diff --git a/docs/source/conventions/computed_identifiers.rst b/docs/source/conventions/computed_identifiers.rst index 0568f616..af53211a 100644 --- a/docs/source/conventions/computed_identifiers.rst +++ b/docs/source/conventions/computed_identifiers.rst @@ -78,7 +78,7 @@ Implementations MUST adhere to the following requirements: be provided in other fields as decorative metadata, alongside object IDs. Implementations may freely implement such fields without impacting computed identifiers. Implementations are therefore encouraged (but not - required) to use the ``id`` field strictly for computed identifiers and + required) to use the *id* field strictly for computed identifiers and use decorative fields for alternate accessions, to reduce computational complexity. diff --git a/docs/source/conventions/example.rst b/docs/source/conventions/example.rst index 0d40919b..65e1e181 100644 --- a/docs/source/conventions/example.rst +++ b/docs/source/conventions/example.rst @@ -29,7 +29,7 @@ sequence derived from another source. In this example, we will use a :ref:`SequenceLocation`, which is composed of a :ref:`SequenceReference` and start and end coordinates. -In VRS, the :ref:`SequenceReference` object's ``refgetAccession`` +In VRS, the :ref:`SequenceReference` object's *refgetAccession* attribute MUST use a `GA4GH RefGet `_ identifier. Therefore, ``NC_000019.10`` MUST be written as the string @@ -125,9 +125,9 @@ identifiers enables the use of custom reference sequences. .. important:: VRS permits the use of conventional sequence accessions from RefSeq, Ensembl, or other sources by annotating the - :ref:`SequenceReference` object's ``id`` attribute. When + :ref:`SequenceReference` object's *id* attribute. When generating computed identifiers, the - :ref:`SequenceReference` object's ``refgetAccession`` + :ref:`SequenceReference` object's *refgetAccession* attribute MUST use a `GA4GH RefGet `_ identifier. @@ -166,7 +166,7 @@ following computed identifier for our example:: Importantly, GA4GH computed identifiers may be used literally (without escaping) in URIs. -Variation and Location objects contain an OPTIONAL ``id`` attribute +Variation and Location objects contain an OPTIONAL *id* attribute which implementations may use to store any CURIE-formatted identifier. *If* an implementation returns a computed identifier with objects, the object might look like the following: @@ -192,11 +192,11 @@ object might look like the following: This example provides a full VRS-compliant Allele with a computed identifier. -.. note:: The ``id`` attribute is optional. If it is used, the value +.. note:: The *id* attribute is optional. If it is used, the value MUST be a string, but it does NOT need to be a GA4GH Computed Identifier. Applications MAY choose to implement their own identifier scheme for private or public use. For example, - the above ``id`` could be a serial number assigned by an + the above *id* could be a serial number assigned by an application, such as ``acmecorp:v0000123``.