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Utilized workflow systems and integration tools therefore need to process large amounts of heterogeneous data formats, check for data source updates, and find suitable mapping methods to cross-reference entities from different databases. This article presents BioDWH2, an open-source, graph-based data warehouse and mapping tool, capable of helping researchers with these issues. A workspace centered approach allows project-specific data source selections and Neo4j or GraphQL server tools enable quick access to the database for analysis. The BioDWH2 tools are available to the scientific community at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/BioDWH2\">https:\/\/github.com\/BioDWH2<\/jats:ext-link>.<\/jats:p>","DOI":"10.1515\/jib-2020-0033","type":"journal-article","created":{"date-parts":[[2021,2,22]],"date-time":"2021-02-22T23:18:21Z","timestamp":1614035901000},"page":"167-176","source":"Crossref","is-referenced-by-count":11,"title":["BioDWH2: an automated graph-based data warehouse and mapping tool"],"prefix":"10.1515","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9846-7212","authenticated-orcid":false,"given":"Marcel","family":"Friedrichs","sequence":"first","affiliation":[{"name":"Bielefeld University, Faculty of Technology, Bioinformatics \/ Medical Informatics Department , Bielefeld , Germany"}]}],"member":"374","published-online":{"date-parts":[[2021,2,22]]},"reference":[{"key":"2023033120073843701_j_jib-2020-0033_ref_001","doi-asserted-by":"crossref","unstructured":"Imker, HJ. 25 Years of molecular biology databases: a study of proliferation, impact, and maintenance. 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