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Integration of Structured Biological Data Sources using Biological Expression Language | bioRxiv
New Results
Integration of Structured Biological Data Sources using Biological Expression Language
View ORCID ProfileCharles Tapley Hoyt, View ORCID ProfileDaniel Domingo-Fernández, View ORCID ProfileSarah Mubeen, View ORCID ProfileJosep Marin Llaó, View ORCID ProfileAndrej Konotopez, View ORCID ProfileChristian Ebeling, View ORCID ProfileColin Birkenbihl, View ORCID ProfileÖzlem Muslu, View ORCID ProfileBradley English, View ORCID ProfileSimon Müller, View ORCID ProfileMauricio Pio de Lacerda, View ORCID ProfileMehdi Ali, View ORCID ProfileScott Colby, View ORCID ProfileDénes Türei, View ORCID ProfileNicolàs Palacio-Escat, View ORCID ProfileMartin Hofmann-Apitius
doi: https://doi.org/10.1101/631812
Abstract
Background The 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.
Results We 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.
Conclusions The 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.
Tweet A suite of independent Python packages for downloading, parsing, warehousing, and converting multi-modal and multi-scale biological databases to Biological Expression Language
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
It is made available under a CC-BY 4.0 International license.
