Tutorial
Last updated
Last updated
You can input CMNPD ID (compound ID, organism ID, target ID or document ID), compound name, organism name, or target name in the search bar for quick search. The bar will provide some suitable suggestions as you type. You can do a quick search at any time because the search bar appears on all pages.
Use the Query Builder to create or modify queries. Specify the domain you want to query, you can search by structure, compound representations, physicochemical properties, ADMET prediction, resources, bioactivities and bibliography separately or in combination.
Before using Query Builder, you should understand the meaning and threshold of each parameter. The FAQ-Parameter Questions section will provide you with some reference information. You can also learn more by browsing the database.
You can draw a structure by Marvin JS sketcher and then do an exact search, substructure search or similarity search. In addition, you can upload a molecular file or paste SMILES to import a chemical structure.
You can select several query conditions to do a text search. Some of them have both text entry and browse functions so that you have the choice of typing in a search term or selecting from the index.
You can search by combining a drawn structure with another parameter or set of parameters.
All query conditions are connected via the Boolean operator AND (OR and NOT are optional). Drag and drop one condition onto another to group them together. The internal Boolean operations of the grouped conditions will be executed first. Using Boolean operators and conditions grouping effectively will greatly improve your search results, by making the results more specific.
Understanding the concept of Set (mathematics) will help you make better use of our Query Builder. Here we will use an example to illustrate how to obtain specific search results with Boolean operators.
e.g. If you want to search for compounds produced by organisms other than bacteria and fungi and whose molecular weight ≤ 500, you can use the following query settings:
In Boolean operations, CMNPD is regarded as the universal set U, and different query conditions are considered as subsets A, B, C, etc. Therefore, this search can be represented by the following Venn diagram:
Subset A (circle) represents bacterial compounds
Subset B (circle) represents fungal compounds
Subset C (rectangle) represents compounds with molecular weight ≤ 500
The logic of Boolean operations is as follows:
Step 1. Boolean operation OR. As you group the query conditions A and B together, the system preferentially calculates the union of A and B.
Step 2. Boolean operation NOT. Next, the calculation is performed in order from top to bottom to get the complement of (A∪B) in U.
Step 3. Boolean operation AND. Finally the system calculates the intersection of C and the above subset.
You can quickly view the list of all compounds, documents, targets and organisms in CMNPD through the Browse button on the toolbar.
There are four types of report card pages that can provide you with detailed information about each compound, document, organism and target. You can enter relevant pages through internal links in the full list page, search results page, and another report card page.
In order to show in a better way what is inside CMNPD we have created some data visualizations. You can see them by Visualization button on the toolbar.
There will be a short instruction above each chart to guide you how to use the visualization tools.
A visual overview of the topological relationship between organisms, compounds and targets. Select a master node and then click the submit button to generate a network. Click on a node to explore the details.
CMNPD data is available for bulk download in the Downloads section.
You can customize the compound download list through the advanced search and manual selection.
A deposit account is required in order to submit data to CMNPD. You must agree to the Submission Policy when you create an account.
After logging in, you will see the submission interface. In the upper left corner, you can choose to submit new compounds, new data for existing compounds or corrections. The submission history can be viewed by clicking Your deposit.
