What is it?
BChemXtract is open-source, community-led software, including curated look up tables (libraries), to assist in the transformation of chemical structures into FAIR machine-readable data.
Tool ID card
- Main purpose: to provide a fully open source workflow for the digitalization and FAIRification of chemical information
- Who is it for? Our current software is intended for use by chemistry journals and experts in cheminformatics. However, we are currently preparing a webdemo version where anyone, including users with no programming expertise, can use the app to digitize their chemical structures
- Skill level: currently for researchers with knowledge of ChemDraw files and programming skills; soon to be available for all skill levels
- Access:
- Description: Open Source - Beilstein-Institut
- Download the open source project: GitHub - Beilstein-Institut/BChemXtract: Pure-Java ChemDraw Parser and Extraction Software · GitHub
- Key features: The open-source Java-based tool BChemXtract allows for paring and extraction of chemical structures and reactions from ChemDraw (CDX and CDXML) files and calculates important information for the digitization of chemical structures (e.g. InChI, SMILES).
What can I do with it?
- Read ChemDraw files as well as extract and validate chemical structures and reactions from the parsed file
- Enrich structures and reactions with calculated chemical descriptors such as InChI and SMILES
- Process your chemical structure information within the limits of current chemical standards
- Contribute to standardization and FAIRification of chemical data, enabling other users to access, reuse and build on what is already available
Good to know
Although BChemXtract was initially conceptualized with the purpose of extracting chemical structures, making them machine-readable and FAIR to be embedded back into the Beilstein diamond-open-access journals, this tool was developed and released as a stand-alone software toolkit with an MIT license. Therefore, it could be integrated into any publishing system or publishing workflow. However, it is not limited to journal publishing. Other applications may include extraction of structures related to dissertations or other documents. Given that the CDX/CDXML file format is by far the most popular format that chemists use to draw their structures, the applications are far reaching.
Try it if you…
… work as (or with):
- Publishers and editorial teams: by integrating the toolkit into publishing platforms to automatically extract and standardize chemical structures from submitted manuscripts
- Cheminformaticians and software developers: by using the tool to parse ChemDraw files
- Researchers and data scientists in chemistry: by processing and turning visual/static chemical drawings into machine-readable curated and FAIR data.
- Educators: by utilizing the open-source toolkit to convert ChemDraw laboratory reactions and molecular structures into clean, standardized formats to teach cheminformatics or improve currently available datasets.