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de-workflow

A ToolBox for fuzzily extracting drugs mentions from text.

https://github.com/uk-ipop/drug-extraction

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary

Keywords

drug-discovery fuzzy-search rust-lang text-processing
Last synced: 6 months ago · JSON representation

Repository

A ToolBox for fuzzily extracting drugs mentions from text.

Basic Info
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 15
Topics
drug-discovery fuzzy-search rust-lang text-processing
Created over 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Stargazers Issues MIT License


Logo

Drug Extraction ToolBox

A suite of tools to extract drugs from text records.

Explore the docs >> CLI | Web
Report Bug | Request Feature

WEBSITE

This project uses string similarity metrics to detect drug mentions inside text records.

Researchers at the University of Kentucky College of Pharmacy had a need for a simple, fast, intuitive interface to extract drug mentions in text records. This project takes text records and detects drug mentions (including misspellings) and then extracts the drug and the corresponding record for analysis.

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Getting Started

In order to set clear expectations for the development of the toolbox and to keep feature requests in scope it is good to set some guidelines.

What this project IS:

  • A suite of tools to extract drug mentions from text records
  • A string parsing tool
  • An interactive playground website

What this project is NOT:

  • An analytical tool
  • A business intelligence tool
  • A preprocessing tool

This toolbox contains multiple projects:

  • A command line tool (available via pipx or cargo install)
  • An interactive website for exploring string similarity metrics

In v1.0.0 we have dropped support for both the de-workflow CLI and the drug-extraction-core library. Both are still available on PyPI.org and crates.io respectively but are not considered to be maintained.

For more information on the reasons for these significant changes, see the CHANGELOG.md.

We utilize string similarity algorithms as defined and implemented by Danny Guo in the str-sim package. For more information on string similarity algorithms, please consult this Wikipedia page for a comparison/list of algorithms and this page for an explanation of string metrics more generally.

The decision to use Rust was based on a series of performance comparison benchmarks and analysis which can be found on the perf-comp branch .

Take a quick look : screen recording

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RoadMap

As of v1.0.0 we are considered stable and will prioritize not breaking features. Most new releases will come via performance improvements or new features (without breaking existing UI).

See the open issues for a full list of proposed features (and known issues).

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Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

  1. Fork the Project
  2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
  3. Commit your Changes (git commit -m 'Add some AmazingFeature')
  4. Push to the Branch (git push origin feature/AmazingFeature)
  5. Open a Pull Request

We use gh release create to make new github releases, cargo release to release to crates.io, and maturin release to release to PyPI.org.

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License

Distributed under the MIT License. See LICENSE for more information.

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Contact

Nick Anthony - @nanthony95 - nicholas.anthony@uky.edu

Project Link: https://github.com/uk-ipop/drug-extraction

Owner

  • Name: UK IPOP
  • Login: UK-IPOP
  • Kind: organization
  • Location: Lexington, KY

University of Kentucky IPOP

GitHub Events

Total
  • Issues event: 3
  • Issue comment event: 10
Last Year
  • Issues event: 3
  • Issue comment event: 10

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 336
  • Total Committers: 2
  • Avg Commits per committer: 168.0
  • Development Distribution Score (DDS): 0.003
Past Year
  • Commits: 25
  • Committers: 1
  • Avg Commits per committer: 25.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nick Anthony n****7@g****m 335
cdelcher 4****r 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 58
  • Total pull requests: 22
  • Average time to close issues: 25 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 0.97
  • Average comments per pull request: 0.68
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 19 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nanthony007 (51)
  • cdelcher (4)
  • Knoxort (3)
Pull Request Authors
  • nanthony007 (23)
Top Labels
Issue Labels
enhancement (23) bug (16) cli (12) documentation (9) workflow (5) help wanted (3) CodeCleanup (3) web (2) good first issue (2) core (1) performance (1) analysis (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 6
  • Total downloads:
    • cargo 12,950 total
    • pypi 132 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 57
  • Total maintainers: 2
proxy.golang.org: github.com/uk-ipop/drug-extraction
  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 6 months ago
proxy.golang.org: github.com/UK-IPOP/drug-extraction

Package main runs the CLI.

  • Versions: 15
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 6 months ago
pypi.org: de-workflow
  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 63 Last month
Rankings
Dependent packages count: 10.1%
Average: 20.3%
Dependent repos count: 21.6%
Downloads: 29.2%
Maintainers (1)
nanthony007
Last synced: 11 months ago
pypi.org: extract-drugs

A CLI for extracting drugs from text records

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 69 Last month
Rankings
Dependent packages count: 7.3%
Average: 24.3%
Dependent repos count: 41.4%
Maintainers (1)
nanthony007
Last synced: 6 months ago
crates.io: drug-extraction-core

A core library for extracting drugs from text records

  • Versions: 3
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 4,172 Total
Rankings
Dependent packages count: 17.0%
Dependent repos count: 29.3%
Average: 36.6%
Forks count: 37.5%
Stargazers count: 43.6%
Downloads: 55.8%
Maintainers (1)
nanthony007
Last synced: 6 months ago
crates.io: drug-extraction-cli

A CLI for extracting drugs from text records

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,778 Total
Rankings
Dependent repos count: 29.3%
Dependent packages count: 33.8%
Forks count: 37.5%
Average: 40.8%
Stargazers count: 43.6%
Downloads: 60.0%
Maintainers (1)
nanthony007
Last synced: 6 months ago

Dependencies

web/package.json npm
  • @types/node 17.0.29 development
  • @types/react 18.0.8 development
  • @types/react-dom 18.0.0 development
  • eslint 8.14.0 development
  • eslint-config-next 12.1.5 development
  • typescript 4.6.3 development
  • @emotion/react ^11.9.0
  • @emotion/styled ^11.8.1
  • @mui/icons-material ^5.6.2
  • @mui/material ^5.6.3
  • @nextui-org/react ^1.0.0-beta.6
  • fast-levenshtein ^3.0.0
  • next 12.1.5
  • react 18.1.0
  • react-dom 18.1.0
  • react-select ^5.3.0
  • sharp ^0.30.4
cli/Cargo.lock cargo
  • addr2line 0.19.0
  • adler 1.0.2
  • anstream 0.3.2
  • anstyle 1.0.0
  • anstyle-parse 0.2.0
  • anstyle-query 1.0.0
  • anstyle-wincon 1.0.1
  • backtrace 0.3.67
  • bitflags 1.3.2
  • bstr 0.2.17
  • cc 1.0.79
  • cfg-if 1.0.0
  • clap 4.3.0
  • clap_builder 4.3.0
  • clap_derive 4.3.0
  • clap_lex 0.5.0
  • color-eyre 0.6.2
  • colorchoice 1.0.0
  • console 0.15.5
  • csv 1.1.6
  • csv-core 0.1.10
  • dialoguer 0.10.3
  • either 1.8.1
  • encode_unicode 0.3.6
  • errno 0.3.1
  • errno-dragonfly 0.1.2
  • eyre 0.6.8
  • gimli 0.27.2
  • heck 0.4.1
  • hermit-abi 0.3.1
  • indenter 0.3.3
  • indicatif 0.17.3
  • io-lifetimes 1.0.5
  • is-terminal 0.4.7
  • itertools 0.10.5
  • itoa 0.4.8
  • lazy_static 1.4.0
  • libc 0.2.144
  • linux-raw-sys 0.3.8
  • memchr 2.5.0
  • miniz_oxide 0.6.2
  • number_prefix 0.4.0
  • object 0.30.3
  • once_cell 1.17.0
  • owo-colors 3.5.0
  • portable-atomic 0.3.19
  • proc-macro2 1.0.59
  • quote 1.0.28
  • regex-automata 0.1.10
  • rustc-demangle 0.1.21
  • rustix 0.37.7
  • ryu 1.0.12
  • serde 1.0.152
  • serde_derive 1.0.152
  • shell-words 1.1.0
  • strsim 0.10.0
  • strsim 0.11.0
  • syn 1.0.107
  • syn 2.0.18
  • unicode-ident 1.0.6
  • unicode-width 0.1.10
  • utf8parse 0.2.1
  • windows-sys 0.42.0
  • windows-sys 0.45.0
  • windows-sys 0.48.0
  • windows-targets 0.42.1
  • windows-targets 0.48.0
  • windows_aarch64_gnullvm 0.42.1
  • windows_aarch64_gnullvm 0.48.0
  • windows_aarch64_msvc 0.42.1
  • windows_aarch64_msvc 0.48.0
  • windows_i686_gnu 0.42.1
  • windows_i686_gnu 0.48.0
  • windows_i686_msvc 0.42.1
  • windows_i686_msvc 0.48.0
  • windows_x86_64_gnu 0.42.1
  • windows_x86_64_gnu 0.48.0
  • windows_x86_64_gnullvm 0.42.1
  • windows_x86_64_gnullvm 0.48.0
  • windows_x86_64_msvc 0.42.1
  • windows_x86_64_msvc 0.48.0
cli/Cargo.toml cargo
web/package-lock.json npm
  • 346 dependencies
cli/pyproject.toml pypi
environment.yml pypi