Crate obofoundry

Expand description

§`obofoundry.rs`

Structures to deserialize OBO Foundry listings into.

§Usage

Add the obofoundry crate to the Cargo.toml manifest, as well as either serde_yaml or serde_json:

[dependencies]
obofoundry = "0.11"
serde_yaml = "0.8"

Then use the serde framework to load the listings:

extern crate obofoundry;
extern crate serde_yaml;

let yaml_data = include_str!("...");
let foundry: obofoundry::Foundry = serde_yaml::from_str(&yml).unwrap();

It’s also possible to use an HTTP library to load the listings from the OBO Foundry website directly, for instance using ureq:

extern crate obofoundry;
extern crate ureq;
extern crate serde_yaml;

let url = "http://www.obofoundry.org/registry/ontologies.yml";

let res = ureq::get(url).call();
let reader = res.unwrap().into_reader();
let foundry: obofoundry::Foundry = serde_yaml::from_reader(reader).unwrap();

§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)
            }
        }
    }
}

See the online documentation at docs.rs for more examples.

§Changelog

This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.

§License

This library is provided under the open-source MIT license.

Structs§

Browser: A reference to a browser for the ontology.
Build: Information about the way an ontology is built.
Contact: The corresponding editor of an ontology.
Dependency: Reference to a particular dependency.
Development: Metadata concerning the development of the ontology.
Document: A review document.
Example: A reference to an example usage of the ontology.
Foundry: An index of ontologies following the OBO Foundry principles.
Funding: A funding reference.
Job: A CI/CD job pipeline running for the ontology.
License: The legal information about an ontology.
Ontology: A comprehensive table of informations about an ontology.
Product: A released product of an ontology.
Publication: A publication relevant to the ontology.
Redirect: A redirection to another location.
Review: A review for a particular ontology.
Taxon: A taxon specifically relevant to the ontology.
Usage: A relevant project an ontology is used in.

Enums§

ActivityStatus: The current development status of the ontology development.
BuildMethod: The build method for an ontology build.
BuildSystem: The build system for an ontology build.
JobType: The type of a job pipeline.
UsageType: The way an ontology can be used in a project.