RareLinkCDM-LinkML

[aslgraefe]

RareLinkCDM-Schema:

• develop reusable classes and functions, also usable for CDM-extensions when exporting REDCap data to schema/ preproccesing #105
• preprocess rarelink-cdm schema with more granularity so that it is ready to be processed to Phenopackets
• fetching displays implemented,
• include conversion of REDCap codes,
• revise modularity for function preprocess_redcap_json.py and other way round,
• add eveytghing necessary for Phenopackets)
• write classes and functionalities so that Rarelink-cdm extensions can also use the API
• Implement OAK and fetch displays ( https://github.com/INCATools/ontology-access-kit / https://incatools.github.io/ontology-access-kit/ ): API request via BioPortal to fetch displays
• ImportMapper: Implement SchemaAutomator ( https://github.com/linkml/schema-automator / https://linkml.io/schema-automator/introduction.html#generalization-from-instance-data )
  targetSchema: from schema viewer to definition (linkml), format tabular data to TSV for schema-automator
• revise Schema PythonGenerator: check for pydanticgen, check how to use & reuse the generated python classes

[aslgraefe]

closed, remainer now only in issue #122