Crate oboannotation 

This library simplifies accessing annotations of biomedical ontologies.

Supported ontologies

The library supports the following ontologies

• Human Phenotype Ontology (HPO)
• Gene Ontology (GO)

Examples

Load HPO annotations

Load a toy HPO annotation file:

use oboannotation::io::AnnotationLoader;
use oboannotation::hpo::HpoAnnotation;
use oboannotation::hpo::io::{HpoAnnotationLines, HpoAnnotationLoader};

// 👇 Replace with path to a real file 👇
let fpath_hpoa = "data/phenotype.real-shortlist.hpoa";

let loader = HpoAnnotationLoader::default();
let data: HpoAnnotationLines = loader.load_from_path(fpath_hpoa)
                                 .expect("Toy HPOA should be well formatted");

assert_eq!(data.lines.len(), 86); // Toy HPOA includes 86 records

See HpoAnnotationLines and HpoAnnotation to learn more about the data format.

Load GO annotations

Load a toy GO annotation file containing annotations of FBN1 and SURF1 genes for Homo sapiens.

use oboannotation::io::AnnotationLoader;
use oboannotation::go::{GoAnnotations, GoGafAnnotationLoader};

// 👇 Replace with path to a real file 👇
let fpath_goa = "data/goa_human.SURF1_FBN1.gaf";

let loader = GoGafAnnotationLoader;
let data: GoAnnotations = loader.load_from_path(fpath_goa)
                            .expect("Toy GO annotations should be well formatted");

assert_eq!(data.annotations.len(), 156); // Toy GO annotations include 156 records

See GoAnnotations and GoAnnotation to learn more about the data format.

Modules

go

Parse Gene Ontology annotations.

hpo

Types and I/O for working with HPO Annotations.

io

Load ontology annotations.