pybiodatafuse

Python package for biodatafuse project.

https://github.com/biodatafuse/pybiodatafuse

Science Score: 57.0%

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CITATION.cff file
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codemeta.json file
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DOI references
Found 2 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (14.9%) to scientific vocabulary

Keywords

biomedical data-integration data-mining graph-algorithms graphs knowledge-graph rdf

Last synced: 6 months ago · JSON representation ·

Repository

Python package for biodatafuse project.

Basic Info

Host: GitHub
Owner: BioDataFuse
License: mit
Language: Python
Default Branch: main
Homepage: https://biodatafuse.org
Size: 47.6 MB

Statistics

Stars: 7
Watchers: 2
Forks: 10
Open Issues: 35
Releases: 1

Topics

biomedical data-integration data-mining graph-algorithms graphs knowledge-graph rdf

Created over 2 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

pyBioDataFuse

💪 Getting Started

We introduce BioDataFuse, a query-based Python tool for seamless integration of biomedical databases. BioDataFuse establishes a modular framework for efficient data wrangling, enabling context-specific knowledge graph creation and supporting graph-based analyses. With a user-friendly interface, it enables users to dynamically create knowledge graphs from their input data. Supported by a robust Python package, pyBiodatafuse, this tool excels in data harmonization, aggregating diverse sources through modular queries. Moreover, BioDataFuse provides plugin capabilities for Cytoscape and Neo4j, allowing local graph hosting. Ongoing refinements enhance the graph utility through tasks like link prediction, making BioDataFuse a versatile solution for efficient and effective biological data integration.

To know more about the package, read our documentation here.

Creating your own graph

To generate your own graph, check out our tutorial notebook in examples.

We support exporting of the graphs in Cytoscape, Neo4J and GraphDB. You can use the following functions:

```python

on neo4j

neo4j.loadgraph(pygraph, uri="bolt://localhost:7687", username="YOURUSERNAME", password="YOUR_PASSWORD") # change username and password

on cytoscape

cytoscape.loadgraph(pygraph, networkname="YOURCUSTOMNAME")

rdf ttl files

bdf = BDFGraph( baseuri="https://biodatafuse.org/YOURCUSTOMNAME/", versioniri="https://biodatafuse.org/example/YOURCUSTOMNAME.ttl", orcid="YOURORCID", author="YOURNAME", )

bdf.generaterdf(combineddf, combinedmetadata) # Generate the RDF from the (meta)data files from the example runs bdf.serialize( "YOURCUSTOM_NAME.ttl", format="ttl", ) ```

🚀 Installation

The most recent release can be installed from PyPI with:

shell $ pip install pyBiodatafuse

The most recent code and data can be installed directly from GitHub with:

bash $ pip install git+https://github.com/BioDataFuse/pyBiodatafuse.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

📖 Citation

The work was started as part of the Elixir BioHackathon 2023 integrating and bringing together multiple Core Data Resources together.

Gadiya, Y., Ammar, A., Willighagen, E., Martinat, D., Sima, A. C., Balci, H., & Abbassi Daloii, T. (2023). BioHackEU23 report: Extending interoperability of experimental data using modular queries across biomedical resources. BioHackrXiv Preprints. https://doi.org/10.37044/osf.io/mhsqp

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution. ### Development Installation To install in development mode, use the following: ```bash $ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git $ cd pyBiodatafuse $ pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell $ tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/BioDataFuse/pyBiodatafuse/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git $ cd pyBiodatafuse $ tox -e docs $ open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins like `texext` can be added there. Additionally, they need to be added to the `extensions` list in [`docs/source/conf.py`](docs/source/conf.py). ### 📦 Making a Release After installing the package in development mode and installing `tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment in `tox.ini`. Run the following from the shell: ```shell $ tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/pyBiodatafuse/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this step 4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. 5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use `tox -e bumpversion -- minor` after.

Owner

Name: BioDataFuse
Login: BioDataFuse
Kind: organization

Repositories: 1
Profile: https://github.com/BioDataFuse

Citation (CITATION.cff)

cff-version: 1.0.2
message: "If you use this software, please cite it as below."
title: "pyBioDataFuse"
authors:
  - name: "Tooba Abbassi-Daloii"
version: 0.0.1-dev
doi:
url: "https://github.com/BioDataFuse/pyBiodatafuse"

GitHub Events

Total

Create event: 43
Issues event: 27
Watch event: 3
Delete event: 55
Member event: 1
Issue comment event: 56
Push event: 292
Pull request review comment event: 26
Pull request review event: 54
Pull request event: 102
Fork event: 2

Last Year

Create event: 43
Issues event: 27
Watch event: 3
Delete event: 55
Member event: 1
Issue comment event: 56
Push event: 292
Pull request review comment event: 26
Pull request review event: 54
Pull request event: 102
Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 11
Total pull requests: 45
Average time to close issues: 8 months
Average time to close pull requests: 18 days
Total issue authors: 5
Total pull request authors: 6
Average comments per issue: 0.91
Average comments per pull request: 0.36
Merged pull requests: 21
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 9
Pull requests: 45
Average time to close issues: about 1 month
Average time to close pull requests: 18 days
Issue authors: 4
Pull request authors: 6
Average comments per issue: 0.56
Average comments per pull request: 0.36
Merged pull requests: 21
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

tabbassidaloii (26)
jmillanacosta (12)
YojanaGadiya (5)
DominikMartinat (3)
adriaque (3)
djwetstede (1)
dssib (1)

Pull Request Authors

tabbassidaloii (40)
jmillanacosta (27)
YojanaGadiya (21)
adriaque (11)
ammar257ammar (10)
djwetstede (9)
DominikMartinat (7)
dssib (7)
egonw (2)
cthoyt (1)
dependabot[bot] (1)

Top Labels

Issue Labels

enhancement (9) bug (8) update annotator (7) annotator (6) rdf (4) database (3) id mapper (2) new annotator (2) analyser (2) biohack2024 (1) package (1) documentation (1) generator (1) biohack2023 (1) input type (1) VHP4Safty (1)

Pull Request Labels

new annotator (4) rdf (3) bug (2) update annotator (2) VHP4Safety (1) enhancement (1) id mapper (1) new species (1) annotator (1) analyser (1) graph-exporter (1) dependencies (1)

Packages

Total packages: 1
Total downloads:
- pypi 272 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 8
Total maintainers: 3

pypi.org: pybiodatafuse

A python package for integrating data from multiple resources

Homepage: https://github.com/BioDataFuse/pyBiodatafuse
Documentation: https://pyBiodatafuse.readthedocs.io
License: MIT
Latest release: 1.2.0
published 8 months ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 272 Last month

Rankings

Dependent packages count: 9.1%

Average: 38.7%

Dependent repos count: 68.3%

Maintainers (3)

Yojana tabbassidaloi jmillanacosta