Merge pull request #48 from TheJacksonLaboratory/small-fixes

Enhance the documentation

README.md

@@ -4,7 +4,7 @@
 ![PyPi downloads](https://img.shields.io/pypi/dm/hpo-toolkit.svg?label=Pypi%20downloads)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/hpo-toolkit)
 
-A toolkit for working with Human Phenotype Ontology in Python.
+A toolkit for working with Human Phenotype Ontology (HPO) and HPO disease annotations in Python.
 
 Loading HPO is as simple as:
 
@@ -14,7 +14,7 @@ import hpotk
 hpo = hpotk.load_ontology('http://purl.obolibrary.org/obo/hp.json')
 ```
 
-Loading HPO annotations is accomplished by running:
+The HPO disease annotations are loaded by running:
 
 ```python
 from hpotk.annotations.load.hpoa import SimpleHpoaDiseaseLoader
@@ -28,7 +28,7 @@ diseases = loader.load(hpoa_path)
 assert len(diseases) == 12_468
 ```
 
-Check out the User guide and the API reference for more info:
+Find more info in our detailed documentation:
 
 - [Stable documentation](https://thejacksonlaboratory.github.io/hpo-toolkit/stable) (last release on `main` branch)
 - [Latest documentation](https://thejacksonlaboratory.github.io/hpo-toolkit/latest) (bleeding edge, latest commit on `development` branch)

docs/setup.rst

@@ -31,14 +31,26 @@ the active Python environment, assuming you have privileges to install packages.
 Run tests
 ^^^^^^^^^
 
-The contributors may want to run the unit tests and the integration tests to ensure the features work as expected.
-Hpo-toolkit's tests use a combination of `unittest` and `ddt`. The tests are run as::
+The contributors may want to run the unit tests and the integration tests to ensure all features work as expected.
+
+Before running tests, make sure you install HPO toolkit with `test` and `docs` dependencies::
+
+  python3 -m pip install .[test,docs]
+
+The unit tests and the integration tests can the be running by invoking::
 
   python3 -m unittest discover -s src -p _test*.py
   python3 -m unittest discover -s tests
 
+We go extra mile to ensure the documentation is always up-to-date, and, therefore, we also run the documentation tests.
+The documentation tests are run by::
+
+  cd docs
+  sphinx-apidoc --separate --module-first -d 2 -H "API reference" -o apidocs ../src/hpotk
+  make doctest
+
 .. note::
 
-  The library *must* be installed in the environment before running the tests. Otherwise, the test discovery will fail.
+  The library *must* be installed in the environment before running all tests. Otherwise, the test discovery will fail.
 
 That's about it!

docs/user-guide/index.rst

@@ -13,5 +13,6 @@ This guide includes self-contained tutorials for using HPO toolkit to work with
   load-ontology
   use-hierarchy
   load-hpo-annotations
+  validate-phenotypic-features
   sort-term-ids
 

docs/user-guide/validate-phenotypic-features.rst

@@ -0,0 +1,150 @@
+.. _validate-phenotypic-features:
+
+============================
+Validate phenotypic features
+============================
+
+One of the most convenient benefits of using ontology concepts for annotation of items with features and properties
+is that one can leverage the information encoded in the semantic relationships of the ontology hierarchy.
+Among other things, the semantic relationships empower fuzzy searches and similarity measures that have found
+broad usage in many fields, such as biomedicine.
+
+HPO became a *de facto* standard for representing phenotypic features - the signs and symptoms of an individual.
+However, unlike in the case of other ontologies, several unique rules should be followed to maximize the benefits
+of HPO annotations. In the sections below, we describe the rules and show how HPO toolkit can reveal their violations.
+
+For the sake of this guide, let's assume we have an individual annotated with the following four phenotypic features:
+
+* *Arachnodactyly*
+* *Seizure*
+* *Focal clonic seizure*
+* *Enuresis nocturna*
+
+.. doctest:: check-consistency
+
+  >>> curies = [
+  ...   'HP:0001505',  # Arachnodactyly
+  ...   'HP:0001250',  # Seizure
+  ...   'HP:0002266',  # Focal clonic seizure
+  ...   'HP:0010677'   # Enuresis nocturna
+  ... ]
+
+Let's convert the CURIEs into term ids:
+
+.. doctest:: check-consistency
+
+  >>> import hpotk
+  >>> term_ids = [hpotk.TermId.from_curie(curie) for curie in curies]
+
+and let's finish the setup by loading the toy HPO shipped with the documentation.
+
+.. doctest:: check-consistency
+
+  >>> hpo = hpotk.load_minimal_ontology('data/hp.toy.json')
+
+
+Do not use obsolete term ids
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As the first rule, the annotations should always use the current identifier. During ontology development,
+some concepts may become obsolete and later be removed from the ontology altogether.
+Most of the time, however, the removed concepts have a straightforward replacement.
+
+The :class:`hpotk.validate.ObsoleteTermIdsValidator` points out the usage of obsolete term ids
+and suggests the replacement.
+
+Let's create the validator and check if the phenotypic features are OK:
+
+.. doctest:: check-consistency
+
+  >>> from hpotk.validate import ObsoleteTermIdsValidator
+  >>> obs_val = ObsoleteTermIdsValidator(hpo)
+
+  >>> vr = obs_val.validate(term_ids)
+
+The validator returns back an instance of :class:`hpotk.validate.ValidationResults` with the validation output.
+We can check for presence of issues in the input:
+
+.. doctest:: check-consistency
+
+  >>> vr.is_ok()
+  False
+
+The input is *not* OK, so we should look at the issues in greater detail:
+
+.. doctest:: check-consistency
+
+  >>> for validation_result in vr.results:
+  ...   print(validation_result)
+  ValidationResult(level=<ValidationLevel.WARNING: 1>, category='obsolete_term_id_is_used', message='Using the obsolete HP:0001505 instead of HP:0001166 for Arachnodactyly')
+
+We see that the `HP:0001505` is obsolete and `HP:0001166` should be used as the new *Arachnodactyly* identifier.
+
+
+Phenotypic features should be descendants of *Phenotypic abnormality*
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+HPO hierarchy has several major branches to uniquely represent concepts such as clinical modifiers, modes of inheritance,
+and past medical medical history. However, the signs and symptoms should be encoded into descendants
+of *Phenotypic abnormality*.
+
+:class:`hpotk.validate.PhenotypicAbnormalityValidator` checks that all identifiers correspond to descendants
+of *Phenotypic abnormality*:
+
+Let's test that this is valid for the patient features:
+
+.. doctest:: check-consistency
+
+  >>> from hpotk.validate import PhenotypicAbnormalityValidator
+  >>> pa_val = PhenotypicAbnormalityValidator(hpo)
+
+  >>> vr = pa_val.validate(term_ids)
+  >>> vr.is_ok()
+  True
+
+Yes, the all term ids represent the descendants of *Phenotypic abnormality*.
+
+
+Phenotypic features should not violate the annotation propagation rule
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Last and most importantly, let's discuss the concept of annotation redundancy.
+HPO uses `is_a` to represent the edges of the ontology hierarchy graph. The edges model the "parent-child"
+relationships between two ontology concepts (the object subsumes the subject).
+
+When using HPO concepts to encode clinical features of an individual, presence of a concept implies presence
+of all ancestral concepts. This is also known as the "True path rule", where the annotation "propagates" across
+the concept ancestors.
+
+In general, using the same annotation more than once is considered an error (e.g. annotate the subject with *Focal clonic seizure*
+and *Focal clonic seizure*). However, thanks to the True path rule, using a concept and its ancestor is an offender
+of a similar kind.
+
+:class:`hpotk.validate.AnnotationPropagationValidator` checks if a set of terms violate the annotation propagation rule
+- if a collection of concepts contains a term and its ancestor.
+
+.. doctest:: check-consistency
+
+  >>> from hpotk.validate import AnnotationPropagationValidator
+  >>> ap_val = AnnotationPropagationValidator(hpo)
+
+  >>> vr = ap_val.validate(term_ids)
+  >>> vr.is_ok()
+  False
+
+There seems to an issue. Let's break it down:
+
+.. doctest:: check-consistency
+
+  >>> for validation_result in vr.results:
+  ...   print(validation_result.level)
+  ...   print(validation_result.category)
+  ...   print(validation_result.message)
+  ValidationLevel.ERROR
+  annotation_propagation
+  Terms should not contain both present Focal clonic seizure [HP:0002266] and its present or excluded ancestor Seizure [HP:0001250]
+
+The validator points out that *Seizure* is an ancestor of *Focal clonic seizure* and should, therefore, not be used
+as an annotation of the individual.
+
+That's it for now. There are more validators to come!