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Merge pull request #385 from ielis/fix-doc-bugs
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Fixing several small documentation bugs
pnrobinson authored Jul 4, 2024
2 parents 804a217 + 9e08152 commit d69fc9e
Showing 8 changed files with 14 additions and 10 deletions.
2 changes: 1 addition & 1 deletion docs/cancer-example.rst
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@@ -78,7 +78,7 @@ each :ref:`rstbiosample` in turn. The entire collection of biosamples is represe
biosample 1: Infiltrating Urothelial Carcinoma
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The first biosample is a biopsy taken from the wall of the urinary bladder. The histologuical diagnosis is represented
The first biosample is a biopsy taken from the wall of the urinary bladder. The histological diagnosis is represented
by a National Cancer Institute's Thesaurus code. This is a primary malignant neoplasm with stage T2bN2. A VCF file
representing a paired normal germline sample is located at ``/data/genomes/urothelial_ca_wgs.vcf.gz`` on the file system.
In order to specify the procedure used to remove the bladder and prostate gland,
4 changes: 4 additions & 0 deletions docs/family.rst
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@@ -44,6 +44,10 @@ Data model
- :ref:`rstphenopacket` (list)
- 0..*
- list of Phenopackets for family members other than the proband
* - consanguinous_parents
- bool
- 0..1
- flag to indicate that the parents of the proband are consanguinous
* - pedigree
- :ref:`rstpedigree`
- 1..1
6 changes: 3 additions & 3 deletions docs/interpretation.rst
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@@ -136,7 +136,7 @@ other researchers with similar cases in order to subsequently share detailed inf
a collaborative project.

In this case, the gene should be marked as ``CANDIDATE``. Here is an example of an interpretation
with the hypothetical gene YFG42.
with the gene *DHODH*.



@@ -150,7 +150,7 @@ with the hypothetical gene YFG42.
id: "OMIM:263750"
label: "Miller syndrome"
genomicInterpretations:
- interpretationStatus: "CONTRIBUTORY"
- interpretationStatus: "CANDIDATE"
gene:
valueId: "HGNC:2867"
symbol: "DHODH"
@@ -237,7 +237,7 @@ Diagnostic finding in a cancer

Cancer cases are not generally solved by genomic analysis. Instead, the intention is often to
identify actionable variants that represent potential indications for targeted therapy. In
this example, a BRAF variant is interpreted as being actionable in this sense.
this example, a *BRAF* variant is interpreted as being actionable in this sense.

.. code-block:: yaml
2 changes: 1 addition & 1 deletion docs/requirements.rst
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@@ -5,7 +5,7 @@ Requirement Levels
##################


The schema is formally defined using `protobuf3 <rstprotobuf>`_. In protobuf3, all elements are optional, and so there is no mechanism
The schema is formally defined using :ref:`protobuf3 <rstprotobuf>`. In protobuf3, all elements are optional, and so there is no mechanism
within protobuf to declare that a certain field is required. The Phenopacket schema does require some fields to be
present and in some cases additionally requires that these fields have a certain format (syntax) or intended meaning
(semantics). Software that uses Phenopackets should check the validity of the data with other means. We provide a Java
2 changes: 1 addition & 1 deletion docs/therapeutic-regimen.rst
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@@ -35,7 +35,7 @@ TherapeuticRegimen
- :ref:`rsttimeelement`
- 0..1
- When the regimen ended. An empty `end_time` with a populated `start_time` would indicate the regimen was ongoing. RECOMMENDED.
* - status
* - regimen_status
- :ref:`rstregimenstatus`
- 1..1
- Current status of the regimen for the enclosing :ref:`rstmedicalaction` on the :ref:`rstindividual`. REQUIRED.
4 changes: 2 additions & 2 deletions docs/value.rst
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@@ -5,7 +5,7 @@ Value
#####

The value element is meant to be used as part of the :ref:`rstmeasurement` element, and it
represents the outcome of a measurment.
represents the outcome of a measurement.


Data model
@@ -60,7 +60,7 @@ The following example shows a Value used for an ordinal measurement.
Explanations
############

See :ref:`rstquantity` for explanations of how to contruct that element. For ordinal measurements,
See :ref:`rstquantity` for explanations of how to construct that element. For ordinal measurements,
the following terms may be useful.


2 changes: 1 addition & 1 deletion docs/variant.rst
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@@ -6,7 +6,7 @@ VariationDescriptor

Variation Descriptors are part of the `VRSATILE framework <https://vrsatile.readthedocs.io>`_, a set of
conventions extending the GA4GH `Variation Representation Specification (VRS) <https://vrs.ga4gh.org>`_.
Descriptors allow for the complemetary use of human-readable labels, descriptions, alternate contexts,
Descriptors allow for the complementary use of human-readable labels, descriptions, alternate contexts,
and identifier cross-references alongside the precise computable representation of variation concepts
provided by VRS.

2 changes: 1 addition & 1 deletion docs/working.rst
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@@ -12,7 +12,7 @@ language implementations.
Example code
~~~~~~~~~~~~
We provide several examples that demonstrate how to work with Phenopackets in Java and C++.
There are also Python examples in the source code test directory. All three langauge implementations are automatically
There are also Python examples in the source code test directory. All three language implementations are automatically
produced as part of the build (:ref:`rstjavabuild`).


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