Release 3.4.2

Support for deploying the e2e pipeline using the docker image.

Release 3.4.0

Added the End-to-end REST pipeline service, described here: https://nlpie.github.io/biomedicus/docs/deploy-pipeline.html.

Release 3.3.0

What's Changed

• Updated concepts to UMLS 2023AA
• Fixed an issue with overlapping annotations for the same concepts
• Dependency Updates

Breaking Changes

• Removed support for Python 3.8 from biomedicus (deprecated, numpy no longer receiving updates on 3.8)

Full Changelog: v3.2.1...v3.3.0

Release 3.2.1

What's Changed

• Dependency Updates (Torch 2.0, rocksdb 8.0)
• Supports Python 3.8-3.11 now
• Switched to performing negation detection using only negex by default.
• Updated to MTAP 1.2.1. This introduces some breaking changes, click on the link for more info.
• Moved everything in biomedicus_client.pipeline to biomedicus_client package.
• Renamed some built-in pipeline and deployment configuration files (-conf.yml to .yml)

Release Milestone: https://github.com/nlpie/biomedicus/milestone/15?closed=1
Full Changelog: v3.1.0...v3.2.1

3.1.0

What's Changed

• Dependencies for release versions are now pinned for more stable releases.
• Fix for a number of RTF reader formatting issues. (#140, #141)
• Fixed an issue where the sentences processor would fail when CUDA is available (#142)
• Fixed an issue where deepen was failing due to incorrect offset indices on dependencies (#138)

Full Changelog: v3.0.0...v3.1.0

3.0.0

Initial public release.

3.0 Release Candidate 4

What's Changed

• Downloads stanza models earlier by @benknoll-umn in #117

Full Changelog: v3.0.0-rc.3...v3.0.0-rc.4

3.0 Release Candidate 3

Various bug fixes (Mainly RTF). Made it easier to programmatically create pipelines and use custom input sources. Better logging messages around configuration.

Breaking change:
The biomedicus run command argument for the output directory has switched to an option -o. The correct syntax is now

biomedicus run /path_to/input_dir/ -o /path_to/output_dir/ 

This is because the option is only used in the case of a serializer (default: json) and if the serializer is set to none the option will not be used.

3.0 Beta #6

This update contains the following enhancements for BioMedICUS

• Better negation detection via an adapted implementation of parsing-sensitive DEEPEN algorithm.
• Improvements to concept detection and vocabularies updated to UMLS 2020AA.
• BioMedICUS 2.x simple rule-based regex patterns section header detection.
• Fixed a bug which could potentially cause time-outs during deployment.

3.0 Beta #5

The fifth beta release for biomedicus 3.0.

• Negation via NegEx algorithm.
• Fixed an issue with normalized term concept detection.
• Added --host parameters to both "biomedicus deploy" and "biomedicus run". To host on the public IP use "biomedicus deploy 0.0.0.0".
• Fixed an issue where downloading would fail if ~/.biomedicus/data existed without a version file.
• Added dependency parsing via Stanford Stanza.
• Can execute java applications against a classpath containing the biomedicus Java jar by using "biomedicus java -- edu.umn.biomedicus.rtf.RtfProcessor --events localhost:50100 --port 50101" for example.
• Various other bug fixes.