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PyBEL: a computational framework for Biological Expression Language.
Hoyt CT, Konotopez A, Ebeling C, Wren J. Hoyt CT, et al. Bioinformatics. 2018 Feb 15;34(4):703-704. doi: 10.1093/bioinformatics/btx660. Bioinformatics. 2018. PMID: 29048466 Free PMC article.
SUMMARY: Biological Expression Language (BEL) assembles knowledge networks from biological relations across multiple modes and scales. ...
SUMMARY: Biological Expression Language (BEL) assembles knowledge networks from biological relations across mult …
BEL2ABM: agent-based simulation of static models in Biological Expression Language.
Gündel M, Hoyt CT, Hofmann-Apitius M. Gündel M, et al. Bioinformatics. 2018 Jul 1;34(13):2316-2318. doi: 10.1093/bioinformatics/bty107. Bioinformatics. 2018. PMID: 29949955 Free PMC article.
SUMMARY: While cause-and-effect knowledge assembly models encoded in Biological Expression Language are able to support generation of mechanistic hypotheses, they are static and limited in their ability to encode temporality. ...
SUMMARY: While cause-and-effect knowledge assembly models encoded in Biological Expression Language are able to support …
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.
Hoyt CT, Domingo-Fernández D, Hofmann-Apitius M. Hoyt CT, et al. Database (Oxford). 2018 Jan 1;2018:bay126. doi: 10.1093/database/bay126. Database (Oxford). 2018. PMID: 30576488 Free PMC article.
While several web applications exist with various focuses on creation, revision, curation, storage, integration, collaboration, exploration, visualization and analysis, many of these services remain disjoint and have yet to be packaged into a cohesive environment.Here, we present …
While several web applications exist with various focuses on creation, revision, curation, storage, integration, collaboration, exploration, …
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.
Hoyt CT, Domingo-Fernández D, Aldisi R, Xu L, Kolpeja K, Spalek S, Wollert E, Bachman J, Gyori BM, Greene P, Hofmann-Apitius M. Hoyt CT, et al. Database (Oxford). 2019 Jan 1;2019:baz068. doi: 10.1093/database/baz068. Database (Oxford). 2019. PMID: 31225582 Free PMC article.
We applied these workflows to the KGs encoded in Biological Expression Language from the NeuroMMSig database using content that was pre-extracted from MEDLINE abstracts and PubMed Central full-text articles using text mining output integrated by INDRA. ...
We applied these workflows to the KGs encoded in Biological Expression Language from the NeuroMMSig database using cont …
Coreference resolution improves extraction of Biological Expression Language statements from texts.
Choi M, Liu H, Baumgartner W, Zobel J, Verspoor K. Choi M, et al. Database (Oxford). 2016 Jul 3;2016:baw076. doi: 10.1093/database/baw076. Print 2016. Database (Oxford). 2016. PMID: 27374122 Free PMC article.
We describe a system that automatically extracts biological events from biomedical journal articles, and translates those events into Biological Expression Language (BEL) statements. The system incorporates existing text mining components for coreferen …
We describe a system that automatically extracts biological events from biomedical journal articles, and translates those events into …
The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track.
Madan S, Szostak J, Komandur Elayavilli R, Tsai RT, Ali M, Qian L, Rastegar-Mojarad M, Hoeng J, Fluck J. Madan S, et al. Database (Oxford). 2019 Jan 1;2019:baz084. doi: 10.1093/database/baz084. Database (Oxford). 2019. PMID: 31603193 Free PMC article.
Knowledge of the molecular interactions of biological and chemical entities and their involvement in biological processes or clinical phenotypes is important for data interpretation. ...Biological expression language (BEL) is a syntax representa …
Knowledge of the molecular interactions of biological and chemical entities and their involvement in biological processes or c …
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.
Rinaldi F, Ellendorff TR, Madan S, Clematide S, van der Lek A, Mevissen T, Fluck J. Rinaldi F, et al. Database (Oxford). 2016 Jul 9;2016:baw067. doi: 10.1093/database/baw067. Print 2016. Database (Oxford). 2016. PMID: 27402677 Free PMC article.
Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biologica
Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and med …
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL).
Fluck J, Madan S, Ansari S, Kodamullil AT, Karki R, Rastegar-Mojarad M, Catlett NL, Hayes W, Szostak J, Hoeng J, Peitsch M. Fluck J, et al. Database (Oxford). 2016 Aug 23;2016:baw113. doi: 10.1093/database/baw113. Print 2016. Database (Oxford). 2016. PMID: 27554092 Free PMC article.
Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high-quality training data. Here, we describe the new corpora in the systems biology modeling language BEL for training and testing bio
Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high- …
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences.
Ravikumar KE, Rastegar-Mojarad M, Liu H. Ravikumar KE, et al. Database (Oxford). 2017 Jan 1;2017(1):baw156. doi: 10.1093/database/baw156. Database (Oxford). 2017. PMID: 28365720 Free PMC article.
In this work, we tested the ability of a rule-based semantic parser to extract Biological Expression Language (BEL) statements from evidence sentences culled out of biomedical literature as part of BioCreative V Track4 challenge. ...
In this work, we tested the ability of a rule-based semantic parser to extract Biological Expression Language (BEL) sta …
BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text.
Lai PT, Lo YY, Huang MS, Hsiao YC, Tsai RT. Lai PT, et al. Database (Oxford). 2016 May 12;2016:baw064. doi: 10.1093/database/baw064. Print 2016. Database (Oxford). 2016. PMID: 27173520 Free PMC article.
Biological expression language (BEL) is one of the most popular languages to represent the causal and correlative relationships among biological events. ...
Biological expression language (BEL) is one of the most popular languages to represent the causal and correlative relat
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