Integration of Structured Biological Data Sources using Biological Expression Language

Hoyt, C.; Domingo-Fernandez, D.; Mubeen, S.; Marin, J.; Konotopez, A.; Ebeling, C.; Birkenbihl, C.; Muslu, O.; English, B.; Mueller, S.; Pio De Lacerda, M.; Ali, M.; Colby, S.; Turei, D.; Palacio-Escat, N.; Hofmann-Apitius, M.

doi:10.1101/631812

bioRxiv · 10.1101/631812

Integration of Structured Biological Data Sources using Biological Expression Language

Hoyt, C.·Domingo-Fernandez, D.·Mubeen, S.·Marin, J.·Konotopez, A.·Ebeling, C.·Birkenbihl, C.·Muslu, O.·English, B.·Mueller, S.·Pio De Lacerda, M.·Ali, M.·Colby, S.·Turei, D.·Palacio-Escat, N.·Hofmann-Apitius, M.

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Abstract

BackgroundThe integration of heterogeneous, multiscale, and multimodal knowledge and data has become a common prerequisite for joint analysis to unravel the mechanisms and aetiologies of complex diseases. Because of its unique ability to capture this variety, Biological Expression Language (BEL) is well suited to be further used as a platform for semantic integration and harmonization in networks and systems biology.\n\nResultsWe have developed numerous independent packages capable of downloading, structuring, and serializing various biological data sources to BEL. Each Bio2BEL package is implemented in the Python programming language and distributed through GitHub (https://github.com/bio2bel) and PyPI.\n\nConclusionsThe philosophy of Bio2BEL encourages reproducibility, accessibility, and democratization of biological databases. We present several applications of Bio2BEL packages including their ability to support the curation of pathway mappings, integration of pathway databases, and machine learning applications.\n\nTweetA suite of independent Python packages for downloading, parsing, warehousing, and converting multi-modal and multi-scale biological databases to Biological Expression Language

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Hoyt, C., Domingo-Fernandez, D., Mubeen, S., Marin, J., Konotopez, A., Ebeling, C., Birkenbihl, C., Muslu, O., English, B., Mueller, S., Pio De Lacerda, M., Ali, M., Colby, S., Turei, D., Palacio-Escat, N., Hofmann-Apitius, M.. 2019-05-08. Integration of Structured Biological Data Sources using Biological Expression Language. https://doi.org/10.1101/631812

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