https://github.com/althonos/obofoundry.rs

Structures to deserialize OBO Foundry listings into.

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
1 of 3 committers (33.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (9.1%) to scientific vocabulary

Keywords

berkeley-bop obo obofoundry rust serde

Keywords from Contributors

annotation bioinformatics filesystem pyfilesystem2 progress-bar archive biopython moclo modular-cloning plasmids

Last synced: 6 months ago · JSON representation

Repository

Structures to deserialize OBO Foundry listings into.

Basic Info

Host: GitHub
Owner: althonos
License: mit
Language: Rust
Default Branch: master
Size: 64.5 KB

Statistics

Stars: 0
Watchers: 2
Forks: 0
Open Issues: 1
Releases: 16

Topics

berkeley-bop obo obofoundry rust serde

Created almost 7 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog License

README.md

`obofoundry.rs`

Structures to deserialize OBO Foundry listings into.

Usage

Add the obofoundry crate to the Cargo.toml manifest, as well as either serde_yaml or serde_json:

toml [dependencies] obofoundry = "0.8" serde_yaml = "0.8"

Then use the serde framework to load the listings:

```rust,ignore extern crate obofoundry; extern crate serde_yaml;

let yamldata = includestr!("..."); let foundry: obofoundry::Foundry = serdeyaml::fromstr(&yml).unwrap(); ```

It's also possible to use an HTTP library to load the listings from the OBO Foundry website directly, for instance using ureq:

```rust extern crate obofoundry; extern crate ureq; extern crate serde_yaml;

let url = "http://www.obofoundry.org/registry/ontologies.yml";

let res = ureq::get(url).call(); let reader = res.unwrap().intoreader(); let foundry: obofoundry::Foundry = serdeyaml::from_reader(reader).unwrap(); ```

Example

Download the ontologies.yml table from the OBO Foundry and use it to extract all PURLs to ontologies in the OBO format:

```rust extern crate obofoundry; extern crate ureq; extern crate serde_yaml; use std::io::Read;

const URL: &'static str = "http://www.obofoundry.org/registry/ontologies.yml";

fn main() { let res = ureq::get(URL).call(); let reader = res.unwrap().into_reader();

let foundry: obofoundry::Foundry = serde_yaml::from_reader(reader).unwrap();
for ontology in &foundry.ontologies {
    for product in &ontology.products {
        if product.id.ends_with(".obo") {
            println!("{} - {}", product.id, product.ontology_purl)
        }
    }
}

} ```

See the online documentation at docs.rs for more examples.

Changelog

This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.

License

This library is provided under the open-source MIT license.

Owner

Name: Martin Larralde
Login: althonos
Kind: user
Location: Heidelberg, Germany
Company: EMBL / LUMC, @zellerlab

Twitter: althonos
Repositories: 91
Profile: https://github.com/althonos

PhD candidate in Bioinformatics, passionate about programming, SIMD-enthusiast, Pythonista, Rustacean. I write poems, and sometimes they are executable.

GitHub Events

Total

Pull request event: 1
Create event: 1

Last Year

Pull request event: 1
Create event: 1

Committers

Last synced: 11 months ago

All Time

Total Commits: 78
Total Committers: 3
Avg Commits per committer: 26.0
Development Distribution Score (DDS): 0.397

Past Year

Commits: 3
Committers: 1
Avg Commits per committer: 3.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Martin Larralde	m**e@e**e	47
Martin Larralde	m**e@e**r	30
dependabot-preview[bot]	2****]	1

Committer Domains (Top 20 + Academic)

ens-cachan.fr: 1 embl.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 0
Total pull requests: 8
Average time to close issues: N/A
Average time to close pull requests: about 2 months
Total issue authors: 0
Total pull request authors: 2
Average comments per issue: 0
Average comments per pull request: 0.75
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 8

Past Year

Issues: 0
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 2

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Top Authors

Issue Authors

Pull Request Authors

dependabot-preview[bot] (5)
dependabot[bot] (3)

Top Labels

Issue Labels

Pull Request Labels

dependencies (8)

Packages

Total packages: 1
Total downloads:
- cargo 25,492 total

Total dependent packages: 2
Total dependent repositories: 2
Total versions: 16
Total maintainers: 1

crates.io: obofoundry

Structures to deserialize OBO Foundry listings into.

Documentation: https://docs.rs/obofoundry/
License: MIT
Latest release: 0.11.0
published over 1 year ago

Versions: 16
Dependent Packages: 2
Dependent Repositories: 2
Downloads: 25,492 Total

Rankings

Dependent packages count: 10.4%

Dependent repos count: 13.6%

Downloads: 14.6%

Average: 27.1%

Forks count: 40.8%

Stargazers count: 56.1%

Maintainers (1)

althonos

Last synced: 6 months ago

Dependencies

Cargo.toml cargo

serde_json 1.0 development
serde_yaml 0.8 development
ureq 2.0 development
serde 1.0
url 2.1

.github/workflows/test.yml actions

actions-rs/cargo v1 composite
actions-rs/tarpaulin v0.1 composite
actions-rs/toolchain v1 composite
actions/cache v2 composite
actions/checkout v1 composite
codecov/codecov-action v1 composite
rasmus-saks/release-a-changelog-action v1.0.1 composite