34 releases
0.15.2 | May 3, 2023 |
---|---|
0.15.1 | Dec 5, 2022 |
0.15.0 | Feb 15, 2022 |
0.13.1 | Mar 30, 2021 |
0.6.1 | Jul 24, 2019 |
#7 in #obo
345 downloads per month
Used in 5 crates
(via fastobo)
12KB
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fastobo
Faultless AST for Open Biomedical Ontologies.
Overview
This library provides a mostly-complete implementation of the OBO flat file format 1.4.
- Data structures -
fastobo
provides a complete owned AST for the OBO language, with constructors and covenience traits where applicable. There is a plan to provide borrowed data structures as well, to be able to build a view of an OBO document from borrowed data. - Parsing - The parser is implemented using pest,
and is reexported from the
fastobo-syntax
crate. Most structures implement theFromPair
trait which allows to build a data structure from a stream of pest tokens. - Errors - All functions in that crate that return a
Result
will always use theError
struct defined in theerror
module. Errors reported by pest are very meaningful, and can give the exact location of a syntax error encountered by the parser. - Semantics - This library exports specific methods that can be used
to edit an OBO syntax tree with the semantics expected in the format
guide: mapping identifiers to URLs, adding default namespaces, or
expanding entity frames using
treat-xrefs
macros.
Warning: this project adheres to Semantic Versioning, but the API is likely to change a lot before the release of a stable 1.0.
Features
All the following features are enabled by default, but can be disabled and
cherry-picked using the default-features = false
option in the Cargo.toml
manifest of your project:
memchr
- Use thememchr
library to improve parser speed when searching for a particular character in a buffer.threading
- Use a multi-threaded parser (additionally depending oncrossbeam-channel
), which can greatly improve the parser speed if parsing is CPU-bound.smartstring
- Use thesmartstring
library to reduce heap allocation for identifiers and string data.
Usage
Add fastobo
to the [dependencies]
sections of your Cargo.toml
manifest:
[dependencies]
fastobo = "0.15.2"
The top-level fastobo
module provides several functions to parse an OboDoc
.
Use fastobo::from_reader
to load an OBO document from a
BufRead
implementor
(use std::io::BufReader
if needed):
extern crate fastobo;
extern crate ureq;
fn main() {
let response = ureq::get("http://purl.obolibrary.org/obo/ms.obo").call();
let mut reader = std::io::BufReader::new(response.unwrap().into_reader());
match fastobo::from_reader(&mut reader) {
Ok(doc) => println!("Number of MS entities: {}", doc.entities().len()),
Err(e) => panic!("Could not parse the Mass-Spec Ontology: {}", e),
}
}
See also
fastobo-syntax
: Standalonepest
parser for the OBO format version 1.4.fastobo-graphs
: Data model andserde
implementation of the OBO graphs specification, with conversion traits from and to OBO.fastobo-py
: Idiomatic Python bindings to this crate.fastobo-validator
: Standalone CLI to validate OBO files against the specification.horned-functional
: Parser for OWL2 Functional Syntax (can be used to parseowl-axioms
clauses).
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)
Dependencies
~0.6–1.1MB
~25K SLoC