Query builder

The query builder panel is located (by default) in the lower left corner of the IJC window. If it is not present it can be displayed using the Window menu.

A query is built from "query terms" which are described below.

Field Operator Value Query Term

This is the basic query condition used in a query. It comprises a simple query condition such as 'MolWeight < 300', but also includes structure search terms (including Chemical Terms filters). Once added you typically select from the available operators (e.g. '<' in the above example) and enter the value(s) ('300' in the above example). The field is pre-determined when you add the query element and cannot be changed.

In future IJC will support other types of constructs such as Field operator Field e.g. Assay1_IC50 < Assay2_IC50.

Querying with Standard Fields

For each standard field present in a table, the field name is displayed along with a drop-down list for defining the query operator (=, <, <=, Between, etc.) as well as one or more elements for specifying the values for the query.

Specify the appropriate operator in the drop-down list and enter the value(s) for the query in text box(es).

Most operators take a single value. Exceptions are:

The BETWEEN operator which provides you with 2 text boxes, the first for the minimum and the second for the maximum value.
The IN LIST (and NOT IN LIST) operator which requires you to enter a comma separated list of values (e.g. 1,2,4,8,16).
If the field is defined as containing a 'discrete set of values' then those values are presented in a multi-select list allowing you to specify them without typing.

Querying with Structure Fields

Structure fields let you specify a structure query, which can be of type:

Substructure: target contains the specified substructure
Superstructure: target is contained within the query structure
Similarity: target is similar to the query
Perfect: target is identical to query, including things like stereochemistry and isotopes
Exact: target is identical to query, allowing user to define things like stereochemistry and isotope matching
Exact Fragment: as for Exact, but match only has to be for one component of the target (target can contain multiple molecules)

In order to edit the structure of the queried field, double-click the structure panel to open Marvin Sketch.

Check the 'Return non-hits' check box if you want to reverse the meaning of the search e.g. find all the structures that don't match the specified structure query.

Click on the options button () for a popup menu that allows you to specify advanced searching settings, such as stereochemistry options and similarity search threshold.

Specifying a Chemical Terms filter

With structures you can also specify a Chemical Terms filter that can be applied to the query. To do this, enter the Chemical Terms expression into the Chemical Terms filter box located beneath the Marvin Sketch panel; alternately, click on the advanced button () to open the Chemical Terms editor which will allow you to enter the expression or use one of the pre-defined favourites. This filter is applied to each result of the search and used as an additional filter for the search results. An example would be to retrieve only structures that have a logP of less that 5 by entering the expression logP() < 5.

Note: Chemical Terms filters are applied dynamically to the query results. If you have lots of results the search will be much slower with a Chemical Terms expression as part of the query. If you are frequently using the same Chemical Terms expressions, you should probably use a Chemical Terms Field instead so that the values are present in the database and so can be queried directly without being recalculated each time a query is run.

Query term validity

To be executed all elements of the query must be valid. When a term is first added to the query it may be in an invalid state because you have not specified the requried values.

The elements of the query term you can specify depend on the Field type. Typically you will specify the operator and one or more values. Once the terms have been correctly specified the query element will be valid.

Repeat this for all the Fields which you want to include in the complete query. If you wish to exclude a Field from the query set its operator to 'Ignore'.

Any part of the query can be collapsed to take up less space. Collapsed elements display a text summary of the current query criteria. Elements that are set to ignore are displayed as collapsed by default.

AND and OR elements

AND query term

This is a composite query term that contains simple query conditions or other composite query terms as child elements. As implied by the name all the child conditions must apply for for this type of query element. e.g. it has a meaning like this: MolWeight < 300 AND logP > 2. This type of query term must be added to another AND or OR parent element, or be the root element of the query tree. To add and AND query element you select the Entity for which you want the AND to apply (see house rule #1) from the Entity selector in the control panel and click on the 'AND' button. This allows you to build up relational queries where conditions from mulitple Entities are part of the total query. The new AND query term will be added to (or after) the currently selected element in the query tree.

OR query term

This is a composite query term that is very similar to the AND query term. The difference is that only one of the child elements needs to match for the query to apply. So the equivalet to the previous example would be MolWeight < 300 OR logP > 2, meaning that only one of the conditions need to be true, not all of them.

Expanding and collapsing query nodes

All the elements in the query tree can be expanded or collapsed as needed. Expanding showns the full details, and allows editing. Collapsing provides a descriptive summary that allows a more compact display of the query.