Refactor/reorder ontology

Cargo.toml

@@ -36,9 +36,5 @@ harness = false
 name = "ancestors"
 harness = false
 
-[[bench]]
-name = "parser"
-harness = false
-
 [profile.release]
 lto = true

src/annotations/gene.rs

@@ -119,11 +119,6 @@ impl Gene {
         &self.name
     }
 
-    /// Connect another [HPO term](`crate::HpoTerm`) to the gene
-    pub fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
-        self.hpos.insert(term_id)
-    }
-
     /// The set of connected HPO terms
     pub fn hpo_terms(&self) -> &HpoGroup {
         &self.hpos
@@ -193,6 +188,16 @@ impl Gene {
     pub fn to_hpo_set<'a>(&self, ontology: &'a Ontology) -> HpoSet<'a> {
         HpoSet::new(ontology, self.hpos.clone())
     }
+
+    /// Connect another [HPO term](`crate::HpoTerm`) to the gene
+    ///
+    /// # Note
+    ///
+    /// This method does **not** add the [`Gene`] to the [HPO term](`crate::HpoTerm`).
+    /// Clients should not use this method, unless they are creating their own Ontology.
+    pub fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
+        self.hpos.insert(term_id)
+    }
 }
 
 impl PartialEq for Gene {

src/annotations/omim_disease.rs

@@ -95,11 +95,6 @@ impl OmimDisease {
         &self.name
     }
 
-    /// Connect another [HPO term](`crate::HpoTerm`) to the disease
-    pub fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
-        self.hpos.insert(term_id)
-    }
-
     /// The set of connected HPO terms
     pub fn hpo_terms(&self) -> &HpoGroup {
         &self.hpos
@@ -167,6 +162,16 @@ impl OmimDisease {
     pub fn to_hpo_set<'a>(&self, ontology: &'a Ontology) -> HpoSet<'a> {
         HpoSet::new(ontology, self.hpos.clone())
     }
+
+    /// Connect another [HPO term](`crate::HpoTerm`) to the disease
+    ///
+    /// # Note
+    ///
+    /// This method does **not** add the [`OmimDisease`] to the [HPO term](`crate::HpoTerm`).
+    /// Clients should not use this method, unless they are creating their own Ontology.
+    pub fn add_term<I: Into<HpoTermId>>(&mut self, term_id: I) -> bool {
+        self.hpos.insert(term_id)
+    }
 }
 
 impl PartialEq for OmimDisease {

src/lib.rs

@@ -21,6 +21,7 @@ pub mod utils;
 pub use ontology::comparison;
 pub use ontology::Ontology;
 pub use set::HpoSet;
+#[doc(inline)]
 pub use term::{HpoTerm, HpoTermId};
 
 const DEFAULT_NUM_PARENTS: usize = 10;