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.

3.0 Beta #3

Third Beta release for BioMedICUS 3.0.

• Fixed an issue that caused the sentences module to fail on unknown characters.
• Wrapper script which enables launching java against the included biomedicus jar.
• Initial baseline negation module provided by NegEx.

To install:

pip install biomedicus==3.0b3\[torch]

Installation instructions are available on our website.

More-comprehensive models are available from https://athena.ahc.umn.edu/biomedicus-downloads/ for verified UMLS licensees.

3.0 Beta 2

The second beta release for biomedicus 3.0.

Includes the multithreaded pipeline runner from MTAP.

3.0 Beta 0

First beta release of BioMedICUS 3.0 using our new processing framework MTAP.

Installation instructions are available on our website.

More-comprehensive models are available from https://athena.ahc.umn.edu/biomedicus-downloads/ for verified UMLS licensees.