nwb-linkml/docs/_notes/translation.md

translation

what operations do we need when translating between schema languages?

• Iteration - control over "for what" in the source or target domain. eg. we need to map "all attributes and properties to slots" but then the other direction of selection where we need to do one of everything per item in the source domain as well
• dependence - source and target domain have different notions of linking
• level shifting - need to translate when something is a language-level item to a schema-level item/object/class

Steps:

• each namespaces or schema object creates one linkml schema file

• namespaces: one map, just imports all the other schema

• schema: actually create the object in the schema.

  • Classes:
    • Groups
    • Enums (see below)
  • Slots
    • Attributes

• new files: files not in the source domain

  • enum classes

• Rename items

Translation choices

We aren't doing a 1:1 translation of NWB! The goal is to make something that is import backwards-compatible - ie. we can read NWB traditional nwb files - but not necessarily export for now. We will get to that eventually. NWB as it is now is highly tied to hdf5 in multiple places - from the hdmf-common namespace to the nwb file classes, we want to instead abstract the structure of NWB so the schema can be used as a programming element (ie. labs can write their own schema extensions in yaml, generate pydantic modules for them, and they should Just Work TM) with various different storage backends.

• Don't try and emulate the nwb.file schema - it is basically a file layout that indicates what should go where. We are moving I/O out of the schema: storage layout is at a different level than the schema
• Don't worry about most of hdmf-common: instead create sensible generics that can be implemented in different ways by different storage mediums