Update documentation for Orpha related content

docs/annotations.rst

@@ -5,6 +5,10 @@ Annotations
    :members:
    :inherited-members:
 
+.. autoclass:: pyhpo.Orpha
+   :members:
+   :inherited-members:
+
 .. autoclass:: pyhpo.Gene
    :members:
    :inherited-members:

docs/helper.rst

@@ -11,4 +11,6 @@ Methods
 .. autofunction:: pyhpo.helper.batch_similarity
 .. autofunction:: pyhpo.helper.batch_set_similarity
 .. autofunction:: pyhpo.helper.batch_disease_enrichment
+.. autofunction:: pyhpo.helper.batch_omim_disease_enrichment
+.. autofunction:: pyhpo.helper.batch_orpha_disease_enrichment
 .. autofunction:: pyhpo.helper.batch_gene_enrichment

docs/hposet.rst

@@ -16,7 +16,7 @@ Instantiation
 Instance methods
 ----------------
 .. autoclass:: pyhpo.HPOSet
-    :members:   add, child_nodes, remove_modifier, replace_obsolete, terms, all_genes, omim_diseases, information_content, similarity, similarity_scores, toJSON, serialize
+    :members:   add, child_nodes, remove_modifier, replace_obsolete, terms, all_genes, omim_diseases, orpha_diseases, information_content, similarity, similarity_scores, toJSON, serialize
 
 
 Not yet implemented

docs/ontology.rst

@@ -70,6 +70,7 @@ Attributes
 ----------
 .. autoattribute:: pyhpo.Ontology.__class__.genes
 .. autoattribute:: pyhpo.Ontology.__class__.omim_diseases
+.. autoattribute:: pyhpo.Ontology.__class__.orpha_diseases
 
 
 Methods

src/linkage.rs

@@ -37,6 +37,7 @@ use crate::{get_ontology, information_content::PyInformationContentKind, set::Py
 ///     Available options:
 ///
 ///     * **omim**
+///     * **orpha**
 ///     * **gene**
 ///
 /// similarity_method: `str`, default `graphic`

src/term.rs

@@ -13,6 +13,7 @@ use hpo::annotations::AnnotationId;
 use hpo::similarity::Similarity;
 use hpo::term::HpoTermId;
 
+use crate::annotations::PyOrphaDisease;
 use crate::pyterm_from_id;
 use crate::term_from_id;
 use crate::ONTOLOGY;
@@ -279,7 +280,7 @@ impl PyHpoTerm {
     ///         print(disease.name)
     ///
     #[getter(omim_diseases)]
-    fn diseases(&self) -> HashSet<PyOmimDisease> {
+    fn omim_diseases(&self) -> HashSet<PyOmimDisease> {
         self.hpo()
             .omim_diseases()
             .fold(HashSet::new(), |mut set, disease| {
@@ -288,6 +289,37 @@ impl PyHpoTerm {
             })
     }
 
+    /// Returns a set of associated ORPHA diseases
+    ///
+    /// The list includes "inherited" diseases that are not directly
+    /// linked to the term, but to one of its children
+    ///
+    /// Returns
+    /// -------
+    /// Set[:class:`pyhpo.Orpha`]
+    ///     All associated Orpha diseases
+    ///
+    /// Examples
+    /// --------
+    ///
+    /// .. code-block:: python
+    ///
+    ///     from pyhpo import Ontology
+    ///     Ontology()
+    ///     term = Ontology.hpo(188)
+    ///     for disease in term.orpha_diseases:
+    ///         print(disease.name)
+    ///
+    #[getter(orpha_diseases)]
+    fn orpha_diseases(&self) -> HashSet<PyOrphaDisease> {
+        self.hpo()
+            .orpha_diseases()
+            .fold(HashSet::new(), |mut set, disease| {
+                set.insert(PyOrphaDisease::from(disease));
+                set
+            })
+    }
+
     /// A list of the root phenotypical or modifier categories the term
     /// belongs to
     ///