v0.5.0

Highlights

caDSR CDE JSON imports

Ingests the output of caDSR API <https://cadsrapi.cancer.gov/rad/NCIAPI/1.0/api>_.

Note: this doesn't yet talk to the API so you need to download these yourself. See the Makefiles in https://github.com/monarch-initiative/cde-harmonization for examples.

• Each CDE becomes a unique slot
• the CDE is added as a lot of a context-specific class
• the context-specific class is a subclass of the CDE's DataElementConcept

Note that this creates a lot of 1-1 classes, as in many cases there is no
attempt to group concepts. However, this is not always the case.

E.g. the concept with publicId 2012668 (Access Route) is used in 5 contexts
(AHRQ, CCR, ...)

Each context-specific concept has its own set of CDEs

The resulting LinkML can also be converted to OWL for easier browsing:

What's Changed

• bump to linkml 1.7.x series
• Adding myst parser by @cmungall in #128
• cadsr importer by @cmungall in #132
• Add codespell config and workflow and fix a few typos by @yarikoptic in #129

New Contributors

• @yarikoptic made their first contribution in #129

Full Changelog: v0.4.0...v0.5.0