https://github.com/fastobo/fastobo
Faultless AST for Open Biomedical Ontologies.
https://github.com/fastobo/fastobo
ast obo obofoundry ontology
Last synced: about 1 month ago
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Faultless AST for Open Biomedical Ontologies.
- Host: GitHub
- URL: https://github.com/fastobo/fastobo
- Owner: fastobo
- License: mit
- Created: 2019-03-19T02:47:15.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2025-02-19T22:08:42.000Z (2 months ago)
- Last Synced: 2025-02-28T05:30:50.419Z (about 2 months ago)
- Topics: ast, obo, obofoundry, ontology
- Language: Rust
- Homepage:
- Size: 1.27 MB
- Stars: 28
- Watchers: 2
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: COPYING
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README
# `fastobo` [](https://github.com/fastobo/fastobo/stargazers)
*Faultless AST for Open Biomedical Ontologies.*
[](https://github.com/fastobo/fastobo/actions)
[](https://codecov.io/gh/fastobo/fastobo)
[](https://choosealicense.com/licenses/mit/)
[](https://github.com/fastobo/fastobo)
[](https://crates.io/crates/fastobo)
[](https://docs.rs/fastobo)
[](https://github.com/fastobo/fastobo/blob/master/CHANGELOG.md)
[](https://github.com/fastobo/fastobo/issues)
[](https://f1000research.com/posters/8-1500)
## Overview
This library provides a mostly-complete implementation of the
[OBO flat file format 1.4](http://owlcollab.github.io/oboformat/doc/obo-syntax.html).
* **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](http://pest.rs/),
and is reexported from the [`fastobo-syntax`](https://crates.io/crates/fastobo-syntax)
crate. Most structures implement the [`FromPair`](./parser/trait.FromPair.html)
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 the `Error` struct defined in the `error` 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](http://semver.org/spec/v2.0.0.html),
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 the [`memchr`](https://docs.rs/memchr/) library to improve
parser speed when searching for a particular character in a buffer.
* **`threading`** - Use a multi-threaded parser (additionally depending on
[`crossbeam-channel`](https://docs.rs/crossbeam-channel)), which can greatly
improve the parser speed if parsing is CPU-bound.
* **`smartstring`** - Use the [`smartstring`](https://docs.rs/smartstring)
library to reduce heap allocation for identifiers and string data.
## Usage
Add `fastobo` to the `[dependencies]` sections of your `Cargo.toml` manifest:
```toml
[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`](https://doc.rust-lang.org/std/io/trait.BufRead.html) implementor
(use [`std::io::BufReader`](https://doc.rust-lang.org/std/io/struct.BufReader.html)
if needed):
```rust
extern crate fastobo;
extern crate ureq;
fn main() {
let mut response = ureq::get("http://purl.obolibrary.org/obo/ms.obo").call().unwrap();
let mut reader = std::io::BufReader::new(response.body_mut().as_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`](https://crates.io/crates/fastobo-syntax): Standalone `pest` parser
for the OBO format version 1.4.
* [`fastobo-graphs`](https://crates.io/crates/fastobo-graphs): Data model and `serde`
implementation of the OBO graphs specification, with conversion traits from and to OBO.
* [`fastobo-py`](https://pypi.org/project/fastobo/): Idiomatic Python bindings to
this crate.
* [`fastobo-validator`](https://crates.io/crates/fastobo-validator): Standalone CLI
to validate OBO files against the specification.
* [`horned-functional`](https://crates.io/crates/horned-functional): Parser for
OWL2 Functional Syntax (can be used to parse `owl-axioms` clauses).
## Feedback
Found a bug ? Have an enhancement request ? Head over to the
[GitHub issue tracker](https://github.com/fastobo/fastobo/issues) 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](https://github.com/althonos)
as part of a Master's Degree internship in the [BBOP team](http://berkeleybop.org/) of the
[Lawrence Berkeley National Laboratory](https://www.lbl.gov/), under the supervision of
[Chris Mungall](http://biosciences.lbl.gov/profiles/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](https://doi.org/10.7490/f1000research.1117405.1))