https://github.com/cancervariants/disease-normalization
Services and guidelines for normalizing disease terms
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.1%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Services and guidelines for normalizing disease terms
Basic Info
- Host: GitHub
- Owner: cancervariants
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://disease-normalizer.readthedocs.io/latest/
- Size: 4.38 MB
Statistics
- Stars: 6
- Watchers: 4
- Forks: 0
- Open Issues: 31
- Releases: 36
Topics
Metadata Files
README.md
Disease Normalizer
The Disease Normalizer resolves ambiguous references and descriptions of human diseases to consistently-structured, normalized terms. For concepts extracted from NCIt, Mondo Disease Ontology, The Human Disease Ontology, OMIM, and OncoTree, it designates a CURIE, and provides additional metadata like aliases and cross-references. <!-- /description -->
Documentation · Installation · API reference
Installation
The Disease Normalizer is available via PyPI:
```commandline
python3 -m pip install disease-normalizer ```
See installation instructions in the documentation for a description of installation options and data setup requirements.
Examples
Use the live service to programmatically normalize disease terms, as in the following truncated example:
shell
$ curl -s 'https://normalize.cancervariants.org/disease/normalize?q=liver%20cancer' | python -m json.tool
{
"query": "liver cancer",
"warnings": null,
"match_type": 80,
"disease": {
"conceptType": "Disease",
"primaryCoding": {
"id": "ncit:C34803",
"code": "C34803",
"system": "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=",
},
"id": "normalize.disease:liver%20cancer",
"name": "Primary Malignant Liver Neoplasm",
# ...
}
}
Or utilize the Python API for fast local access:
```pycon
from disease.query import QueryHandler from disease.database import createdb q = QueryHandler(createdb()) result = q.normalize("NSCLC") result.disease.primaryCoding.id 'ncit:C2926' ```
Feedback and contributing
We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The documentation contains guidance for submitting feedback and contributing new code.
Owner
- Name: VICC
- Login: cancervariants
- Kind: organization
- Website: http://cancervariants.org
- Repositories: 14
- Profile: https://github.com/cancervariants
The Variant Interpretation for Cancer Consortium
GitHub Events
Total
- Create event: 30
- Release event: 7
- Issues event: 34
- Delete event: 25
- Issue comment event: 40
- Push event: 81
- Pull request review comment event: 34
- Pull request review event: 75
- Pull request event: 62
Last Year
- Create event: 30
- Release event: 7
- Issues event: 34
- Delete event: 25
- Issue comment event: 40
- Push event: 81
- Pull request review comment event: 34
- Pull request review event: 75
- Pull request event: 62
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 330
- Total Committers: 3
- Avg Commits per committer: 110.0
- Development Distribution Score (DDS): 0.148
Top Committers
| Name | Commits | |
|---|---|---|
| James Stevenson | j****n@n****g | 281 |
| korikuzma | k****a@g****m | 42 |
| Kori Kuzma | 4****a@u****m | 7 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 85
- Total pull requests: 181
- Average time to close issues: 4 months
- Average time to close pull requests: 7 days
- Total issue authors: 5
- Total pull request authors: 3
- Average comments per issue: 0.92
- Average comments per pull request: 0.21
- Merged pull requests: 157
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 20
- Pull requests: 60
- Average time to close issues: 6 days
- Average time to close pull requests: 4 days
- Issue authors: 4
- Pull request authors: 2
- Average comments per issue: 0.05
- Average comments per pull request: 0.42
- Merged pull requests: 48
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jsstevenson (51)
- korikuzma (31)
- JackCuihfb (1)
- mcannon068nw (1)
- bwalsh (1)
Pull Request Authors
- jsstevenson (121)
- korikuzma (59)
- bwalsh (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 2,235 last-month
- Total dependent packages: 2
- Total dependent repositories: 3
- Total versions: 36
- Total maintainers: 3
pypi.org: disease-normalizer
VICC normalization routines for diseases
- Homepage: https://github.com/cancervariants/disease-normalization
- Documentation: https://disease-normalizer.readthedocs.io
- License: MIT License Copyright (c) 2021-2024 VICC Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 0.11.2
published 8 months ago
Rankings
Maintainers (3)
Dependencies
- coverage * develop
- coveralls * develop
- disease-normalizer * develop
- flake8 * develop
- flake8-docstrings * develop
- ipykernel * develop
- matplotlib * develop
- pre-commit * develop
- pytest * develop
- pytest-cov * develop
- boto3 *
- click *
- fastapi >=0.72.0
- ga4gh.vrsatile.pydantic >=0.0.5
- httptools *
- owlready2 *
- pydantic *
- pyparsing ==2.4.7
- rdflib *
- requests *
- typing-extensions *
- uvicorn *
- uvloop *
- websockets *
- actions/checkout v2 composite
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- postgres 14 docker