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QIAGEN Biomedical Knowledge Base

Release date: 2022-09-27

What’s New in the QIAGEN Biomedical Knowledge Base Release 2022.3 (October 2022)

The latest release of the QIAGEN Biomedical Knowledge Base contains updates to nearly all content tables and now includes biomarker information as well. As part of the software update, we added Python implementations of the Upstream Regulator Analysis, Downstream Effect Analysis and Causal Networks Analysis known from QIAGEN Ingenuity Pathway Analysis (IPA) (see Krämer, A., Green, J., Pollard, Jr., J. and Tugendreich, S. (2014) Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics 30:5230). We also offer functionality for programmatically visualizing genes and pathways in IPA. Additionally, the Neo4j export functionality has been extended with more content and new configuration options.

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 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.