From 6f77101f7752b96ca2d1759c2aa3f7a567636096 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Apr 2024 21:40:54 -0400 Subject: [PATCH 1/9] Fix #344 --- docs/therapeutic-regimen.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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. From 751ef5a545cc8fc0338e7e422575e82baac2ea1f Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Apr 2024 21:45:31 -0400 Subject: [PATCH 2/9] Fix #350, indicating that `consanguinous_parents` is not required. --- docs/family.rst | 4 ++++ 1 file changed, 4 insertions(+) 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 From b33ce26298329c57718a6724d087842997987fef Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Apr 2024 21:47:24 -0400 Subject: [PATCH 3/9] Fix #351 --- docs/variant-interpretation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/variant-interpretation.rst b/docs/variant-interpretation.rst index 34046fd..5b2d2da 100644 --- a/docs/variant-interpretation.rst +++ b/docs/variant-interpretation.rst @@ -30,7 +30,7 @@ VariantInterpretation - :ref:`rsttherapeuticactionability` - 1..1 - The therapeutic actionability of the variant, default is UNKNOWN_ACTIONABILITY - * - variant + * - variation_descriptor - :ref:`rstvariant` - 1..1 - a genetic/genomic variant From 3332f1224c7f9871347485d7e1671e7c9240b94d Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Apr 2024 21:57:36 -0400 Subject: [PATCH 4/9] Fix #339, thank you @M-casado --- docs/interpretation.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/interpretation.rst b/docs/interpretation.rst index eae1ef8..ea03738 100644 --- a/docs/interpretation.rst +++ b/docs/interpretation.rst @@ -150,10 +150,10 @@ with the hypothetical gene YFG42. id: "OMIM:263750" label: "Miller syndrome" genomicInterpretations: - - interpretationStatus: "CONTRIBUTORY" + - interpretationStatus: "CANDIDATE" gene: - valueId: "HGNC:2867" - symbol: "DHODH" + valueId: "HGNC:11234" + symbol: "YFG42" Diagnostic finding in an autosomal dominant disease From 975a114e000e93a7e51fa57f624baf4014b5fec7 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Apr 2024 22:10:41 -0400 Subject: [PATCH 5/9] Fix cross-reference to address #316, thank you @micheldumontier --- docs/requirements.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 08c16dd3105433c818971a165a0596ee8a11098d Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Jul 2024 09:43:02 +0200 Subject: [PATCH 6/9] Revert the gene identifier in `Interpretation > Candidate genes` section. --- docs/interpretation.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/interpretation.rst b/docs/interpretation.rst index ea03738..92206f6 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. @@ -152,8 +152,8 @@ with the hypothetical gene YFG42. genomicInterpretations: - interpretationStatus: "CANDIDATE" gene: - valueId: "HGNC:11234" - symbol: "YFG42" + valueId: "HGNC:2867" + symbol: "DHODH" Diagnostic finding in an autosomal dominant disease From 73a3b1fc500f97bea9c8559fcfea206392c6022e Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Jul 2024 13:41:07 +0200 Subject: [PATCH 7/9] Italicize gene symbols. --- docs/gene.rst | 2 +- docs/interpretation.rst | 4 ++-- docs/rd-example.rst | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/gene.rst b/docs/gene.rst index 7d69027..05f7fa3 100644 --- a/docs/gene.rst +++ b/docs/gene.rst @@ -110,7 +110,7 @@ the case of Humans, this is the `HGNC `_, e.g. `HGNC symbol ~~~~~~ This SHOULD use official gene symbol as designated by the organism gene nomenclature committee. In the case of human -this is the `HUGO Gene Nomenclature Committee `_ e.g. `ETF1 `_. +this is the `HUGO Gene Nomenclature Committee `_ e.g. `*ETF1* `_. description ~~~~~~~~~~~ diff --git a/docs/interpretation.rst b/docs/interpretation.rst index 92206f6..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 gene DHODH. +with the gene *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/rd-example.rst b/docs/rd-example.rst index 2160442..f7054ea 100644 --- a/docs/rd-example.rst +++ b/docs/rd-example.rst @@ -14,7 +14,7 @@ Phenopacket). We show how to create this phenopacket in Java :ref:`here`. -COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report +*COL6A1* mutation leading to Bethlem myopathy with recurrent hematuria: a case report ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We present an example that summarizes the data presented in a `case report `_ about a boy with Bethlem myopathy. For simplicity's sake, From abd7b51ba0e8a78067e5259c2cfe004c33b81594 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Jul 2024 13:41:26 +0200 Subject: [PATCH 8/9] Fix doc typos. --- docs/cancer-example.rst | 2 +- docs/value.rst | 4 ++-- docs/variant.rst | 2 +- docs/working.rst | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) 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/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 e29a88c..e73fc88 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 3122073..5ae4b1e 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`). From 9e08152f812b374b1e09f3075a7795255d34a9af Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 4 Jul 2024 14:00:43 +0200 Subject: [PATCH 9/9] Revert inappropriate italics. --- docs/gene.rst | 2 +- docs/rd-example.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/gene.rst b/docs/gene.rst index 05f7fa3..7d69027 100644 --- a/docs/gene.rst +++ b/docs/gene.rst @@ -110,7 +110,7 @@ the case of Humans, this is the `HGNC `_, e.g. `HGNC symbol ~~~~~~ This SHOULD use official gene symbol as designated by the organism gene nomenclature committee. In the case of human -this is the `HUGO Gene Nomenclature Committee `_ e.g. `*ETF1* `_. +this is the `HUGO Gene Nomenclature Committee `_ e.g. `ETF1 `_. description ~~~~~~~~~~~ diff --git a/docs/rd-example.rst b/docs/rd-example.rst index f7054ea..2160442 100644 --- a/docs/rd-example.rst +++ b/docs/rd-example.rst @@ -14,7 +14,7 @@ Phenopacket). We show how to create this phenopacket in Java :ref:`here`. -*COL6A1* mutation leading to Bethlem myopathy with recurrent hematuria: a case report +COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We present an example that summarizes the data presented in a `case report `_ about a boy with Bethlem myopathy. For simplicity's sake,