publication-figure-retrieval
This tool provides a method for retrieving publication figure images from NIH's Entrez API based on a list of species.
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: ncbi.nlm.nih.gov -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.4%) to scientific vocabulary
Keywords
Repository
This tool provides a method for retrieving publication figure images from NIH's Entrez API based on a list of species.
Basic Info
- Host: GitHub
- Owner: AlexJSully
- License: gpl-2.0
- Language: TypeScript
- Default Branch: master
- Homepage: https://github.com/AlexJSully/Publication-Figure-Retrieval
- Size: 3.12 MB
Statistics
- Stars: 5
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Publication Figure Retrieval Tool
This tool provides a method for retrieving figures from NCBI's PMC publications using the Entrez API.
Disclaimer
This code is maintained for educational and historical reference purposes only. The tool was originally developed for academic research. Please note that the use of this tool for retrieving figures from PMC publications is subject to NCBI's policies. Use at own risk.
Requirements
- Node.js >= 20
- RAM >= 4GB
- Internet connection with greater than 7mb/s download speed
Installation & Setup
If you would like to run or modify the publication figure retrieval tool locally, clone the repository with git by running the following command:
bash
git clone https://github.com/AlexJSully/Publication-Figure-Retrieval.git
Then run
bash
npm ci
Running locally
To start and run the publication figure retrieval tool, run the following command:
bash
npm run start
If you chose to cancel this process at any time, you can resume and continue where you left off by running the same command. It will store the already processed PMC IDs in build/output/cache/id.json. To reset the cache, delete the id.json file.
Usage
The images are downloaded locally within the build/output directory. They are organized by species then by publication ID.
API Key
If you have an API key, create a .env file in the root directory and add your API key as follows:
bash
NCBI_API_KEY=your_api_key_here
With an API key, the tool can retrieve up to 10 calls per second instead of 3. Details on obtaining an API key can be found in the NCBI API key documentation.
Known Issues
We aim to make this tool as perfect as possible but unfortunately, there may be some unforeseen bugs. If you manage to find one that is not here, feel free to create a bug report so we can fix it.
- None at the moment... Help us find some!
Contributing
Please read CONTRIBUTING.md for more details.
Before contributing, ensure that all tests pass by running:
bash
npm run validate
License
Maintenance Mode
This project is currently in maintenance mode. This means that:
- Only critical bug fixes and security updates will be addressed.
- New feature requests are unlikely to be implemented.
Sponsorship
If you want to support my work, you can do so through the following methods:
Authors
Owner
- Name: Alexander Sullivan
- Login: AlexJSully
- Kind: user
- Location: Canada
- Company: Verily
- Website: https://alexjsully.me/
- Twitter: AlexJSully
- Repositories: 5
- Profile: https://github.com/AlexJSully
Software Developer @verily-src | Bioinformatician | MSc @BioAnalyticResource
Citation (CITATION.cff)
cff-version: 1.2.0
title: Publication Figure Retrieval Tool
message: >-
Open-source code for the Publication Figure Retrieval CLI
tool, which retrieves publication figure images from NIH's Entrez
API based on a list of species.
type: software
authors:
- given-names: Alexander
family-names: Sullivan
orcid: "https://orcid.org/0000-0002-4463-4473"
email: alexjsully.connect@outlook.com
contact:
- email: alexjsully.connect@outlook.com
family-names: Sullivan
given-names: Alexander
country: CA
orcid: "https://orcid.org/0000-0002-4463-4473"
website: "https://alexjsully.me/"
identifiers:
- type: url
value: "https://github.com/AlexJSully/Publication-Figure-Retrieval"
repository-code: "https://github.com/AlexJSully/Publication-Figure-Retrieval"
url: "https://github.com/AlexJSully/Publication-Figure-Retrieval"
abstract: >-
This tool provides a method for retrieving publication figure images from NIH's Entrez API based on a list of species.
keywords:
- bioinformatics
- publication data
- science
license: GPL-2.0
commit: 740b403cf6575e00471013b1664339caa8ad61c3
version: 3.0.1
date-released: "2024-08-26"
GitHub Events
Total
- Delete event: 3
- Issue comment event: 1
- Push event: 5
- Pull request review comment event: 3
- Pull request event: 6
- Pull request review event: 8
- Create event: 4
Last Year
- Delete event: 3
- Issue comment event: 1
- Push event: 5
- Pull request review comment event: 3
- Pull request event: 6
- Pull request review event: 8
- Create event: 4
Dependencies
- prettier 2.7.1 development
- @sentry/core 7.8.0
- @sentry/hub 7.8.0
- @sentry/node 7.8.0
- @sentry/tracing 7.8.0
- @sentry/types 7.8.0
- @sentry/utils 7.8.0
- @tootallnate/once 2.0.0
- abab 2.0.6
- acorn 8.7.1
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- asynckit 0.4.0
- axios 0.27.2
- browser-process-hrtime 1.0.0
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- dotenv 16.0.1
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- escodegen 2.0.0
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- esutils 2.0.3
- fast-levenshtein 2.0.6
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- iconv-lite 0.6.3
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- jsdom 20.0.0
- levn 0.3.0
- lodash 4.17.21
- lru_map 0.3.3
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- ws 8.8.0
- xml-name-validator 4.0.0
- xmlchars 2.2.0
- prettier ^2.7.1 development
- @sentry/node ^7.8.0
- @sentry/tracing ^7.8.0
- axios ^0.27.2
- dotenv ^16.0.1
- jsdom ^20.0.0
- lodash ^4.17.21
- throttled-queue ^2.1.4
- actions/checkout v2 composite
- github/codeql-action/analyze v2 composite
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