diff --git a/docs/source/recipes/index.rst b/docs/source/recipes/index.rst deleted file mode 100644 index 1611e6e5..00000000 --- a/docs/source/recipes/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. `Profiles`: - -Profiles -!!!!!!!! - - -.. TODO:: Add more information about the profiles. \ No newline at end of file diff --git a/docs/source/rst_epilog b/docs/source/rst_epilog index fdfe7c1e..ad33c395 100644 --- a/docs/source/rst_epilog +++ b/docs/source/rst_epilog @@ -19,7 +19,6 @@ .. _polymeric chain: https://en.wikipedia.org/wiki/Polymer .. _protein: https://en.wikipedia.org/wiki/Protein .. _vrs-issues: https://github.com/ga4gh/vrs/issues/ -.. _VRSATILE: https://vrsatile.readthedocs.io/en/latest/index.html .. _cat-vrs: https://cat-vrs.readthedocs.io/en/latest/index.html .. |curie| replace:: `Compact URI (CURIE)`_ diff --git a/docs/source/style.rst b/docs/source/style.rst deleted file mode 100644 index bad6562b..00000000 --- a/docs/source/style.rst +++ /dev/null @@ -1,81 +0,0 @@ -:orphan: - -This page shows style conventions used in these docs. It will be -built with other pages and you can view it (at -docs/build/html/style.html). Unfortunately, because it's intentionally -not included in the published docs, it generates the annoying warning -"WARNING: document isn't included in any toctree". - - -Headings -!!!!!!!! - -ReST heading levels are determined by the character used beneath text. -Within a file, each new character creates a new heading level. - -This documentation uses the characters ``!``, ``@``, ``#``, and ``$``. -That is, the first four shifted digit characters across a US keyboard. - -For example:: - - A Heading - !!!!!!!!! - - The first subheading - @@@@@@@@@@@@@@@@@@@@ - - The first subsubeheading - ######################## - - The second subheading - @@@@@@@@@@@@@@@@@@@@@ - - Another Heading - !!!!!!!!!!!!!!! - - -To aid comprehension, the Text Styles section source looks like this:: - - .. _text-styles-target: - - Text Styles - !!!!!!!!!!! - - -.. _text-styles-target: - -Text Styles -!!!!!!!!!!! - -A cheat sheet for making references, links, and literals in sphinx. - -* For external links, use ``target_``. - - * See ``epilog.rst`` for pre-defined links. - * e.g, ``Base64_`` renders as Base64_ and ```Compact URI (CURIE)`_`` - renders as `Compact URI (CURIE)`_. - -* *Within* VRS documentation, use ``.. _refname:`` to create link - target, and use ``:ref:`refname``` to reference it. - - * Create explicit link targets for all headings. - * Do not rely on the implicit targets created by sphinx because - changing the heading will break the link. - * e.g., ``:ref:`text-styles-target``` renders as - :ref:`text-styles-target` and uses the heading text as - the link name. - * e.g., ``:ref:`Alleles ``` renders as :ref:`Alleles - `, with custom link text. - * Use class names verbatim when making link targets (e.g., - ``.. _SequenceLocation:``). Use (lowercase) kebab-case for other - sections (e.g., ``.. computed-identifiers:``). - -* Use \* for attributes. - - * ``*attribute*`` renders as *attribute*. - * e.g., The :ref:`Allele` *location* attribute must be set. - -* Use double backticks for literals. - - * ````literal```` renders as ``literal`` - * e.g., The :ref:`Allele` *type* attribute must be set to ``"Allele"``. diff --git a/docs/source/terms_and_model.rst b/docs/source/terms_and_model.rst deleted file mode 100644 index e134516e..00000000 --- a/docs/source/terms_and_model.rst +++ /dev/null @@ -1,81 +0,0 @@ -Terminology & Information Model -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -When biologists define terms in order to describe phenomena and -observations, they rely on a background of human experience and -intelligence for interpretation. Definitions may be abstract, perhaps -correctly reflecting uncertainty of our understanding at the -time. Unfortunately, such terms are not readily translatable into an -unambiguous representation of knowledge. - -For example, "allele" might refer to "an alternative form of a gene or -locus" [`Wikipedia`_], "one of two or more forms of the DNA sequence -of a particular gene" [`ISOGG`_], or "one of a set of coexisting -sequence alleles of a gene" [`Sequence Ontology`_]. Even for human -interpretation, these definitions are inconsistent: does the -definition precisely describe a specific change on a specific -sequence, or, rather, a more general change on an undefined sequence? -In addition, all three definitions are inconsistent with the practical -need for a way to describe sequence changes outside regions associated -with genes. - -**The computational representation of biological concepts requires -translating precise biological definitions into information models and -data structures that may be used in software.** This translation -should result in a representation of information that is consistent -with conventional biological understanding and, ideally, be able to -accommodate future data as well. The resulting *computational -representation* of information should also be cognizant of -computational performance, the minimization of opportunities for -misunderstanding, and ease of manipulating and transforming data. - -Accordingly, for each term we define below, we begin by describing the -term as used by the genetics and/or bioinformatics communities as -available. When a term has multiple such definitions, we -explicitly choose one of them for the purposes of computational -modelling. We then define the **computational definition** that -reformulates the community definition in terms of information content. -Finally, we translate each of these computational definitions into precise -specifications for the (**information model**). Terms are ordered -"bottom-up" so that definitions depend only on previously-defined terms. - -.. note:: The keywords "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL - NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and - "OPTIONAL" in this document are to be interpreted as - described in `RFC 2119`_. - - -Information Model Principles -@@@@@@@@@@@@@@@@@@@@@@@@@@@@ - -* **VRS objects are minimal** `value objects - `_. Two objects are - considered equal if and only if their respective attributes are - equal. As value objects, VRS objects are used as primitive types - and MUST NOT be used as containers for related data, such as primary - database accessions, representations in particular formats, or links - to external data. Instead, related data should be associated with - VRS objects through identifiers. See :ref:`computed-identifiers`. - -* **VRS uses polymorphism.** VRS uses polymorphism extensively in - order to provide a coherent top-down structure for variation while - enabling precise models for variation data. For example, Allele is - a kind of Variation, SequenceLocation is a kind of Location, and - SequenceState is a kind of State. See :ref:`future-plans` for the - roadmap of VRS data classes and relationships. All VRS objects - contain a *type* attribute, which is used to discriminate - polymorphic objects. - -* **Error handling is intentionally unspecified and delegated to - implementation.** VRS provides foundational data types that - enable significant flexibility. Except where required by this - specification, implementations may choose whether and how to - validate data. For example, implementations MAY choose to validate - that particular combinations of objects are compatible, but such - validation is not required. - -* **VRS uses** `snake_case - `__ **to represent - compound words.** Although the schema is currently JSON-based (which - would typically use camelCase), VRS itself is intended to be neutral - with respect to languages and database.