diff --git a/docs/cancer-example.rst b/docs/cancer-example.rst index bcecf3a..f5b48c6 100644 --- 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 index 17abd37..bcacd2e 100644 --- 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 index eae1ef8..ac03a65 100644 --- 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 index 522cf48..99c95e5 100644 --- a/docs/requirements.rst +++ b/docs/requirements.rst @@ -5,7 +5,7 @@ Requirement Levels ################## -The schema is formally defined using `protobuf3 `_. In protobuf3, all elements are optional, and so there is no mechanism +The schema is formally defined using :ref:`protobuf3 `. 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 index aed14a5..a6113bc 100644 --- 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 index cb2c04f..8573730 100644 --- 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 index cf2d3a9..6290393 100644 --- a/docs/variant.rst +++ b/docs/variant.rst @@ -6,7 +6,7 @@ VariationDescriptor Variation Descriptors are part of the `VRSATILE framework `_, a set of conventions extending the GA4GH `Variation Representation Specification (VRS) `_. -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 index bef5e6b..7c1f048 100644 --- 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`).