WIP: RFC: Axis Anatomical Orientation

rfc/x/markdown/Orientation.md

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+
+# Enum: Orientation
+
+Anatomical orientation refers to the specific arrangement and directional alignment of anatomical structures within an imaging dataset. It is crucial for ensuring accurate alignment and comparison of images to anatomical atlases, facilitating consistent analysis and interpretation of biological data.
+
+URI: [ngff:Orientation](https://w3id.org/ome/ngff/Orientation)
+
+
+## Permissible Values
+
+| Text | Description | Meaning | Other Information |
+| :--- | :---: | :---: | ---: |
+| left-to-right | Describes the directional orientation from the left side to the right side of an anatomical structure or body. |  |  |
+| right-to-left | Describes the directional orientation from the right side to the left side of an anatomical structure or body. |  |  |
+| anterior-to-posterior | Describes the directional orientation from the front (anterior) to the back (posterior) of an anatomical structure or body. |  |  |
+| posterior-to-anterior | Describes the directional orientation from the back (posterior) to the front (anterior) of an anatomical structure or body. |  |  |
+| inferior-to-superior | Describes the directional orientation from the lower (inferior) to the upper (superior) part of an anatomical structure or body. |  |  |
+| superior-to-inferior | Describes the directional orientation from the upper (superior) to the lower (inferior) part of an anatomical structure or body. |  |  |
+| dorsal-to-ventral | Describes the directional orientation from the back (dorsal) to the front (ventral) of an anatomical structure or body. |  |  |
+| ventral-to-dorsal | Describes the directional orientation from the front (ventral) to the back (dorsal) of an anatomical structure or body. |  |  |
+| rostral-to-caudal | Describes the directional orientation from the front (rostral) to the back (caudal) end of an anatomical structure, typically used in reference to the central nervous system. |  |  |
+| caudal-to-rostral | Describes the directional orientation from the back (caudal) to the front (rostral) end of an anatomical structure, typically used in reference to the central nervous system. |  |  |
+

rfc/x/markdown/index.md

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+
+# orientation
+
+
+**metamodel version:** 1.7.0
+
+**version:** 0.1.0
+
+
+The orientation field provides explicit metadata about the anatomical orientation in an image using a controlled vocabulary. The goal is to preserve essential biological information and eliminate assumptions about orientation which can lead to errors in downstream analysis and alignment to anatomical atlases.
+
+
+### Classes
+
+
+### Mixins
+
+
+### Slots
+
+
+### Enums
+
+ * [Orientation](Orientation.md) - Anatomical orientation refers to the specific arrangement and directional alignment of anatomical structures within an imaging dataset. It is crucial for ensuring accurate alignment and comparison of images to anatomical atlases, facilitating consistent analysis and interpretation of biological data.
+
+### Subsets
+
+
+### Types
+
+
+#### Built in
+
+ * **Bool**
+ * **Curie**
+ * **Decimal**
+ * **ElementIdentifier**
+ * **NCName**
+ * **NodeIdentifier**
+ * **URI**
+ * **URIorCURIE**
+ * **XSDDate**
+ * **XSDDateTime**
+ * **XSDTime**
+ * **float**
+ * **int**
+ * **str**
+
+#### Defined
+
+ * [Boolean](types/Boolean.md)  (**Bool**)  - A binary (true or false) value
+ * [Curie](types/Curie.md)  (**Curie**)  - a compact URI
+ * [Date](types/Date.md)  (**XSDDate**)  - a date (year, month and day) in an idealized calendar
+ * [DateOrDatetime](types/DateOrDatetime.md)  (**str**)  - Either a date or a datetime
+ * [Datetime](types/Datetime.md)  (**XSDDateTime**)  - The combination of a date and time
+ * [Decimal](types/Decimal.md)  (**Decimal**)  - A real number with arbitrary precision that conforms to the xsd:decimal specification
+ * [Double](types/Double.md)  (**float**)  - A real number that conforms to the xsd:double specification
+ * [Float](types/Float.md)  (**float**)  - A real number that conforms to the xsd:float specification
+ * [Integer](types/Integer.md)  (**int**)  - An integer
+ * [Jsonpath](types/Jsonpath.md)  (**str**)  - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
+ * [Jsonpointer](types/Jsonpointer.md)  (**str**)  - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
+ * [Ncname](types/Ncname.md)  (**NCName**)  - Prefix part of CURIE
+ * [Nodeidentifier](types/Nodeidentifier.md)  (**NodeIdentifier**)  - A URI, CURIE or BNODE that represents a node in a model.
+ * [Objectidentifier](types/Objectidentifier.md)  (**ElementIdentifier**)  - A URI or CURIE that represents an object in the model.
+ * [Sparqlpath](types/Sparqlpath.md)  (**str**)  - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
+ * [String](types/String.md)  (**str**)  - A character string
+ * [Time](types/Time.md)  (**XSDTime**)  - A time object represents a (local) time of day, independent of any particular day
+ * [Uri](types/Uri.md)  (**URI**)  - a complete URI
+ * [Uriorcurie](types/Uriorcurie.md)  (**URIorCURIE**)  - a URI or a CURIE

rfc/x/markdown/types/Boolean.md

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+
+# Type: boolean
+
+A binary (true or false) value
+
+URI: [linkml:Boolean](https://w3id.org/linkml/Boolean)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **Bool** |
+| Representation | | bool |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Exact Mappings:** | | schema:Boolean |

rfc/x/markdown/types/Curie.md

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+
+# Type: curie
+
+a compact URI
+
+URI: [linkml:Curie](https://w3id.org/linkml/Curie)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **Curie** |
+| Representation | | str |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Comments:** | | in RDF serializations this MUST be expanded to a URI |
+|  | | in non-RDF serializations MAY be serialized as the compact representation |

rfc/x/markdown/types/Date.md

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+
+# Type: date
+
+a date (year, month and day) in an idealized calendar
+
+URI: [linkml:Date](https://w3id.org/linkml/Date)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **XSDDate** |
+| Representation | | str |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Exact Mappings:** | | schema:Date |

rfc/x/markdown/types/DateOrDatetime.md

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+
+# Type: date_or_datetime
+
+Either a date or a datetime
+
+URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **str** |
+| Representation | | str |

rfc/x/markdown/types/Datetime.md

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+
+# Type: datetime
+
+The combination of a date and time
+
+URI: [linkml:Datetime](https://w3id.org/linkml/Datetime)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **XSDDateTime** |
+| Representation | | str |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Exact Mappings:** | | schema:DateTime |

rfc/x/markdown/types/Decimal.md

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+
+# Type: decimal
+
+A real number with arbitrary precision that conforms to the xsd:decimal specification
+
+URI: [linkml:Decimal](https://w3id.org/linkml/Decimal)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **Decimal** |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Broad Mappings:** | | schema:Number |

rfc/x/markdown/types/Double.md

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+
+# Type: double
+
+A real number that conforms to the xsd:double specification
+
+URI: [linkml:Double](https://w3id.org/linkml/Double)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **float** |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Close Mappings:** | | schema:Float |

rfc/x/markdown/types/Float.md

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+
+# Type: float
+
+A real number that conforms to the xsd:float specification
+
+URI: [linkml:Float](https://w3id.org/linkml/Float)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **float** |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Exact Mappings:** | | schema:Float |

rfc/x/markdown/types/Integer.md

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+
+# Type: integer
+
+An integer
+
+URI: [linkml:Integer](https://w3id.org/linkml/Integer)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **int** |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Exact Mappings:** | | schema:Integer |

rfc/x/markdown/types/Jsonpath.md

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+
+# Type: jsonpath
+
+A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
+
+URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **str** |
+| Representation | | str |

rfc/x/markdown/types/Jsonpointer.md

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+
+# Type: jsonpointer
+
+A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
+
+URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **str** |
+| Representation | | str |

rfc/x/markdown/types/Ncname.md

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+
+# Type: ncname
+
+Prefix part of CURIE
+
+URI: [linkml:Ncname](https://w3id.org/linkml/Ncname)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **NCName** |
+| Representation | | str |

rfc/x/markdown/types/Nodeidentifier.md

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+
+# Type: nodeidentifier
+
+A URI, CURIE or BNODE that represents a node in a model.
+
+URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **NodeIdentifier** |
+| Representation | | str |

rfc/x/markdown/types/Objectidentifier.md

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+
+# Type: objectidentifier
+
+A URI or CURIE that represents an object in the model.
+
+URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **ElementIdentifier** |
+| Representation | | str |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Comments:** | | Used for inheritance and type checking |

rfc/x/markdown/types/Sparqlpath.md

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+
+# Type: sparqlpath
+
+A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
+
+URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **str** |
+| Representation | | str |

rfc/x/markdown/types/String.md

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+
+# Type: string
+
+A character string
+
+URI: [linkml:String](https://w3id.org/linkml/String)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **str** |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Exact Mappings:** | | schema:Text |

rfc/x/markdown/types/Time.md

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+
+# Type: time
+
+A time object represents a (local) time of day, independent of any particular day
+
+URI: [linkml:Time](https://w3id.org/linkml/Time)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **XSDTime** |
+| Representation | | str |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Exact Mappings:** | | schema:Time |

rfc/x/markdown/types/Uri.md

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+
+# Type: uri
+
+a complete URI
+
+URI: [linkml:Uri](https://w3id.org/linkml/Uri)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **URI** |
+| Representation | | str |
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node |
+| **Close Mappings:** | | schema:URL |

rfc/x/markdown/types/Uriorcurie.md

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+
+# Type: uriorcurie
+
+a URI or a CURIE
+
+URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie)
+
+|  |  |  |
+| --- | --- | --- |
+| Root (builtin) type | | **URIorCURIE** |
+| Representation | | str |