biocypher
A unifying framework for biomedical research knowledge graphs
Science Score: 59.0%
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
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: arxiv.org, nature.com, zenodo.org -
✓Committers with academic emails
5 of 21 committers (23.8%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (10.4%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A unifying framework for biomedical research knowledge graphs
Basic Info
- Host: GitHub
- Owner: biocypher
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://biocypher.org
- Size: 24.3 MB
Statistics
- Stars: 262
- Watchers: 8
- Forks: 40
- Open Issues: 183
- Releases: 49
Topics
Metadata Files
README.md
BioCypher
| | | | |
| --- | --- | --- | --- |
| License | 
| Python | 
| Build status | 
|
| Tests | 
| Docker | 
| Contributions | 
❓ Description
Knowledge graphs (KGs) are an approach to knowledge representation that uses graph structure to facilitate exploration and analysis of complex data, often leveraging semantic information. They are popular in many research areas, including the life sciences, due to their versatile use, for instance in data storage, integration, reasoning, and more recently in artificial intelligence. The creation of KGs is a complex task; BioCypher helps you in creating and maintaining your own KG. For more overview, usage notes, and a tutorial, read the docs here.
📖 Documentation
Tutorial and developer docs at https://biocypher.org. For a quickstart into your own pipeline, you can refer to our project template, and for an overview of existing and planned adapters for resources and outputs, as well as other features, visit our GitHub Project Board.
⚙️ Installation / Usage
Install the package from PyPI using pip install biocypher. More comprehensive
installation and configuration instructions can be found
here.
Exemplary usage of BioCypher to build a graph database is shown in our tutorial and the various pipelines we have created. You can find these on the Components Project Board.
🤝 Getting involved
We are very happy about contributions from the community, large and small! If you would like to contribute to BioCypher development, please refer to our contribution guidelines. :)
If you want to ask informal questions, talk about dev things, or just chat, please join our community at https://biocypher.zulipchat.com!
Imposter syndrome disclaimer: We want your help. No, really. There may be a little voice inside your head that is telling you that you're not ready, that you aren't skilled enough to contribute. We assure you that the little voice in your head is wrong. Most importantly, there are many valuable ways to contribute besides writing code.
This disclaimer was adapted from the Pooch project.
✍️ Citation
The BioCypher paper has been peer-reviewed in Nature Biotechnology. It is available as a self-archived version on Zenodo, online version here. Before, it was available as a preprint at https://arxiv.org/abs/2212.13543.
Acknowledgements
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 965193 for DECIDER and No 116030 for TransQST.
Owner
- Name: biocypher
- Login: biocypher
- Kind: organization
- Website: https://biocypher.org
- Repositories: 1
- Profile: https://github.com/biocypher
GitHub Events
Total
- Create event: 30
- Release event: 11
- Issues event: 51
- Watch event: 41
- Delete event: 20
- Member event: 3
- Issue comment event: 85
- Push event: 147
- Pull request review comment event: 64
- Pull request review event: 64
- Pull request event: 46
- Fork event: 10
Last Year
- Create event: 30
- Release event: 11
- Issues event: 51
- Watch event: 41
- Delete event: 20
- Member event: 3
- Issue comment event: 85
- Push event: 147
- Pull request review comment event: 64
- Pull request review event: 64
- Pull request event: 46
- Fork event: 10
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Sebastian Lobentanzer | s****r@g****m | 1,204 |
| Nils Krehl | n****l@p****e | 171 |
| deeenes | t****s@g****m | 101 |
| ryxx0811 | y****1@g****m | 17 |
| loesvdbiggelaar | l****s@t****l | 14 |
| Hartung, Michael | m****g@u****e | 13 |
| Marko Baric | m****c@p****r | 12 |
| bnymnsen | 1****n | 10 |
| Edwin Carreño | e****o@g****m | 8 |
| Johann Dreo | j****o@p****r | 8 |
| ahmetrifaioglu | a****u@g****m | 8 |
| dbdimitrov | d****f@g****m | 5 |
| fengsh | s****8@g****m | 3 |
| Vincent Vialard | v****d@d****e | 2 |
| Paul TO | k****o@e****k | 2 |
| Hakan Çelik | h****v@g****m | 1 |
| Valeriia Dragan | 4****1 | 1 |
| dependabot[bot] | 4****] | 1 |
| fengsh27 | 1****7 | 1 |
| Edwin Carreno | e****o@i****e | 1 |
| supermaxiste | s****e@h****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 272
- Total pull requests: 102
- Average time to close issues: 3 months
- Average time to close pull requests: 21 days
- Total issue authors: 31
- Total pull request authors: 17
- Average comments per issue: 0.92
- Average comments per pull request: 2.54
- Merged pull requests: 87
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 43
- Pull requests: 54
- Average time to close issues: 10 days
- Average time to close pull requests: 6 days
- Issue authors: 12
- Pull request authors: 7
- Average comments per issue: 0.47
- Average comments per pull request: 1.72
- Merged pull requests: 44
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- slobentanzer (181)
- nilskre (26)
- bnymnsen (11)
- vd-dragan21 (6)
- jdreo (3)
- adhalanay (2)
- mbaric758 (2)
- rahulmaurya1507 (2)
- JPonsa (2)
- Valentijn000 (1)
- flalix (1)
- dgg32 (1)
- marco-brandizi (1)
- shaileshchaudhary11 (1)
- johndef64 (1)
Pull Request Authors
- slobentanzer (37)
- nilskre (27)
- ecarrenolozano (16)
- jdreo (8)
- ryxx0811 (7)
- vd-dragan21 (5)
- kpto (4)
- mbaric758 (4)
- dbdimitrov (2)
- bnymnsen (2)
- Mjvolk3 (2)
- lvvittor (2)
- Maiykol (1)
- supermaxiste (1)
- vincentvialard (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 1,775 last-month
- Total dependent packages: 2
- Total dependent repositories: 4
- Total versions: 54
- Total maintainers: 1
pypi.org: biocypher
A unifying framework for biomedical research knowledge graphs
- Homepage: https://github.com/biocypher/biocypher
- Documentation: https://biocypher.readthedocs.io/
- License: MIT
-
Latest release: 0.10.1
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- 159 dependencies
- PyYAML >=5.0
- appdirs *
- more_itertools *
- neo4j-utils 0.0.7
- networkx ^3.0
- pandas ^2.0.1
- pooch ^1.7.0
- python ^3.9
- rdflib ^6.2.0
- stringcase ^1.2.0
- tqdm ^4.65.0
- treelib 1.6.4
- actions/cache v3 composite
- actions/cache v3 composite
- actions/setup-python v4 composite
- snok/install-poetry v1 composite
- douglascamata/setup-docker-macos-action v1-alpha composite
- pre-commit/action v3.0.0 composite
- s0/git-publish-subdir-action develop composite
- ./.github/actions/build_docs * composite
- ./.github/actions/install * composite
- ./.github/actions/setup * composite
- actions/checkout v4 composite
- s0/git-publish-subdir-action develop composite
- ./.github/actions/install * composite
- ./.github/actions/setup * composite
- ./.github/actions/test * composite
- actions/checkout v4 composite
- ./.github/actions/install * composite
- ./.github/actions/setup * composite
- actions/checkout v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- ./.github/actions/install * composite
- ./.github/actions/setup * composite
- ./.github/actions/test * composite
- ./.github/actions/test_coverage * composite
- actions/checkout v4 composite