v0.5.1

What's Changed

• metamodel docs by @cmungall in #133
• kwalify importer by @cmungall in #136

Full Changelog: v0.5.0...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

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

• @cthoyt made their first contribution in #121

Full Changelog: v0.3.0...v0.4.0

v0.3.1

What's Changed

• Remove Bioregistry dependency and update OAK dependency by @cthoyt in #121

New Contributors

• @cthoyt made their first contribution in #121

Full Changelog: v0.3.0...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

• @dalito made their first contribution in #104

Full Changelog: v0.2.0...v0.3.0

v0.2.11

What's Changed

• Added ability to import multiple jsonschema files organized in a project. by @cmungall and @dalito in #113

Full Changelog: v0.2.10...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

• @dalito made their first contribution in #104

Full Changelog: v0.2.9...v0.2.10

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

v0.2.8

What's Changed

• Additional tests and documentation by @cmungall in #86
• Added toml generalizer by @cmungall in #90

Full Changelog: v0.2.7...v0.2.8

v0.2.7

Highlights

Generation of LinkML schemas by generalizing from tables in web pages

For example, given this table:

https://www.nature.com/articles/s41467-022-31626-4/tables/1

Run:

schemauto  generalize-htmltable  https://www.nature.com/articles/s41467-022-31626-4/tables/1

To get

name: example
description: example
id: https://w3id.org/example
imports:
- linkml:types
prefixes:
  linkml: https://w3id.org/linkml/
  example: https://w3id.org/example
default_prefix: example
slots:
  GWAS trait:
    examples:
    - value: "\xC2"
    range: string
  Peak GWAS SNP:
    examples:
    - value: rs2974298
    range: string
  Gene:
    examples:
    - value: SMIM19
    range: string
  NK cell cis eSNP:
    examples:
    - value: rs2974348
    range: string
  TWAS Z score:
    examples:
    - value: '3.809'
    range: string
  TWAS P value:
    examples:
    - value: '0.0001'
    range: string
classes:
  example:
    slots:
    - GWAS trait
    - Peak GWAS SNP
    - Gene
    - NK cell cis eSNP
    - TWAS Z score
    - TWAS P value

What's Changed

• Enhancing sphinx docs by @cmungall in #80
• Re committing sql_importer. by @sierra-moxon @cmungall in #82
• Added generalization using panderas by @cmungall in #84

Full Changelog: v0.2.6...v0.2.7