coconut
COCONUT (COlleCtion of Open Natural prodUcTs): A comprehensive platform facilitating natural product research by providing data, tools, and services for deposition, curation, and reuse.
Science Score: 75.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 7 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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✓Institutional organization owner
Organization steinbeck-lab has institutional domain (cheminf.uni-jena.de) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.2%) to scientific vocabulary
Keywords
cheminformatics
natural-products
Last synced: 6 months ago
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Repository
COCONUT (COlleCtion of Open Natural prodUcTs): A comprehensive platform facilitating natural product research by providing data, tools, and services for deposition, curation, and reuse.
Basic Info
- Host: GitHub
- Owner: Steinbeck-Lab
- Language: PHP
- Default Branch: main
- Homepage: https://coconut.naturalproducts.net
- Size: 37.9 MB
Statistics
- Stars: 34
- Watchers: 2
- Forks: 3
- Open Issues: 84
- Releases: 3
Topics
cheminformatics
natural-products
Created almost 2 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Citation
README.md
COlleCtion of Open Natural prodUcTs
[](https://opensource.org/licenses/MIT)
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[](https://GitHub.com/Steinbeck-Lab/coconut/issues/)
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[](https://www.rdkit.org/)
[](https://laravel.com)
[](https://doi.org/10.5281/zenodo.13382750)
About
A comprehensive platform facilitating natural product research by providing data, tools, and services for deposition, curation, and reuse. It aims to provide researchers, scientists, and enthusiasts with comprehensive and easily accessible data on a wide variety of natural compounds. The database includes detailed information on the chemical structures, literature references and sources of these compounds, facilitating research and discovery in natural products.
https://coconut.naturalproducts.net/
Features
- Standardised data aggregation: COCONUT 2.0 aggregates data from more than 63 sources using ChEMBL curation pipeline with RDKit post-processing, standardizing molecular structures and metadata while preserving stereochemistry from sources.
- Descriptor calculations: COCONUT data curation and descriptors calculation are performed using Cheminformatics microservice.
- Comprehensive download options: The database offers downloads in CSV, SDF, and SQL dump formats, with specialized CSV files for mass spectrometry, molecular descriptors, and substructure analyses accessible here.
- Search and Filtering: Users can search by chemical structure (exact, substructure, similarity), text-based queries for names/SMILES, and filter by organism, chemical class, or literature references.
- Online Submission and Curation: Features community-driven data submission and curation through a web interface, allowing users to submit new structures, report issues, and request changes with full audit trail tracking.
- API Access: Provides a REST API compliant with OpenAPI specifications for programmatic access to chemical structures, metadata, and audit information with real-time data updates - API documentation.
License
COCONUT infrastructure code is licensed under the MIT license - see the LICENSE. Every source on COCONUT comes with its own specific license. It is essential to review the license details for each dataset before using it.
Citations
COCONUT 2.0
- Venkata Chandrasekhar, Kohulan Rajan, Sri Ram Sagar Kanakam, Nisha Sharma, Viktor Weienborn, Jonas Schaub, Christoph Steinbeck, COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database, Nucleic Acids Research, 2024;, gkae1063, https://doi.org/10.1093/nar/gkae1063
COCONUT (Legacy)
- Sorokina, M., Merseburger, P., Rajan, K. et al. (2021). COCONUT online: COlleCtion of Open Natural prodUcTs database. Journal of Cheminformatics, 13, 2. https://doi.org/10.1186/s13321-020-00478-9
Maintained by
The COCONUT database and its infrastructure are developed and maintained by the Steinbeck group at the Friedrich Schiller University Jena, Germany.
The code for this web application is released under the MIT license. Copyright CC-BY-SA 2024
Acknowledgments
Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the ChemBioSys (Project INF) - Project number: 239748522 - SFB 1127.
Owner
- Name: Steinbeck-Lab
- Login: Steinbeck-Lab
- Kind: organization
- Website: https://cheminf.uni-jena.de
- Repositories: 28
- Profile: https://github.com/Steinbeck-Lab
Official GitHub organization for the Steinbeck group Jena, Germany
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Venkata" given-names: "Chandrasekhar" orcid: "https://orcid.org/0000-0002-2564-3243" - family-names: "Kanakam" given-names: "Sri Ram Sagar" orcid: "https://orcid.org/0009-0004-7934-5876" - family-names: "Sharma" given-names: "Nisha" orcid: "https://orcid.org/0009-0006-4755-1039" - family-names: "Schaub" given-names: "Jonas" orcid: "https://orcid.org/0000-0003-1554-6666" - family-names: "Steinbeck" given-names: "Christoph" orcid: "https://orcid.org/0000-0001-6966-0814" - family-names: "Rajan" given-names: "Kohulan" orcid: "https://orcid.org/0000-0003-1066-7792" title: "COCONUT" version: v0.0.1 - prerelease doi: 10.5281/zenodo.13283949 date-released: 2023-05-03 url: "https://github.com/Steinbeck-Lab/coconut"
GitHub Events
Total
- Issues event: 298
- Watch event: 22
- Delete event: 34
- Issue comment event: 76
- Push event: 250
- Pull request review comment event: 3
- Pull request review event: 47
- Pull request event: 127
- Fork event: 1
- Create event: 52
Last Year
- Issues event: 298
- Watch event: 22
- Delete event: 34
- Issue comment event: 76
- Push event: 250
- Pull request review comment event: 3
- Pull request review event: 47
- Pull request event: 127
- Fork event: 1
- Create event: 52
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 136
- Total pull requests: 35
- Average time to close issues: 13 days
- Average time to close pull requests: 4 days
- Total issue authors: 8
- Total pull request authors: 4
- Average comments per issue: 0.19
- Average comments per pull request: 0.03
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 135
- Pull requests: 35
- Average time to close issues: 11 days
- Average time to close pull requests: 4 days
- Issue authors: 8
- Pull request authors: 4
- Average comments per issue: 0.17
- Average comments per pull request: 0.03
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- CS76 (118)
- sriramkanakam87 (50)
- vcnainala (35)
- Kohulan (27)
- steinbeck (15)
- JonasSchaub (7)
- NRayya (3)
- NishaSharma14 (3)
- NanoporeAna (1)
- JustinYiChen (1)
- mizzlefeng (1)
- LWdaHustla (1)
Pull Request Authors
- sriramkanakam87 (83)
- Kohulan (21)
- CS76 (20)
- NRayya (2)
- NishaSharma14 (2)
- github-actions[bot] (1)
- ZachBurkhead (1)
Top Labels
Issue Labels
enhancement (23)
high priority (19)
bug (12)
wip (8)
curation (5)
spam (4)
question (2)
documentation (2)
needs discussion (1)
ready to test (1)
performance enhancement (1)
invalid (1)
help wanted (1)
Pull Request Labels
bug (3)
autorelease: pending (3)
high priority (1)
Dependencies
docker/8.0/Dockerfile
docker
- ubuntu 20.04 build
docker/8.1/Dockerfile
docker
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docker/8.2/Dockerfile
docker
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docker/8.3/Dockerfile
docker
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docker-compose.yml
docker
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- nfdi4chem/cheminformatics-microservice dev-latest
- redis alpine
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docs/.vitepress/cache/deps/package.json
npm
package-lock.json
npm
- 250 dependencies
package.json
npm
- @tailwindcss/forms ^0.5.7 development
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composer.json
packagist
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- owen-it/laravel-auditing ^13.6
- php ^8.3
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composer.lock
packagist
- 186 dependencies