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Faultless AST for Open Biomedical Ontologies.

This library provides a mostly-complete implementation of theOBO flat file format 1.4.

• Data structures -fastobo provides a complete owned AST for theOBO language, with constructors and covenience traits where applicable.There is a plan to provide borrowed data structures as well, to be ableto build a view of an OBO document from borrowed data.
• Parsing - The parser is implemented usingpest,and is reexported from thefastobo-syntaxcrate. Most structures implement theFromPairtrait which allows to build a data structure from a stream of pest tokens.
• Errors - All functions in that crate that return aResult willalways use theError struct defined in theerror module. Errorsreported by pest are very meaningful, and can give the exact locationof a syntax error encountered by the parser.
• Semantics - This library exports specific methods that can be usedto edit an OBO syntax tree with the semantics expected in the formatguide: mapping identifiers to URLs, adding default namespaces, orexpanding entity frames usingtreat-xrefs macros.

Warning: this project adheres toSemantic Versioning,but the API is likely to change a lot before the release of a stable 1.0.

All the following features are enabled by default, but can be disabled andcherry-picked using thedefault-features = false option in theCargo.tomlmanifest of your project:

• memchr - Use thememchr library to improveparser speed when searching for a particular character in a buffer.
• threading - Use a multi-threaded parser (additionally depending oncrossbeam-channel), which can greatlyimprove the parser speed if parsing is CPU-bound.
• smartstring - Use thesmartstringlibrary to reduce heap allocation for identifiers and string data.

Addfastobo to the[dependencies] sections of yourCargo.toml manifest:

[dependencies]fastobo ="0.15.2"

The top-levelfastobo module provides several functions to parse anOboDoc.Usefastobo::from_reader to load an OBO document from aBufRead implementor(usestd::io::BufReaderif needed):

externcrate fastobo;externcrate ureq;fnmain(){letmut response = ureq::get("http://purl.obolibrary.org/obo/ms.obo").call().unwrap();letmut 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),}}

• fastobo-syntax: Standalonepest parserfor the OBO format version 1.4.
• fastobo-graphs: Data model andserdeimplementation of the OBO graphs specification, with conversion traits from and to OBO.
• fastobo-py: Idiomatic Python bindings tothis crate.
• fastobo-validator: Standalone CLIto validate OBO files against the specification.
• horned-functional: Parser forOWL2 Functional Syntax (can be used to parseowl-axioms clauses).

Found a bug ? Have an enhancement request ? Head over to theGitHub issue tracker of the project ifyou need to report or ask something. If you are filling in on a bug, please include as muchinformation as you can about the issue, and try to recreate the same bug in a simple, easilyreproducible situation.

This project was developed byMartin Larraldeas part of a Master's Degree internship in theBBOP team of theLawrence Berkeley National Laboratory, under the supervision ofChris 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)