High-Performance Open-Source Archive
Performs biomedical named entity recognition, Unified Medical Language System (UMLS) concept mapping, and negation detection using the Python 'spaCy', 'scispaCy', and 'medspaCy' packages, and transforms extracted data into a wide format for inclusion in machine learning models. The development of the 'scispaCy' package is described by Neumann (2019) <doi:10.18653/v1/W19-5034>. The 'medspacy' package uses 'ConText', an algorithm for determining the context of clinical statements described by Harkema (2009) <doi:10.1016/j.jbi.2009.05.002>. Clinspacy also supports entity embeddings from 'scispaCy' and UMLS 'cui2vec' concept embeddings developed by Beam (2018) <doi:10.48550/arXiv.1804.01486>.
| Version: | 1.0.2 |
| Depends: | R (≥ 2.10) |
| Imports: | reticulate (≥ 1.16), data.table, assertthat, rappdirs, utils, magrittr |
| Suggests: | knitr, rmarkdown |
| Published: | 2021-03-20 |
| DOI: | 10.32614/CRAN.package.clinspacy |
| Author: | Karandeep Singh [aut, cre], Benjamin Kompa [aut], Andrew Beam [aut], Allen Schmaltz [aut] |
| Maintainer: | Karandeep Singh <kdpsingh at umich.edu> |
| BugReports: | https://github.com/ML4LHS/clinspacy/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/ML4LHS/clinspacy |
| NeedsCompilation: | no |
| Materials: | README, NEWS |
| CRAN checks: | clinspacy results |
| Reference manual: | clinspacy.html , clinspacy.pdf |
| Package source: | clinspacy_1.0.2.tar.gz |
| Windows binaries: | r-devel: clinspacy_1.0.2.zip, r-release: clinspacy_1.0.2.zip, r-oldrel: clinspacy_1.0.2.zip |
| macOS binaries: | r-release (arm64): clinspacy_1.0.2.tgz, r-oldrel (arm64): clinspacy_1.0.2.tgz, r-release (x86_64): clinspacy_1.0.2.tgz, r-oldrel (x86_64): clinspacy_1.0.2.tgz |
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