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fastobo-owl Star me

OWL language mapping for ontologies in the OBO flat file format 1.4

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Overview

This library provides an implementation of the OBO to OWL mappings for the OBO format version 1.4 ontology language. It can be used to produce a semantically-equivalent OWL ontology from any OBO ontology.

Usage

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

[dependencies]
fastobo-owl = "0.2.1"

Then use the IntoOwl trait to convert an OboDoc into any OWL ontology (the output type must implement the Default, Ontology and MutableOntology traits). Here's a how you could write a very simple script to load an OBO document from a file, convert it to OWL, and write it to another file in OWL/XML syntax:

extern crate fastobo;
extern crate fastobo_owl;

use fastobo_owl::IntoOwl;

// load an OBO ontology from a file
let obo = fastobo::from_file("tests/data/ms.obo").expect("failed to read OBO file");

// extract prefixes from the OBO header, so that they can be used
// to build abbreviated IRIs when serializing the OWL output
// (note: this contains OBO default prefixes such as xsd, rdf, or oboInOwl)
let prefixes = obo.prefixes();

// convert the ontology to OBO (the ontology type is implied by the later
// call to owx::writer::write which expects an `AxiomMappedOntology`)
let owl = obo.into_owl()
  .expect("failed to convert OBO to OWL");

// write the OWL ontology with abbreviated IRIs
let mut output = std::fs::File::create("tests/data/ms.owx").unwrap();
horned_owl::io::owx::writer::write(&mut output, &owl, Some(&prefixes));

See also

  • fastobo-syntax: Standalone pest parser for the OBO format version 1.4.
  • fastobo: Abstract Syntax Tree and data structures for the OBO format version 1.4.
  • fastobo-py: Idiomatic Python bindings to the fastobo crate.
  • fastobo-graphs: Data model and serde implementation of the OBO graphs specification, with conversion traits from and to OBO.
  • fastobo-validator: Standalone CLI to validate OBO files against the specification.

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)