Releases: linkml/schema-automator
Releases · linkml/schema-automator
v0.5.2
v0.5.1
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
Contributors
yarikoptic and cmungall
Assets 2
v0.4.0
What's Changed
- Remove Bioregistry dependency and update OAK dependency by @cthoyt in #121
- Adding LLMAnnotator by @cmungall in #126
Example:
from schema_automator.utils.schemautils import write_schema
annotator = LLMAnnotator(model_name="gpt-4")
schema = annotator.enrich("tests/resources/biopax3.yaml")
write_schema(schema)New Contributors
Full Changelog: v0.3.0...v0.4.0
Contributors
cmungall and cthoyt
Assets 2
v0.3.1
v0.3.0
What's Changed
- removing unused files by @cmungall in #71
- update pypi release action by @cmungall in #72
- pypi by @cmungall in #73
- refactoring by @cmungall in #75
- Schema enricher and Docker config by @cmungall in #77
- First pass at SQL Importer. See #67 by @cmungall in #78
- Added frictionless importer by @cmungall in #79
- Enhancing sphinx docs by @cmungall in #80
- doc-fixes-bullets by @cmungall in #81
- Re committing sql_importer. by @cmungall in #82
- Added generalization using panderas by @cmungall in #84
- Additional tests and documentation by @cmungall in #86
- Added toml generalizer by @cmungall in #90
- Improved docs for annotator by @cmungall in #92
- Using inflect library to depluralize class names when generalizing. by @cmungall in #94
- update dependencies fixes #95 fixes #97 by @sierra-moxon in #96
- Fixes #99 (logging object contents when None by @matentzn in #101
- Windows fixes (make test suite pass on windows) by @dalito in #104
- CsvGeneralizer: Adding ability to interpret metadata rows - adding docs to parameters - expose more parameters in CLI - additional tests by @cmungall in #106
- Added ability to import multiple jsonschema files organized in a project. by @cmungall in #113
- Implement RDFS importer. Bypasses issues with #114 by @cmungall in #115
- Delete pre_poetry directory by @turbomam in #116
- Adding CLI option from import-from-frictionless. by @cmungall in #118
New Contributors
Full Changelog: v0.2.0...v0.3.0
Contributors
cmungall, dalito, and 3 other contributors
Assets 2
v0.2.11
v0.2.10
What's Changed
- Fixes #99 (logging object contents when None by @matentzn in #101
- Windows fixes (make test suite pass on windows) by @dalito in #104
- CsvGeneralizer: Adding ability to interpret metadata rows - adding docs to parameters - expose more parameters in CLI - additional tests by @cmungall in #106
New Contributors
Full Changelog: v0.2.9...v0.2.10
Contributors
cmungall, dalito, and matentzn
Assets 2
v0.2.9
What's Changed
- Improved docs for annotator by @cmungall in #92
- Using inflect library to depluralize class names when generalizing. by @cmungall in #94
- update dependencies fixes #95 fixes #97 by @sierra-moxon in #96
Full Changelog: v0.2.8...v0.2.9
Contributors
cmungall and sierra-moxon