fastobo

Faultless AST for Open Biomedical Ontologies.

Overview

This library provides an abstract syntax tree for the OBO flat file format 1.4.

Usage

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

[dependencies]
fastobo = "0.1.0"

The OboDoc struct acts as the root of the AST. Use OboDoc::from_stream to load an OBO document from a BufRead implementor (use std::io::BufReader if needed):

extern crate fastobo;
extern crate reqwest;

fn main() {
    let response = reqwest::get("http://purl.obolibrary.org/obo/go.obo").unwrap();
    let mut reader = std::io::BufReader::new(response);

    match fastobo::ast::OboDoc::from_stream(&mut reader) {
        Ok(doc) => println!("Number of GO entities: {}", doc.entities.len()),
        Err(e) => panic!("Could not parse the Gene Ontology: {}", e),
    }
}

Missing features

• Support for comment blocks between frames
• Support for comments in property_value clauses in headers.
• More std traits implementation.

See also

• fastobo-syntax: Standalone pest parser for the OBO format version 1.4.
• fastobo-py: Idiomatic Python bindings to this crate.

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 is currently being 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.