Latest improvements for QIAGEN Biomedical Knowledge Base

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Release date: 2023-09-12

What’s new in the QIAGEN Biomedical Knowledge Base 2023.2.1 release 

We continually develop and improve our software to deliver you, our customer, maximum value. We’re excited to share with you our latest 2023.2.1 release of QIAGEN Biomedical Knowledge Base. It features updated, curated content and third-party databases. Get step-by-step guidance with refreshed tutorials and enhanced documentation and statistics.

As always, we want to know if we can improve something. Please let us know about any feature requests or suggestions by contacting us at ts-bioinformatics@qiagen.com.

Version 2023.2.1 (September 2023)  

The new release introduces support for the QIAGEN Biomedical Knowledge Base (QIAGEN BKB) API, enabling the submission of queries to the QIAGEN-hosted query service using Python or R clients, as well as a REST API. 

 Software and documentation changes 

• Added support for the QIAGEN BKB API query service connections in Python and R clients 
• Introduced query function in R and Python clients as a main interface for query submission 
• Introduced remaining_limit function on Python and R clients that returns information on the remaining query size quota associated with your QIAGEN BKB API license 
• Updated tutorial notebooks to use QIAGEN BKB API for query execution wherever possible 
• Fixed links in QIAGEN BKB schema diagram on the Schema & Data Dictionary page 
• Adjusted query examples page to include QIAGEN BKB API-specific examples for recursive ontology queries
• Moved ontology functions to the knowledge base object and added deprecation notice to the old ontology functions 
• Changed behavior of ontology_get_parents and ontology_get_children functions to return indirect parents and children as a direct link 
• Expanded existing documentation with a section on QIAGEN BKB API service and REST API 
• Expanded causal reasoning notebook with extra statistics and graphs 
• Added support for SQLAlchemy version 2 

 

All above-mentioned materials (schema information, jupyter notebooks, query examples & documentation) are available through your MyQDI page found here: https://my.qiagendigitalinsights.com/bbp/ 

Version 2023.2 (July 2023)

Content changes

• We’ve added more than half a million relationships compared to the previous version of QIAGEN Biomedical Knowledge Base. This includes more than 600,000 findings added from ClinVar.
• To view more detailed changes, see the bkb_statistics.pdf document available from your MyQDI portal.
• This new curated content in QIAGEN Biomedical Knowledge Base matches the 2023 June (Summer) release content for QIAGEN Ingenuity Pathway Analysis.

Software changes

• Extended causal reasoning notebooks provide more graphics.
• Minor corrections have been made to tutorial notebooks and R library documentation.
• The multi_valued property of the synonym attribute of variation_type_metadata is now set correctly.
• The variation_type_metadata_pivot view now includes all related synonym values.