Merge branch 'main' into release/0.10.0

CHANGELOG.md

@@ -2,15 +2,27 @@
 
 All notable changes to this project will be documented in this file.
 
+## Unreleased
+
 ## [0.10.0]
 
+### Feature
+
+- Add Orphante diseases (`OrphaDisease`) to Ontology
+- Filter gene and disease annotations in subontology based on association with phenotypes
+- Add binary version 3
+- Add new example ontology
+
 ### Documentation
 
 - Change orders of methods in `Ontology` to clean up the documentation.
 
 ### Refactor
 
 - Improve the OBO parser with better error handling
+- [**breaking**] Add `Disease` trait that is needed to work with `OmimDisease` and `OrphaDisease`
+- Update example ontology
+- Update unit- and doctests to align with updated example ontology
 
 
 ## [0.9.1] - 2024-03-30

README.md

@@ -33,9 +33,10 @@ The main structs used in `hpo` are:
 - [`HpoSet`](https://docs.rs/hpo/latest/hpo/struct.HpoSet.html) is a collection of `HpoTerm`s, like a patient's clinical information.
 - [`Gene`](https://docs.rs/hpo/latest/hpo/annotations/struct.Gene.html) represents a single gene, including information about associated `HpoTerm`s.
 - [`OmimDisease`](https://docs.rs/hpo/latest/hpo/annotations/struct.OmimDisease.html) represents a single OMIM-diseases, including information about associated `HpoTerm`s.
+- [`OrphaDisease`](https://docs.rs/hpo/latest/hpo/annotations/struct.OrphaDisease.html) represents a single ORPHA-diseases, including information about associated `HpoTerm`s.
 
 The most relevant modules are:
-- [`annotations`](https://docs.rs/hpo/latest/hpo/annotations/index.html) contains the `Gene` and `OmimDisease` structs, and some related important types.
+- [`annotations`](https://docs.rs/hpo/latest/hpo/annotations/index.html) contains the `Gene`, `OmimDisease` and `OrphaDisease` structs, and some related important types.
 - [`similarity`](https://docs.rs/hpo/latest/hpo/similarity/index.html) contains structs and helper functions for similarity comparisons for `HpoTerm` and `HpoSet`.
 - [`stats`](https://docs.rs/hpo/latest/hpo/stats/index.html) contains functions to calculate the hypergeometric enrichment score of genes or diseases.
 
@@ -67,7 +68,7 @@ Finally, load the data using [`Ontology::from_binary`]:
 ### Ontology
 ```rust
 use hpo::{Ontology, HpoTermId};
-use hpo::annotations::{GeneId, OmimDiseaseId};
+use hpo::annotations::{GeneId, OmimDiseaseId, OrphaDiseaseId};
 
 fn example() {
     let ontology = Ontology::from_standard("/path/to/master-data/").unwrap();
@@ -87,6 +88,11 @@ fn example() {
         // do something with disease
     }
 
+    // iterate orpha diseases
+    for disease in ontology.orpha_diseases() {
+        // do something with disease
+    }
+
     // get a single HPO term using HPO ID
     let hpo_id = HpoTermId::try_from("HP:0000123").unwrap();
     let term = ontology.hpo(hpo_id);
@@ -98,6 +104,10 @@ fn example() {
     let disease_id = OmimDiseaseId::from(12345u32);
     let disease = ontology.omim_disease(&disease_id);
 
+    // get a single Orpha disease
+    let disease_id = OrphaDiseaseId::from(12345u32);
+    let disease = ontology.orpha_disease(&disease_id);
+
     // get a single Gene
     let hgnc_id = GeneId::from(12345u32);
     let gene = ontology.gene(&hgnc_id);

examples/bench_compare_gene_to_diseases.rs

@@ -2,6 +2,7 @@ use std::path::Path;
 
 use rayon::prelude::*;
 
+use hpo::annotations::Disease;
 use hpo::similarity::GroupSimilarity;
 use hpo::{HpoSet, Ontology};
 

examples/compare_ontologies.rs

@@ -3,6 +3,7 @@
 //! This is helpful for checking correctness of the parser modules
 //! or to see changes after a new HPO release
 
+use hpo::annotations::Disease;
 use hpo::comparison::Comparison;
 use hpo::{HpoTermId, Ontology};
 use std::{path::Path, process};
@@ -52,6 +53,14 @@ fn overview(diffs: &Comparison) {
     for disease in diffs.removed_omim_diseases() {
         println!("Removed\t{}\t{}", disease.id(), disease.name());
     }
+
+    for disease in diffs.added_orpha_diseases() {
+        println!("Added\t{}\t{}", disease.id(), disease.name());
+    }
+
+    for disease in diffs.removed_orpha_diseases() {
+        println!("Removed\t{}\t{}", disease.id(), disease.name());
+    }
 }
 
 /// Prints info about Term-specific changes
@@ -141,7 +150,11 @@ fn changed_genes(diffs: &Comparison) {
 /// Prints info about Gene-specific changes
 fn changed_diseases(diffs: &Comparison) {
     println!("#Disease Delta\tID\tOld Name:New Name\tn Terms Old\tn Terms New\tAdded Terms\tRemoved Terms");
-    for disease in diffs.changed_omim_diseases() {
+    for disease in diffs
+        .changed_omim_diseases()
+        .iter()
+        .chain(diffs.changed_orpha_diseases().iter())
+    {
         print!("Delta\t{}", disease.id());
         if let Some(names) = disease.changed_name() {
             print!("\t{}:{}", names.0, names.1);

examples/dendogram.rs

@@ -1,7 +1,7 @@
 use std::env::Args;
 use std::path::Path;
 
-use hpo::annotations::OmimDisease;
+use hpo::annotations::{Disease, OmimDisease};
 use rayon::prelude::*;
 
 use hpo::similarity::GroupSimilarity;

examples/disease_similarity.rs

@@ -4,7 +4,7 @@ use std::io::Write;
 use std::{env::Args, time::SystemTime};
 
 use hpo::{
-    annotations::{OmimDisease, OmimDiseaseId},
+    annotations::{Disease, OmimDisease, OmimDiseaseId},
     similarity::{GraphIc, GroupSimilarity, StandardCombiner},
     term::HpoGroup,
     HpoSet, HpoTermId, Ontology,
@@ -120,6 +120,29 @@ fn cross_compare_diseases(
     }
 }
 
+fn compare_omim_to_orpha(ontology: &Ontology, sim: &GroupSimilarity<GraphIc, StandardCombiner>) {
+    let omim: Vec<&OmimDisease> = ontology.omim_diseases().collect();
+
+    let omim_names: Vec<&str> = omim.iter().map(|d| d.name()).collect();
+
+    let omim_sets: Vec<HpoSet> = omim.iter().map(|d| d.to_hpo_set(ontology)).collect();
+
+    println!("Orpha\\Omim\t{}", omim_names.join("\t"));
+
+    ontology
+        .orpha_diseases()
+        .take(100)
+        .par_bridge()
+        .for_each(|orpha| {
+            let orpha_set = orpha.to_hpo_set(ontology);
+            let mut row = orpha.name().to_string();
+            for omim_set in omim_sets.iter() {
+                row.push_str(&format!("\t{}", sim.calculate(&orpha_set, omim_set)));
+            }
+            println!("{row}");
+        })
+}
+
 fn main() {
     let ontology = Ontology::from_binary("tests/ontology.hpo").unwrap();
     let combiner = StandardCombiner::FunSimAvg;
@@ -135,6 +158,12 @@ fn main() {
             if let Ok(num) = arg.parse::<usize>() {
                 // integer provided, using disease x disease comparisons
                 cross_compare_diseases(&ontology, &sim, num);
+            } else if arg == "orpha" {
+                let sim = GroupSimilarity::new(
+                    StandardCombiner::FunSimAvg,
+                    GraphIc::new(hpo::term::InformationContentKind::Gene),
+                );
+                compare_omim_to_orpha(&ontology, &sim);
             } else {
                 // List of HPO terms provided
                 compare_custom_set_to_diseases(&ontology, &sim, arg);
@@ -153,6 +182,9 @@ fn main() {
                 - Cross compare N diseases\n\
                     disease_similarity <NUMBER OF COMPARISONS>\n\
                     disease_similarity 20
+                - Compare all OMIM to all ORPHA diseases\n\
+                    disease_similarity orpha\n\
+                    disease_similarity orpha
             ");
         }
     }

examples/enrichment.rs

@@ -1,6 +1,10 @@
 use std::{env::Args, process};
 
-use hpo::{annotations::OmimDiseaseId, term::HpoGroup, HpoResult, HpoSet, HpoTermId, Ontology};
+use hpo::{
+    annotations::{Disease, OmimDiseaseId},
+    term::HpoGroup,
+    HpoResult, HpoSet, HpoTermId, Ontology,
+};
 
 /// Tries to parse an HpoTermId from a string `HP:0007768` or a `u32`
 fn id_from_freetext(value: &str) -> HpoResult<HpoTermId> {

examples/gene_similarity.rs

@@ -0,0 +1,153 @@
+use rayon::prelude::*;
+use std::io;
+use std::io::Write;
+use std::{env::Args, time::SystemTime};
+
+use hpo::{
+    annotations::{Gene, GeneId},
+    similarity::{GraphIc, GroupSimilarity, StandardCombiner},
+    term::HpoGroup,
+    HpoSet, HpoTermId, Ontology,
+};
+
+/// Calculates the similarity score of two diseases
+/// The two diseases are specified as OMIM-ID via CLI arguments
+fn compare_two_genes(
+    ontology: &Ontology,
+    sim: &GroupSimilarity<GraphIc, StandardCombiner>,
+    mut args: Args,
+) {
+    let symbol_a = args.nth(1).unwrap();
+    let symbol_b = args.next().unwrap();
+
+    let gene_a = ontology
+        .gene_by_name(&symbol_a)
+        .expect("The first gene is not part of the Ontology");
+    let gene_b = ontology
+        .gene_by_name(&symbol_b)
+        .expect("The second gene is not part of the Ontology");
+
+    let set_a = gene_a.to_hpo_set(ontology);
+    let set_b = gene_b.to_hpo_set(ontology);
+
+    let res = sim.calculate(&set_a, &set_b);
+    println!("Similarity is {res}");
+}
+
+/// Calculates the similarity score of a custom HPO-Set
+/// to all OMIM diseases
+/// The HPO-Set is specified as a comma separated list of HPO-Term-IDs
+fn compare_custom_set_to_genes(
+    ontology: &Ontology,
+    sim: &GroupSimilarity<GraphIc, StandardCombiner>,
+    terms: String,
+) {
+    let hpo_terms = terms.split(',');
+    let mut group = HpoGroup::default();
+    for t in hpo_terms {
+        group.insert(HpoTermId::try_from(t).expect("Invalid HpoTermId"));
+    }
+    let set_a = HpoSet::new(ontology, group);
+
+    let start = SystemTime::now();
+    let mut results: Vec<(&Gene, f32)> = ontology
+        .genes()
+        .par_bridge()
+        .map(|gene| {
+            let res = sim.calculate(&set_a, &gene.to_hpo_set(ontology));
+            (gene, res)
+        })
+        .collect();
+    let end = SystemTime::now();
+    let duration = end.duration_since(start).unwrap();
+
+    println!(
+        "Number of comparisons: {} in {} sec",
+        results.len(),
+        duration.as_secs()
+    );
+    results.sort_by(|a, b| b.1.partial_cmp(&a.1).unwrap());
+
+    let mut stdout = io::stdout().lock();
+    for x in results {
+        stdout
+            .write_all(format!("{}\t{}\t{}\n", x.0.id(), x.0.name(), x.1).as_bytes())
+            .unwrap();
+    }
+}
+
+/// Calculate the pairwise similarity of all diseases to <num> other
+/// diseases.
+fn cross_compare_genes(
+    ontology: &Ontology,
+    sim: &GroupSimilarity<GraphIc, StandardCombiner>,
+    num: usize,
+) {
+    let start = SystemTime::now();
+    let results: Vec<(GeneId, GeneId, f32)> = ontology
+        .genes()
+        .par_bridge()
+        .flat_map(|gene_a| {
+            ontology
+                .genes()
+                .take(num)
+                .map(|gene_b| {
+                    let res =
+                        sim.calculate(&gene_a.to_hpo_set(ontology), &gene_b.to_hpo_set(ontology));
+                    (*gene_a.id(), *gene_b.id(), res)
+                })
+                .collect::<Vec<(GeneId, GeneId, f32)>>()
+        })
+        .collect();
+    let end = SystemTime::now();
+    let duration = end.duration_since(start).unwrap();
+
+    println!(
+        "Number of comparisons: {} in {} sec",
+        results.len(),
+        duration.as_secs()
+    );
+
+    let mut stdout = io::stdout().lock();
+    for x in results {
+        stdout
+            .write_all(format!("{}\t{}\t{}\n", x.0, x.1, x.2).as_bytes())
+            .unwrap();
+    }
+}
+
+fn main() {
+    let ontology = Ontology::from_binary("tests/example.hpo").unwrap();
+    let sim = GroupSimilarity::default();
+
+    let mut args = std::env::args();
+
+    match args.len() {
+        3 => compare_two_genes(&ontology, &sim, args),
+        2 => {
+            let arg = args.nth(1).unwrap();
+            if let Ok(num) = arg.parse::<usize>() {
+                // integer provided, using disease x disease comparisons
+                cross_compare_genes(&ontology, &sim, num);
+            } else {
+                // List of HPO terms provided
+                compare_custom_set_to_genes(&ontology, &sim, arg);
+            }
+        }
+        _ => {
+            println!("Calculate similarities of genes\n\n");
+            println!("\
+                There are 3 different options:\n\
+                - Compare 2 genes\n\
+                    gene_similarity <Gene symbol> <Gene symbol>\n\
+                    gene_similarity 618395 615368\n\n\
+                - Compare all genes to a custom HPO-Set\n\
+                    gene_similarity <HPO-TERM-IDs>\n\
+                    gene_similarity HP:0000750,HP:0000752,HP:0001249,HP:0007018,HP:0010818,HP:0011463\n\n\
+                - Cross compare N genes\n\
+                    gene_similarity <NUMBER OF COMPARISONS>\n\
+                    gene_similarity 20
+            ");
+        }
+    }
+}

examples/search_by_name.rs

@@ -1,12 +1,13 @@
 //! Prints every term and its associated genes
 
+use hpo::annotations::Disease;
 use hpo::Ontology;
 
 fn main() {
     let ontology = Ontology::from_binary("tests/ontology.hpo").unwrap();
-    let cystinosis = ontology.omim_disease_by_name("Cystinosis").unwrap();
-    println!("first match: {:?}", cystinosis.name());
-    for result in ontology.omim_diseases_by_name("Cystinosis") {
+    let congenital = ontology.omim_disease_by_name("congenital").unwrap();
+    println!("first match: {:?}", congenital.name());
+    for result in ontology.omim_diseases_by_name("congenital") {
         println!("{:?}", result.name());
     }
 }