clinspacy
Clinical Natural Language Processing using 'spaCy', 'scispaCy', and 'medspaCy'
Description
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) <arXiv:1804.01486>.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
CRAN incoming feasibility
Maintainer: ‘Karandeep Singh <kdpsingh@umich.edu>’ The Description field contains embeddings developed by Beam (2018) <arXiv:1804.01486>. Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
CRAN incoming feasibility
Maintainer: ‘Karandeep Singh <kdpsingh@umich.edu>’ The Description field contains embeddings developed by Beam (2018) <arXiv:1804.01486>. Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
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NOTE 9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
CRAN incoming feasibility
Maintainer: ‘Karandeep Singh <kdpsingh@umich.edu>’ The Description field contains embeddings developed by Beam (2018) <arXiv:1804.01486>. Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
CRAN incoming feasibility
Maintainer: ‘Karandeep Singh <kdpsingh@umich.edu>’ The Description field contains embeddings developed by Beam (2018) <arXiv:1804.01486>. Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
LazyData
'LazyData' is specified without a 'data' directory
LazyData
'LazyData' is specified without a 'data' directory
LazyData
'LazyData' is specified without a 'data' directory