Kelly Peterson

Results 14 issues of Kelly Peterson

This is an initial fix for what @soldni and I have discussed with spacy and overlapping entity spans. We may want to add additional match data later in an extension...

**Describe the bug** When QuickUMLS concept matches occur over the same token, Spacy reports an error like the **To Reproduce** Using QuickUMLS version 1.5 or higher, run the following sample....

At various times, @burgersmoke and @turbosheep have noticed that if you generate QuickUMLS resources on a POSIX system (i.e. MacOS, Linux, etc) and then try to load those resources for...

…her model. This notebook does not currently appear to do anything meaningful with entities, but rather it shows how sections are detected and accessible at a Doc level. As such,...

Currently this notebook (https://github.com/medspacy/medspacy/blob/master/notebooks/section_detection/2-Adding-Sections.ipynb) does not execute because it depends on a model (en_info_3700_i2b2_2012) which has not been re-generated for spacy v3. While we could re-generate this for v3, it...

Today on a presentation from several medical professionals (work in progress so I will not name names) a significant amount of work was recently put in to validate the works...

With spacy 3.1, overlapping sections of text can now be handled. This is a common issue with clinical concepts where they may overlap and with spacy `Entity` we choose only...

These notebooks are currently being skipped for one of the following reasons: - Model used in notebook not currently loading successfully (e.g. `en_info_3700_i2b2_2012`) - Model used in notebook is fairly...

What: Add SemType/SemGroup lookup for Semantic Type IDs in medspacy (i.e. transform `T038` to `Biologic Function`) Why: Currently QuickUMLS only attaches Semantic Type IDs (e.g. T038) to extractions, but these...

enhancement

In a team discussion, we agreed that it would be great to have CI that ensures periodically (maybe every push?) that this runs without problem: ```pip install medspacy```