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Tweak structure add more information
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jfy133 authored Jan 31, 2025
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36 changes: 19 additions & 17 deletions src/docs/mixs-linkml-schema-quickstart.md
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Expand Up @@ -16,23 +16,25 @@ The schema is currently (as of Jan 2025) a very large file of more than 20,000 l

The following table provides a description of each top-level element of the `.yaml` file:

| Element | Description |
|---------|--------------|
| `name:` | name of the overall schema itself |
| `description:` | short description of what the schema is for |
| `comments:` | additional general information about the schema (e.g. like code comments) |
| `source:` | original source of the information encoded in schema (e.g. URL) |
| `id:` | A w3id linked-data URL |
| `version:` | version of the schema |
| `imports:` | specifications of internal linkml packages/modules used |
| `prefixes:` | additional URL prefixes for call out different things within the schema where prefix + object makes a full URL |
| `default_prefix`: | default prefix to append to each 'slot' (term) ID |
| `default_range`: | default slot (term) object type (e.g., integer, string) |
| `subsets`: | section or term group category definitions |
| `enums`: | definitions of drop down menu/fixed lists used by metadata term slots |
| `slots`: | definition of each MIxS metadata term; basic summary information of each MIxS checklist and extension |
| `classes`: | definition of the contents of each checklists, extensions, combinations (e.g., which metadata term slot is included) |
| `settings`: | definitions of regex patterns etc. (a bit like variables) that are then be used inside `string_serialisation:` attribute of a slot |
| Element | Description | Can you modify\* |
|---------|--------------|-------------------|
| `name:` | name of the overall schema itself | No |
| `description:` | short description of what the schema is for | No |
| `comments:` | additional general information about the schema (e.g. like code comments) | No |
| `source:` | original source of the information encoded in schema (e.g. URL) | No |
| `id:` | A w3id linked-data URL | No |
| `version:` | version of the schema | No |
| `imports:` | specifications of internal linkml packages/modules used | No |
| `prefixes:` | additional URL prefixes for call out different things within the schema where prefix + object makes a full URL | No |
| `default_prefix`: | default prefix to append to each 'slot' (term) ID | No |
| `default_range`: | default slot (term) object type (e.g., integer, string) | No |
| `subsets`: | section or term group category definitions | No |
| `enums`: | definitions of drop down menu/fixed lists used by metadata term slots | Yes |
| `slots`: | definition of each MIxS metadata term; basic summary information of each MIxS checklist and extension | Yes |
| `classes`: | definition of the contents of each checklists, extensions, combinations (e.g., which metadata term slot is included) | Yes |
| `settings`: | definitions of regex patterns etc. (a bit like variables) that are then be used inside `string_serialisation:` attribute of a slot | No |

\* where 'you' refers to someone contributing to a occasional contributor of metadata terms, rather than a schema developer.

### Gold MIxS Standard Metadata Slot

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