fastobo-graphs

OBO Graphs decoder and encoder in Rust.

Overview

This library provides an implementation of the OBO Graphs schema specified by the Gene Ontology to provide developers with a data format easier to use than plain ontology files in OBO or OWL format.

• Data structures - the complete OBO Graphs schema is reproduced into Rust data structures with public fields for direct access to the graphs nodes. See fastobo_graphs::model to see the comprehensive list of data structures.
• I/O - structures use serde to implement serialization and deserialization from both YAML and JSON.
• Errors - fallible operations can return an Error with informative messages as well as an std::error::Error implementation.
• Conversion traits - OBO Graphs can be (partially) converted to and from plain OBO documents, using the FromGraph and IntoGraph traits.

Usage

Add fastobo_graphs to the [dependencies] sections of your Cargo.toml manifest:

[dependencies]
fastobo-graphs = "0.4"

Then use one of the top-level functions in fastobo_graphs to load a JSON or YAML serialized OBO Graph:

extern crate fastobo_graphs;
extern crate ureq;

fn main() {
    let response = ureq::get("http://purl.obolibrary.org/obo/zeco.json").call();

    match fastobo_graphs::from_reader(response.unwrap().into_reader()) {
        Ok(doc) => println!("Number of ZECO nodes: {}", doc.graphs[0].nodes.len()),
        Err(e) => panic!("Could not parse ZECO OBO Graph: {}", e),
    }
}

Features

The following feature is enabled by default, but can be disabled if needed:

• obo - compile FromGraph and IntoGraph traits that can be used to convert between a GraphDocument and an OboDoc.

Feedback

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker of the project if you need to report or ask something. If you are filling in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.

About

This project was developed by Martin Larralde as part of a Master's Degree internship in the BBOP team of the Lawrence Berkeley National Laboratory, under the supervision of Chris Mungall. Cite this project as:

Larralde M. Developing Python and Rust libraries to improve the ontology ecosystem [version 1; not peer reviewed]. F1000Research 2019, 8(ISCB Comm J):1500 (poster) (https://doi.org/10.7490/f1000research.1117405.1)