Expand description
Β§horned-functional
An OWL2 Functional-style Syntax parser for horned-owl
.
Β§πΊοΈ Overview
This library provides extensions to the horned-owl
crate to work with the OWL Functional-Style syntax.
It provides a parser written with pest
and a serializer.
Β§π Usage
Add the latest versions of horned-owl
and horned-functional
to the
[dependencies]
sections of your Cargo.toml
manifest:
[dependencies]
horned-owl = "0.11.0"
horned-functional = "0.4.0"
Β§π Parser
To easily read an entire OWL document, including prefixes, use the
horned_functional::to_string
function:
use horned_owl::ontology::set::SetOntology;
let s = std::fs::read_to_string("tests/data/ms.obo.ofn")
.expect("failed to read OWL file");
let (ontology, prefixes) = horned_functional::from_str::<SetOntology, _>(&s)
.expect("failed to parse OWL file");
All OWL elements can be parsed from functional syntax as well, using the
FromFunctional
trait to read a from a serialized string with the from_ofn
method:
use horned_owl::model::Axiom;
use horned_functional::FromFunctional;
let axiom = Axiom::from_ofn("Declaration(Class(<http://purl.obolibrary.org/obo/MS_1000031>))")
.expect("failed to parse axiom");
If the serialized version contains abbreviated IRIs, you can pass a custom
prefix mapping to the from_ofn_ctx
method:
use horned_owl::model::Axiom;
use horned_functional::FromFunctional;
let mut mapping = curie::PrefixMapping::default();
mapping.add_prefix("obo", "http://purl.obolibrary.org/obo/").ok();
let ctx = horned_functional::Context::from(&mapping);
let axiom = Axiom::from_ofn_ctx("Declaration(Class(obo:MS_1000031))", &ctx)
.expect("failed to parse axiom");
Β§βοΈ Serializer
To easily serialize an entire OWL document, including prefixes, use the
horned_functional::to_string
function:
let mut file = std::fs::File::open("tests/data/ms.owx")
.map(std::io::BufReader::new)
.expect("failed to open OWL file");
let (ontology, prefixes) = horned_owl::io::owx::reader::read(&mut file)
.expect("failed to read OWL file");
// `horned_functional::to_string` needs an AxiomMappedOntology
let axiom_mapped = ontology.into();
// serialize using the same prefixes as the input OWL/XML file
let ofn = horned_functional::to_string(&axiom_mapped, &prefixes);
// serialize without abbreviated IRIs
let ofn = horned_functional::to_string(&axiom_mapped, None);
All OWL elements can be displayed in functional syntax as well, using
a custom Display
implementation, allowing the functional syntax in
format!
,
println!
or
write!
macros.
Just add the AsFunctional
trait to the scope, and use the as_ofn
method
to get a displayable type for any supported element:
use horned_owl::model::*;
use horned_functional::AsFunctional;
let build = Build::new();
// build a Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002175>))
let op = build.object_property("http://purl.obolibrary.org/obo/RO_0002175");
let axiom = Axiom::from(DeclareObjectProperty(op));
println!("Axiom: {}", axiom.as_ofn());
Β§π Feedback
Β§β οΈ Issue Tracker
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.
Β§π Changelog
This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.
Β§π License
This library is provided under the open-source MIT license.
Β§π° Citation
This project was developed by Martin Larralde as part of a Masterβs 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)
Structs§
- A context to pass around while parsing and writing OWL functional documents.
- A wrapper for displaying an OWL2 element in functional syntax.
Enums§
- The error type for this crate.
Traits§
- A trait for OWL elements that can be serialized to OWL Functional syntax.
- A trait for OWL elements that can be deserialized from OWL Functional syntax.
Functions§
- Parse an entire OWL document from a file on the local filesystem.
- Parse an entire OWL document from a
Read
implementor. - Parse an entire OWL document from a string.
- Render an entire OWL document to a string.
Type Aliases§
- The result type for this crate.