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Latest improvements for QIAGEN Biomedical Knowledge Base

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Release date: 2022-09-27

Version 2023.2.1 (September 2023)

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.

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

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.

 

Version 2023.1

Content changes

  • We’ve added nearly half a million relationships compared to the previous version of QIAGEN Biomedical Knowledge Base. This includes more than 100,000 findings from gov and more than 150,000 findings added from ClinVar
  • For more detailed changes, please visit the document ‘bkb_statistics.pdf’ via your MyQDI portal)
  • This new curated content in QIAGEN Biomedical Knowledge Base matches the 2023 March release content for QIAGEN Ingenuity Pathway Analysis

Software changes

  • We’ve added new indexes to the SQLite database for faster common queries
  • We’ve improved the Neo4j export functionality, so it now supports the neo4j engine 5

Version 2022.4

We’re excited to announce our latest release featuring updated, curated content and third-party databases. Get step-by-step guidance with refreshed tutorials and enhanced documentation and statistics.

Looking for something specific? Send us your feature requests or suggestions at ts-bioinformatics@qiagen.com and let us help you achieve your research goals.

Content changes

We updated the curated content to match the QIAGEN Ingenuity Pathway Analysis (IPA) 2022 Q4 release content:

  • We added more than 1M Ingenuity Expert Findings to the findings_metadata table
  • We added more than 200K Ingenuity-supported third-party information findings to the findings_metadata table
  • We updated several integrated third-party sources to newer versions, including BioGRID, CDD, ClinVar, ClinicalTrials.gov, Gene Ontology, IntAct and NCI Thesaurus

Software and documentation changes

  • The functionality for causal analysis is now also available for R. For an example of how to use this, see the ‘Causal Reasoning (R)’ R Studio notebook
  • You can now find detailed statistics for the changes of entities and relationships between versions in the bkb_statistics.pdf document
  • The R documentation is now better organized when shown in, e.g., R Studio

Version 2022.3

Content changes:

The curated content has been updated to match the IPA 2022 Q3 release content

  • A new biomarker_disease_drug table has been added. This table describes interactions between biomarker molecules and diseases with or without a drug context for the interaction
  • An issue regarding the gene_cell_line_location, gene_tissue_primary_cell_location, gene_biofluid_location, gene_subcellular_location tables has been fixed. Previously, these tables included experimental observations stating a gene was not observed in the specified location. This observation was only evident from the natural_language_string in the finding_metadata table. These relations have been removed
  • The molecule_disease_and_function_relationships_aggregated_findings, molecule_molecule_relationships_aggregated_findings and pathway_relationships_aggregated_findings tables have been renamed as follows: molecule_disease_and_function_relationships_aggregated_relationships, molecule_molecule_relationships_aggregated_relationships and pathway_relationships_aggregated_relationships. These tables now refer to relationship_ids instead of finding_ids.
  • Additional mappings of entities to Mondo Disease Ontology (MONDO), Experimental Factor Ontology (EFO) and Human Phenotype Ontology (HPO) have been included

Software changes:

  • New Python functions for causal analysis have been added. For an example of how to use these, see the “Causal Reasoning (Python)” Jupyter Notebook
  • New R and Python functions are available for visualizing pathways and genes in IPA. For an example of how to use these, see the IPA integration section on the Example Queries web page
  • Neo4j export has been updated to include new content

 

Version 2022.2.2

Content changes:

The curated content has been updated to match the IPA 2022 Q2 release content

  • New tables have been added for biofluids, cell lines, subcellular location, tissue, primary cell and tox lists: biofluid_metadata, biofluid_ontology, cell_line_metadata, cell_line_ontology, gene_biofluid_location, gene_cell_line_location, gene_subcellular_location, gene_tissue_primary_cell_location, subcellular_location_metadata, subcellular_location_ontology, tissue_primary_cell_metadata, tissue_primary_cell_ontology, gene_toxlist, toxlist_metadata, variation_type_metadata, variation_type_ontology
  • The gene_molecular_function and pathway_node tables now have a different column structure, corresponding to the structure of the existing relationship tables
  • The pathway tables now include metabolic pathways
  • The drug_target_disease_relationships table now includes target_high_level_id and target_high_level_name columns. The table also now includes additional drug-target and drug-disease relationships for which a full drug-target-disease relationship does not exist

Software changes:

  • New example notebooks have been added: GSEA (R), GSEA (Python), Explore a Disease and Explore a Gene
  • New convenience functions for mapping external IDs to QIAGEN IDs (Python, R) have been added. For an example of how to use these, see the new GSEA notebooks
  • New convenience functions for extracting gene sets from pathways, diseases and functions (Python, R) have been added. For an example of how to use these, see the new GSEA notebooks
  • An issue with Neo4j graph export in which relations of the drug_target_disease type were duplicated for each clinical trial sponsor has been fixed

 

Version 2022.2.1

Content changes:

  • New aggregated tables for pathway_relationships have been added: pathway_relationships_aggregated, pathway_relationships_aggregated_findings
  • An issue with molecule_molecule_relationships in which some locations had “shadow filter” labels has been fixed
  • Minor fixes and updates were made to finding_metadata; most notably the source column now refers to the source from which the content was directly acquired
  • An issue with pathway_relationships in which some relationship_type entries would be missing from the table has been fixed

Software changes:

  • R Package error handling when the SQLite database file cannot be found has been improved: instead of creating an empty file, an error message is displayed
  • An issue with Neo4j export in which the drug_target_disease.trial_sponsor property name was suffixed by another column name has been fixed

 

Version 2022.2.0

First release.

Sample to Insight