Compound Registration

Normalize, check, validate and register your chemical compounds.


Streamline your chemical decision-making processes

Compound Registration compares the uniqueness of new small molecules against those already stored in your database. It then kickstarts a decision workflow based on your configured business logic.

The system includes a database (the registry), which stores the relevant structural and accompanying information. Compounds pass through normalization, validation and quality check before registration. If issues can’t be fixed automatically, they fall into a staging area for manual intervention. Upon successful registration, you can store the compound in a three-level hierarchy.

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Why you need Compound Registration


Register compounds individually or in bulk

Add new compounds one-by-one through the web-based registration form or in bulk via the upload page. The system handles single and multi-component structures (two or more independently registered components) with all the validated custom data fields. It supports alternates, mixtures, formulations and polymers.

You can access the registration system from other applications. The publicly available web service API makes integration (typically with an ELN) straightforward, but the service is also accessible via KNIME and Pipeline Pilot workflow tools.



Validate and check unique structures

Compound structures go through a series of standardization, validation and quality checking steps before registration. These include valence error checks and auto-fixes for representation issues.

You can also validate external IDs and other specified data based on your unique business logic. Compounds that don't pass the validation phase or can't be fixed automatically fall into the Staging Area for manual revision.

After validation, the system compares newly submitted chemical structures with the records in the registry. Match types include exact matches, stereoisomers, tautomeric structures and their combinations. If a structure is unknown or only partially known, the system fills gaps with Chemically Significant Text (CST).



Store compounds in a hierarchical structure

The system stores registered compounds in a three-level hierarchical structure of parents, versions and lots (or batches). In this construction, a version may describe an isotopic or salt/solvate variation of a parent, while a lot may represent different production batches of a version.

Salts and solvates are managed in a dedicated dictionary. You can easily specify salts and solvates along with their appropriate multiplicity during the registration, or extract it from the submitted chemical structure.

Read more about parents, versions and lots via the link below



Amend registered entities

Your authorized users can alter the molecular structure or data of a compound in the registry, stored on different hierarchy levels. The amendments you commit to the registry are fully audited. You can also request a complete data history for selected entries.



Deploy, configure and integrate with ease

The Compound Registration system can be deployed to a web server as a typical web application. The publicly available REST API enables simple integration into an existing IT environment. The registration database currently supports Oracle or MySQL RDBMS and utilizes JChem tables and additional relational tables for capturing the data.

To enhance the integration capability with downstream databases and processes, Compound Registration offers a publishing engine to mirror its content in flexible formats (downstream RDBMS, xml, sdf).

You can configure large parts of the internal business logic to facilitate easy adoption and comply with your corporate business rules. The system offers a web interface for all the exposed configuration options. It also provides typical authentication modes, as well as a combination of role-based access control and permission handling based on project memberships.

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Knowledge Hub


Learn more about Compound Registration

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