Merge pull request #385 from ielis/fix-doc-bugs

Fixing several small documentation bugs
phenopackets · Jul 4, 2024 · d69fc9e · d69fc9e
2 parents 804a217 + 9e08152
commit d69fc9e
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diff --git a/docs/cancer-example.rst b/docs/cancer-example.rst
@@ -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,

diff --git a/docs/family.rst b/docs/family.rst
@@ -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

diff --git a/docs/interpretation.rst b/docs/interpretation.rst
@@ -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
 

diff --git a/docs/requirements.rst b/docs/requirements.rst
@@ -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

diff --git a/docs/therapeutic-regimen.rst b/docs/therapeutic-regimen.rst
@@ -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.

diff --git a/docs/value.rst b/docs/value.rst
@@ -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.
 
 

diff --git a/docs/variant.rst b/docs/variant.rst
@@ -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.
 

diff --git a/docs/working.rst b/docs/working.rst
@@ -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`).