BioDWH2: An Automated Graph-Based Data Warehouse and Mapping Tool
BioDWH2 is an easy-to-use, automated, graph-based data warehouse and mapping tool for bioinformatics and medical informatics. It is developed to be usable out of the box without any prerequisites except a suitable Java Runtime.
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Workspace
The simple and clean workspace structure helps you keep all data in one place. Easily configure which data sources you need and BioDWH2 will take care of the rest.
Up-To-Date
Make use of the latest information with automated data source updates. BioDWH2 checks for new data source versions and can update them if necessary. Wish to keep the workspace as it is at the end of a research project? No problem, updates can easily be disabled.
Mapped
The data source modules of BioDWH2 provide mapping descriptions for the most common entities and relationships. A mapping layer is generated automatically, connecting heterogeneous data sources and helping to uncover new and meaningful information.
Ready for Analysis
The resulting graph database is ready to be analyzed with your favorite tools. Starting from the mapping layer, or diving deep into the data sources, all in one graph.
Citing BioDWH2
If you make use of BioDWH2 or it's companion tools as part or your research cite the BioDWH2 manuscript in any resulting publications.
- Friedrichs M. BioDWH2: an automated graph-based data warehouse and mapping tool. Journal of Integrative Bioinformatics. 2021;18(2):167-176. DOI: 10.1515/jib-2020-0033
- Friedrichs M. Automation in graph-based data integration and mapping. In: Chen M, Hofestädt R, eds. Integrative Bioinformatics. Springer Singapore; 2022:97-110. DOI: 10.1007/978-981-16-6795-4_5
Worflow Overview
Analysis & Tools
| BioDWH2-Neo4j-Server | BioDWH2-OrientDB-Server | BioDWH2-ArcadeDB-Server | BioDWH2-GraphQL-Server | BioDWH2-SQL-Exporter | Direct GraphML Access | |
|---|---|---|---|---|---|---|
| Version |  |
 |
 |
 |
 |
- |
| Database | Neo4j Community Embedded | OrientDB Community Embedded | ArcadeDB Embedded | BioDWH2 Graph + GraphQL Java | (Depending on used SQL server) | - |
| Interface | Neo4j Browser | OrientDB Studio | ArcadeDB Studio |
GraphQL Playground, GraphiQL |
(Depending on used SQL server) | - |
| Commercial Use |
Depending on use-case[1] |
Apache 2 License[2] |
Apache 2 License[3] |
MIT License[4] |
(Depending on used SQL server) |
|
| Limitations | - | - | No array property indices | - | Name length limits | No DBMS |