schema Editor and switch to the 'Data Trees' tab. In the Schema Editor toolbar select either the 'New structure entity' icon (images/download/thumbnails/5316554/datatree-jcb-new.png ) or the 'New standard entity' icon (images/download/thumbnails/5316554/datatree-std-new.png ).

    • Open the Schema Editor and switch to the 'Entities' tab. In the Schema Editor toolbar click on the 'New Entity with Data Tree' icon (images/download/thumbnails/5316554/datatree.png ) and then select 'New data tree with new structure entity (table)', 'New data tree with new standard entity (table)', 'New data tree with new SQL entity (virtual view)' or 'New data tree with new Pivot entity (virtual view)' as appropriate .

    The New Entity dialog guides you through the process of entity creating. As well as the entity being created you also get a data tree that will be added to the schema editor and the project window.

    Creating an entity without Data Tree

    To create an entity without a Data Tree, in the schema editor switch to the 'Entities' tab and click on the 'New entity' button in the toolbar ( images/download/thumbnails/5316554/entity-generic.png ). In the pop-down menu choose 'New structure entity (table)', 'New standard entity (table)', 'New SQL entity (virtual view)' or 'New Pivot entity (virtual view)' as appropriate .

    Database table entity

    After selecting New database table as entity type, specify its general settings:

    • In the Display Name text field, enter a name for the new entity.

    • In the Database Table Name text field, the content of the Display Name text field is automatically copied and can’t be changed.

    In the second tab (ID Generation), the value generator type can be set. The default value generator type is Autoincrement. Detailed documentation about value generators available in IJC can be found here.

    After clicking Finish, a new standard entity is created in your project as well as a new database table. If you have requested to create a new data tree together with the new entity, it is also created. The node for a simple Data Tree (images/download/attachments/5316554/datatree-simple-std.png) is displayed under the appropriate database connection in the Projects window and in the 'Data Trees' tab of the schema editor.

    JChem PostgreSQL cartridge entity

    If you are using a PostgreSQL database and have the JChem PostgreSQL Cartridge installed and running, a new JChem PostgreSQL Cartridge entity can be created. (Documentation pages about installation and administration of the JChem PostgreSQL Cartridge can be found here.) After selecting the JChem PostgreSQL Cartridge entity as entity type, the following settings need to be specified:

    • In the Display Name text field, enter a name for the new entity.

    • In the Database Table Name text field, the name of the new entity is automatically copied from the Display Name text field.

    • In the Structure Column field, enter a name for the structure column in the database table.

    • In the ID column field, specify the column name for the identity column (primary key column) in the database table. For a JChem PostgreSQL Cartridge entity, the ID is generated automatically.

    • The default value of the Molecule Type field is ‘sample’. You can add a new molecule type or change the existing one. Detailed documentation about adding and changing molecule types is available in the JChem PostgreSQL Cartridge Manual here.

    Structure entity

    When you’re creating a new structure entity (table), the following dialogue appears:


    Settings and properties of the new structure entity can be adjusted as follows:

    • Tab 1: General Settings

      • In the Display Name text field, enter a name for the new structure entity.

      • In the Database Table Name text field, the name of the new entity is automatically copied from the Display Name text field.

      • Use the Table Contents drop-down box to specify the structure types to be included in the JChem Structure Table. Choices are:

        • Molecules: discrete structures only

        • Reactions: single step reactions

        • Query structures: structures with query features

        • Markush libraries: structures with Markush features

        • Any structures: all types of structures (including reactions, query structures and Markush structures)

    {primary} If 'Any structures' is selected, structure type-specific search functionality (e.g. reaction searching) will be disabled.

    {primary} Markush Libraries requires Markush Enumeration and Markush Search licenses.

    • Specify the settings for the JChem property table and the handling of:

      • Absolute stereo: are chiral structures to be treated as having absolute stereochemistry (the MDL chiral flag option)

      • Empty structures allowed: are empty structures allowed in the table.

      • Duplicate filtering on/off: is duplicate filtering currently enabled.

      • Tautomer duplicate checking: does duplicate filtering consider tautomeric structures (has no effect if the previous option is set to off, but does effect on creating the table).

    {primary} If you are using a JChem cartridge enabled schema, you will be able to choose between different types of structure tables. Some options are available only for specific cartridge tables. Please see the About the JChem cartridge table types documentation page for more details.

    • Tab 2: ID Generation

      • Specify details and the value generation method for the primary key column. In JChemBase, this is set automatically by JChem and there are no user-defined settings. For JChem cartridge indexes on standard tables, you need to define the ID generation method. See the section on primary keys for more details.
    • Tab 3: Fingerprints

      • Optionally, the chemical hashed fingerprint settings can be specified. These affect the structure search performance. The default fingerprint settings are dependent on the table type (e.g. fingerprints for reaction table type are longer than for molecules). The default settings are suitable in most cases. For specific details of fingerprint settings consult the JChem Administration Guide.
    • Tab 4: Standardizer tab

      • Optionally set details for the standardizer. Default standardization will be used if no custom standardization is specified. Default standardization involves conversion to aromatic form and removal of explicit hydrogen atoms. See the section on standardizing structure files for details of using the standardizer editor or the JChem Query Guide for a discussion of standardization and structure searching. Please note, the standardizer actions require a Standardizer license.
    • Click Finish.

      • A new entity is created in your project, as well as a JChem table in the database. A new data tree node for a simple Data Tree (images/download/thumbnails/5316554/datatree-simple-jcb.png) displays under the appropriate database connection in the Projects window and the 'Data Trees' tab of the schema editor.

    For more details regarding the JChem structure tables, please see the JChem Administration Guide.

    SQL entity

    When you’re creating a new SQL entity, the following dialogue appears:

    • Tab 1: General Settings

      • In the Display Name text field, enter a name for the new entity.

      • In the ID Column text field, enter the name of the column with ID values. The ID column must contain unique non-null values. This sets the column as the ID field (primary key column) of the new entity.

      • Choose data type for values in the ID column. IJC supports integer and string ID fields, see the About primary keys and value generators documentation page.

      • In the SQL Select area, specify a SQL SELECT statement to define the new SQL entity. This SELECT must retrieve a column containing the ID column specified in the ID Column text field.

      • Press Next button and continue with promoting fields.

    • Tab 2: Promoting fields

      • All columns retrieved by the SQL SELECT statement are listed and offered for promoting as fields in the new SQL entity.

      • In this step, you can specify which columns you want to promote to fields. The columns can be selected or unselected using the checkboxes next to their names. Additional parameters for each column can be customized by clicking the images/download/thumbnails/5316554/ThreeDotsIcon.png icon in the last column of the table. Columns can be instantly promoted this way. Unpromoted columns can be also added individually to the IJC SQL entity.

    Column aggregation and table pivoting

    Both on Oracle database and SQL entity definition, it is possible to use functions LISTAGG and PIVOT.

    LISTAGG function

    The LISTAGG function rearranges values from a group of rows into a list of values delimited by a separator.

    Value registration_NO Date
    value1 1 Jun 1, 2015
    value2 1 Jun 3, 2015
    value3 1 Jun 2, 2015
    value4 2 Jun 4, 2015
    value5 2 Jun 5, 2015

    To aggregate the values with the same registration_NO and sort them according to the date, the following SQL statement can be used:

    SELECT registration_NO as ID,
        LISTAGG(Value,',')  WITHIN GROUP (ORDER BY Date) "Aggregated Values"
    FROM TableName
    GROUP BY registration_NO

    This will result in the following table:

    ID Aggregated Values
    1 value1, value3, value2
    2 value4, value5

    PIVOT function

    The PIVOT function enables writing queries to transpose rows into columns and aggregating data in the process of transposing.

    registration_ID value assay_id
    1 10 N1
    1 20 N1
    1 30 N1
    2 30 N1
    2 35 N1
    3 35 N2
    4 37 N2

    The pivoted table display s the sum of the values for each registra tion_ ID with the same assay_id and can be created with t he following SQL statement:

        SELECT registration_ID AS ID, value, assay_id
        FROM TableName
        ORDER BY registration_ID
        FOR assay_id IN ('N1','N2')

    This will result in the following table:

    ID N1 N2
    1 60
    2 65
    4 37
    3 35

    The outer SELECT is used to display the data from the pivoted table, the inner SELECT defines the fields to be pivoted and defines the ID field needed for proper functionality of the SQL entity in IJC. Inside of the PIVOT clause, the desired analytic function (SUM) and the pivot condition (inside of the FOR loop) is defined. Unlike SQL, a dynamic statement (subquery) can’t be used in the PIVOT IN clause in Oracle.

    Pivot entity

    Creation of a Pivot entity in IJC and its management is described here.

    Support for database views

    An IJC entity can be created using a database view. A view is a virtual table in the database containing rows and columns, like a real database table. The fields in a view are fields from one or multiple tables in the database. A view is created by CREATE VIEW statement. Data visualized through the view are defined by SELECT statement. For example, a view can be created as follows:

    CREATE VIEW view_name AS
    SELECT * FROM table_name       

    This view shows all fields from the original table. For better readable data representation, additional operations can be added by SELECT statement such as combining data from multiple tables, data filtering or pivoting. A view always represents up-to-date data. The database engine recreates the data every time a user queries a view.

    A database view is not to be confused with IJC views (grid view and form view) as these are visual reports of data.

    The database views are displayed in the ‘Views’ tab of the schema editor and are supported by IJC on a similar way as database tables, with the following limitations:

    • IJC entities, which use views, are read-only.

    • The database views must be created directly in the database, can’t be created in the IJC.

    • The database views are supported only for standard entities in IJC, aren’t supported for structure entities.

    Editing an Entity

    Settings of an entity can be checked and modified from the schema editor. By clicking the entity in the schema editor, the General Settings, ID Generation, Permissions and Extra Attributes tabs are listed in right window. In addition, the Fingerprints, Standardizer and Statistics tabs appear in case of a structure entity. Not all settings are editable once the entity has been created. For instance, the fingerprint settings can be specified when the structure table is being created, afterwards are not editable. The non-editable fields are greyed out in the tabs.

    In the General Settings tab, the entity name and the database table name appear. In case of structure entities, the JChem property table settings become visible as well as flags for allowing empty structures and duplicate filtering and flags for stereochemistry settings (assume absolute stereo and tautomer duplicate checking). Documentation of JChem stereochemistry features can be found here.

    The ID generation tab contains two non-editable fields (ID field and type) in case of both standard and structure entities. The ID field works as primary key column in the database table and the values included in this field are autoincrement (for standard entities) or are automatically generated by JChem (for structure entities).

    Data modification operations for editing, deleting and inserting rows can be set in the Permissions tab.

    A custom row filter for any IJC entity can be added and modified in the Extra Attributes tab. This feature offers restricting access to data at the level of the rows in the database. Instructions for using this feature can be found here.

    The Fingerprints, Standardizer and Statistics tabs are visible only for structure entities. In the Fingerprints and Standardizer tabs, the JChemBase table attributes are displayed. These values can’t be modified. By clicking the ‘Generate’ button in the Statistics tab, descriptive statistics data are calculated for values included in the JChem table (NULL SMILES count and SMILES length, chemical fingerprint settings and distribution). More information about chemical hashed fingerprints can be found here.

    {primary} A pivot entity has limited editing capabilities, the details can be found in the documentation here.

    Deleting an entity

    In the ‘Entities’ tab of the schema editor right-click the entity and choose 'Delete...' from the popup menu. You are presented with a dialog informing you of the other changes that this deletion would cause. The checkbox offers the option of not deleting the actual database table (removing the entity from IJC but leaving the table in the database). Review the settings and click the 'Delete' button to perform the deletion.

    Promoting an entity

    The database may contain tables that are not used by any entity. These might have been in the database before it was used by Instant JChem or might have been created by Instant JChem and then the entity was deleted without the corresponding table being removed. To see these unused tables, use the 'Database Tables' tab of the Schema Editor. For more information on using existing tables in the database see the the Using existing database tables documentation page. Oracle database tables from other database schemas can be also accessed and promoted. See the support for multiple database schemas documentation page for more details.