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update styling for attributes
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follow docs/source/style.rst conventions
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korikuzma committed Aug 27, 2024
1 parent 075f8fa commit 577aa66
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2 changes: 1 addition & 1 deletion docs/source/conventions/computed_identifiers.rst
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Expand Up @@ -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.

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12 changes: 6 additions & 6 deletions docs/source/conventions/example.rst
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Expand Up @@ -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
<http://samtools.github.io/hts-specs/refget.html>`_ identifier.
Therefore, ``NC_000019.10`` MUST be written as the string
Expand Down Expand Up @@ -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
<http://samtools.github.io/hts-specs/refget.html>`_
identifier.
Expand Down Expand Up @@ -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:
Expand All @@ -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``.


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