obook
OBO Organized Knowledge: Training materials for becoming an OBO engineer
Science Score: 59.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
12 of 47 committers (25.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.3%) to scientific vocabulary
Keywords
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Repository
OBO Organized Knowledge: Training materials for becoming an OBO engineer
Basic Info
- Host: GitHub
- Owner: OBOAcademy
- License: cc0-1.0
- Language: Makefile
- Default Branch: master
- Homepage: https://oboacademy.github.io/obook/
- Size: 68.4 MB
Statistics
- Stars: 110
- Watchers: 15
- Forks: 40
- Open Issues: 106
- Releases: 1
Topics
Metadata Files
README.md
Open Biological and Biomedical Ontologies (OBO) Organized Knowledge (OBOOK)
The OBOOK is the main resource for OBOAcademy training materials for Semantic OBO Engineers.
- To get started with learning: https://oboacademy.github.io/obook/getting-started/
- To contribute: https://oboacademy.github.io/obook/contributing/
Running the website locally
Installing dependencies
```bash
Create a virtual environment in the project folder
python -m venv .venv
Activate the virtual environment
in mac/linux
source .venv/bin/activate
in Windows
..venv\Scripts\activate
Install dependencies
pip install mkdocs pip install mkdocs-material ```
Running the site locally
If you haven't, activate the local virtual environment
```bash
in mac/linux
source .venv/bin/activate
in Windows
..venv\Scripts\activate ```
Then run:
mkdocs serve
Go to http://127.0.0.1:8000/, you should see the site.
License
This content is available under the Creative Commons CC0 Public Domain Dedication.
Citation
The conference article describing the OBOOK can be cited with the following:
Nicole Vasilevsky, James Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, & Nicolas Matentzoglu. (2022, August 3). OBO Academy: Training materials for bio-ontologists. 2022 ISMB Bio-Ontologies Community, Madison, WI. https://doi.org/10.5281/zenodo.6955490
Acknowledgements
Critical Path Institute
Critical Path Institute (CPI) is an independent, nonprofit organisation dedicated to bringing together experts from regulatory agencies, industry, and academia to collaborate and improve the medical product development process.
In April 2021, the CPI has commissioned the first version of this OBO course, contributing not only funding for the preparation and delivery of the materials, but also valuable feedback about the course contents and data for the practical exercises. We thank the CPI for contributing significantly to the OBO community and open science!
https://c-path.org/
Owner
- Name: OBOAcademy
- Login: OBOAcademy
- Kind: organization
- Repositories: 1
- Profile: https://github.com/OBOAcademy
GitHub Events
Total
- Issues event: 7
- Watch event: 19
- Delete event: 14
- Issue comment event: 31
- Push event: 64
- Pull request review comment event: 29
- Pull request review event: 44
- Pull request event: 48
- Fork event: 3
- Create event: 19
Last Year
- Issues event: 7
- Watch event: 19
- Delete event: 14
- Issue comment event: 31
- Push event: 64
- Pull request review comment event: 29
- Pull request review event: 44
- Pull request event: 48
- Fork event: 3
- Create event: 19
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Nicole Vasilevsky | n****e@t****g | 902 |
| Nico Matentzoglu | n****u@g****m | 224 |
| Shawn Tan | 7****k | 143 |
| nicolevasilevsky | v****s@o****u | 78 |
| Valentina Cipriani | v****i@q****k | 56 |
| Becky Jackson | r****n@g****m | 46 |
| Sarah Gehrke | 9****e | 43 |
| James A. Overton | j****s@o****a | 32 |
| Jim Balhoff | b****f@g****m | 31 |
| Yasemin Bridges | y****s@q****k | 20 |
| sabrinatoro | s****a@t****g | 17 |
| Nomi Harris | n****s | 16 |
| Chris Mungall | c****m@b****g | 16 |
| bvarner-ebi | b****r@p****u | 14 |
| iQuxLE | c****5@g****m | 10 |
| David Osumi-Sutherland | d****s@g****m | 8 |
| Harry Caufield | j****d@g****m | 7 |
| Anita Caron | a****c@e****k | 7 |
| Manuel Lera Ramirez | m****4@g****m | 6 |
| Ray Stefancsik | r****y@e****k | 4 |
| Damien Goutte-Gattat | d****4@c****k | 4 |
| Vinícius de Souza | s****s@g****m | 3 |
| bvarner-ebi | 9****i | 3 |
| Mark A. Miller | M****M@l****v | 3 |
| Charles Tapley Hoyt | c****t@g****m | 3 |
| henrietteharmse | 3****e | 2 |
| Yasemin Bridges | 9****s | 2 |
| Lauren | 4****n | 2 |
| Sebastian Lobentanzer | s****r@g****m | 2 |
| Philip Strömert | P****t@t****u | 2 |
| and 17 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 57
- Total pull requests: 110
- Average time to close issues: 3 months
- Average time to close pull requests: 5 days
- Total issue authors: 16
- Total pull request authors: 30
- Average comments per issue: 1.74
- Average comments per pull request: 0.53
- Merged pull requests: 99
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 7
- Pull requests: 21
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 5
- Pull request authors: 9
- Average comments per issue: 0.0
- Average comments per pull request: 0.19
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- matentzn (32)
- nicolevasilevsky (9)
- cmungall (6)
- shawntanzk (3)
- paulacalipho (2)
- balhoff (1)
- dosumis (1)
- sagehrke (1)
- sumirp (1)
- souzadevinicius (1)
- ValWood (1)
- lubianat (1)
- gouttegd (1)
- aleixpuigb (1)
- ghost (1)
Pull Request Authors
- sagehrke (50)
- nicolevasilevsky (15)
- matentzn (12)
- nlharris (7)
- timalamenciak (5)
- ghost (5)
- anitacaron (5)
- StroemPhi (4)
- cmungall (4)
- jamesaoverton (3)
- shawntanzk (3)
- cthoyt (3)
- yaseminbridges (2)
- gouttegd (2)
- clnsmth (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- mhausenblas/mkdocs-deploy-gh-pages master composite