Fraunhofer Institute for Algorithms and Scientific Computing SCAI
Fraunhofer Institute for Algorithms and Scientific Computing SCAI

BiK>Mi – Biomedical Knowledge Miner

BiK>Mi


For more information please visit the BiK>Mi Homepage.
 

Please also visit the COVID-19 Biomedical Knowledge Miner

About

The Biological Knowledge Miner (BiK>Mi) is a comprehensive user interface for exploring the annotated and enriched knowledge graphs generated by e(BE:L).
 

In addition to its ability to retrieve key data on specific drugs, proteins, and other biological entities, BiK>Mi also has tools available for extracting BEL statements based on user-defined criteria, for visualizing the embedded subgraphs and networks, and for comparing user-generated gene expression data against the manually curated relationships stored within.

BiK>Mi Features

© Fraunhofer SCAI
© Fraunhofer SCAI

Workspace

Our knowledge graphs are comprised of context-specific biological interactions, and BiK>Mi includes a specialized feature for comparing experimental data against these relationships. Currently, the BiK>Mi Workspace enables one to upload gene expression data and compare the relationship of a given gene pair with that in the knowledge graph. This tool can be modified to work with other experimental data formats upon request.
 

Tools

  • Protein Profiler – Detailed compilation of metadata pertaining to a queried protein. Presented data are comprised of information derived from several notable resources including UniProt, EnsEMBL, OMIM, HGNC, and more.
  • Protein List – Summary table for comparing metadata between a list of proteins. Here, one can also view drugs that target queried proteins derived from DrugBank.
  • BELish – Custom BEL statement builder used to query our knowledge graphs for matching statements.
  • Path – Network visualization comprised of extracted relationships and interactions based on one of the following criteria: paths between a given pair of source and target nodes, the last author of a publication, metadata of a specific publication. Here, one can explore the contextual provenance of individual edges and compare how specific relationships compare against uploaded experimental data.
     

Project-Specific Instances

Because the needed analytical tools will vary from project to project, BiK>Mi can be modified to include novel workflows and pipelines for a given deliverable or milestone. Contact us if you are interested in integrating our knowledge graphs into your project or to inquire what tools can be developed for BiK>Mi to better access and explore the available data.