Merge pull request #401 from ga4gh/typos

pnrobinson · web-flow · commit ccf4bb5fbd60 · 2025-09-30T10:45:48.000+02:00
Fixing five typos
diff --git a/docs/basics.rst b/docs/basics.rst
@@ -37,4 +37,9 @@ to a phenotypic feature, such as `Arachnodactyly <https://hpo.jax.org/app/browse
 component of a disease, such as `Marfan syndrome <https://hpo.jax.org/app/browse/disease/OMIM:154700>`_. The
 Phenopacket proposed here is designed to support `deep phenotyping <https://www.ncbi.nlm.nih.gov/pubmed/22504886>`_, a
 process wherein individual components of each phenotype are observed and documented. The phenotypes may be
-constitutional or those related to a sample (such as from a biopsy).
+constitutional or those related to a sample (such as from a biopsy).
+
+The Phenopacket Schema was developed under the aegis of the `GA4GH <https://www.ga4gh.org/>`_ (2015-2022). 
+
+- `Jacobsen JOB, et al. (2022) The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol <https://pubmed.ncbi.nlm.nih.gov/35705716/>`_ 
+- `Ladewig MS, et al. (2022) GA4GH Phenopackets: A Practical Introduction. Adv Genet (Hoboken) <https://pubmed.ncbi.nlm.nih.gov/36910590/>`_
diff --git a/docs/fhir.rst b/docs/fhir.rst
@@ -6,9 +6,7 @@ FHIR Implementation Guide
 
 Phenopacket on FHIR is a Fast Healthcare Interoperability Resources (FHIR) Implementation Guide (IG) based on the Phenopacket standard. It is meant to be conceptually equivalent but not directly interoperable. The guide is hosted at:
 
-http://phenopackets.org/core-ig/master/
-
-A list of the FHIR artifacts defined as part of this implementation guide can be found at http://phenopackets.org/core-ig/master/artifacts.html
+https://github.com/phenopackets/phenopacket-schema-fhir-implementation-guide
 
 Briefly, the implementation guide includes definitions for the properties by which a RESTFUL server can be queried (Search Parameters), the constraints on FHIR resources for systems (Resource Profiles) and on FHIR data types (Extension Definitions) conforming to this implementation guide, and the existent sets of codes (Value Sets) and new Code Systems used by systems that conform to the Phenopacket FHIR IG.
 
diff --git a/docs/ontologies.rst b/docs/ontologies.rst
@@ -16,7 +16,7 @@ in this recent `review <https://www.ncbi.nlm.nih.gov/pubmed/30304648>`_.
 
 While both terminologies and ontologies can be used, the phenopacket schema recommends the use of specific ontologies in order to maximize utility of performing algorithmic analysis over medically relevant abnormalities.
 
-The `Human Phenotype Ontology (HPO) <http://www.human-phenotype-ontology.org>`_  describes patient phenotypic features and was originally designed for genomic diagnostics, translational research, genomic matchmaking, and systems biology applications in the field of rare disease and other fields of medicine. It is increasinly used within clinical applications today for precision medicine.
+The `Human Phenotype Ontology (HPO) <http://www.human-phenotype-ontology.org>`_  describes patient phenotypic features and was originally designed for genomic diagnostics, translational research, genomic matchmaking, and systems biology applications in the field of rare disease and other fields of medicine. It is increasingly used within clinical applications today for precision medicine.
 
 The HPO is developed in the context of the `Monarch Initiative <https://monarchinitiative.org/>`_, an international team of
 computer scientists, clinicians, and biologists in the United States, Europe, and Australia;
diff --git a/docs/pedigree.rst b/docs/pedigree.rst
@@ -139,8 +139,8 @@ This element is an enumeration to
 In a PED file, affected persons are encoded with "2", and unaffecteds by "1"
 (a "0" is used if no information is available). Instead, Phenopackets uses an enumeration as shown in the table.
 
-In a PED file, the sex of individuals is encoded as a "1" for females, "2" for males, and "0" for unknown. Phenopackets
-uses :ref:`rstsex` instead.
+In a PED file, the sex of individuals is encoded as a "2" for females, "1" for males, and "0" for unknown. Phenopackets
+uses :ref:`rstsex` instead (Note that the enumeration used for Sex by the Phenopacket Schema has 1 for FEMALE and 2 for MALE, but this is internal and is not visible in the JSON-serialized Phenopacket).
 
 The message is made up of a list of ``Person`` elements (the Person element is defined within the Pedigree element).
 Each Person element is equivalent to one row of a PED file.
diff --git a/docs/procedure.rst b/docs/procedure.rst
@@ -7,6 +7,7 @@ Procedure
 The Procedure element represents a clinical procedure performed on a subject. For example a surgical or diagnostic
 procedure such as a biopsy.
 
+
 By preference a single ``code`` to indicate both the procedure and the
 body site should be used. In cases where this is not possible, the body site should be indicated using a separate
 ontology class.
diff --git a/docs/protobuf.rst b/docs/protobuf.rst
@@ -62,9 +62,9 @@ it is not possible to define a field as required.
     syntax = "proto3";
     
     message dog {
-      required string name = 1;
+      string name = 1;
       int32 weight = 2;
-      repeated string toys = 4;
+      repeated string toys = 3;
       }
 
 We can compile this code with the following command
diff --git a/docs/recommended-ontologies.rst b/docs/recommended-ontologies.rst
@@ -127,7 +127,7 @@ medical data. The following table shows some typical examples.
 
 Genotypes
 #########
-GENO is anontology of genotypes their more fundamental sequence components, and links to related biological
+GENO is an ontology of genotypes their more fundamental sequence components, and links to related biological
 and experimental entities. We use GENO terms to denote genotypes.
 
 
diff --git a/docs/resource.rst b/docs/resource.rst
@@ -37,7 +37,7 @@ For an ontology, the url SHALL point to the obo or owl file, e.g. This informati
   resource:
     id: "hp"
     name: "Human Phenotype Ontology"
-    url: "http://www.human-phenotype-ontology.org"
+    url: "http://purl.obolibrary.org/obo/hp.owl"
     version: "2018-03-08"
     namespacePrefix: "HP"
     iriPrefix: "http://purl.obolibrary.org/obo/HP_"
diff --git a/docs/timestamp.rst b/docs/timestamp.rst
@@ -6,7 +6,7 @@ Timestamp
 
 In phenopackets we define the `Timestamp` as an `ISO-8601 date time <https://en.wikipedia.org/wiki/ISO_8601#Combined_date_and_time_representations>`_ string.
 
-The following documentation paraphrases the description of how this is represented in protobuf as JSON `Timestamp <https://developers.google.com/protocol-buffers/docs/reference/java/com/google/protobuf/Timestamp>`_
+The following documentation paraphrases the description of how a Timestamp is represented in protobuf as JSON (See `Timestamp <https://developers.google.com/protocol-buffers/docs/reference/java/com/google/protobuf/Timestamp>`_).
 
 The format for this is "{year}-{month}-{day}T{hour}:{min}:{sec}[.{frac_sec}]Z" where {year} is always expressed using
 four digits while {month}, {day}, {hour}, {min}, and {sec} are zero-padded to two digits each. The fractional seconds,
