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References
==========
If you find PyBEL useful for your work, please consider citing [1]_:
.. [1] Hoyt, C. T., *et al.* (2017). `PyBEL: a Computational Framework for Biological Expression Language
<https://doi.org/10.1093/bioinformatics/btx660>`_. Bioinformatics, 34(December), 1–2.
Related Publications
--------------------
We have used PyBEL in several other projects and publications. Below is a sample:
- Domingo-Fernández, D., Mubeen, S., Marin-Llao, J., Hoyt, C. T., & Hofmann-Apitius, M. (2018). PathMe: Merging and
exploring mechanistic pathway knowledge. bioRxiv, 451625.
- Domingo-Fernández, D., Hoyt, C. T., Alvarez, C. B., Marin-Llao, J., Hofmann-Apitius, M. (2018). ComPath: an ecosystem
for exploring, analyzing, and curating mappings across pathway databases. Npj Systems Biology and Applications,
5(1), 3. https://doi.org/10.1038/s41540-018-0078-8
- Hoyt, C. T., et al. (2018). A systematic approach for identifying shared mechanisms in epilepsy and its
comorbidities. Database, 2018(1). https://doi.org/10.1093/database/bay050
- Hoyt, C. T., et al. (2019). Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression
Language. BioRxiv, 536409. https://doi.org/10.1101/536409
- Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). BEL Commons: an environment for exploration and
analysis of networks encoded in Biological Expression Language. Database, 2018(3), 1–11.
https://doi.org/10.1093/database/bay126
- Ali, M., et al. (2019). BioKEEN: A library for learning and evaluating biological knowledge graph embeddings.
Bioinformatics, btz117. https://doi.org/10.1093/bioinformatics/btz117
Software using PyBEL
--------------------
- https://github.com/cthoyt/bel-repository
- https://github.com/bio2bel
- https://github.com/sorgerlab/indra
- https://github.com/smartDataAnalytics/biokeen
BEL Content
-----------
- https://github.com/neurommsig/neurommsig-knowledge
- https://github.com/pharmacome/knowledge
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