Crate obofoundry

Expand description

Structures to deserialize OBO Foundry listings into.

This library provides structs that can make use of serde_yaml and serde_json to deserialize the table of ontologies provided by the OBO Foundry. It provides a safe and efficient alternative to manually parsing the obtained JSON/YAML, which is actually quite tricky since there is no actual scheme available. Use the Foundry type as an entry point for deserialization.

Example

Download the ontologies.yml table from the OBO Foundry and use it to extract all PURLs to ontologies in the OBO format:

extern crate obofoundry;
extern crate ureq;
extern crate serde_yaml;
use std::io::Read;

const URL: &'static str = "http://www.obofoundry.org/registry/ontologies.yml";

fn main() {

    let res = ureq::get(URL).call();
    let reader = res.unwrap().into_reader();

    let foundry: obofoundry::Foundry = serde_yaml::from_reader(reader).unwrap();
    for ontology in &foundry.ontologies {
        for product in &ontology.products {
            if product.id.ends_with(".obo") {
                println!("{} - {}", product.id, product.ontology_purl)
            }
        }
    }
}