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https://github.com/biolink/biolink-model-toolkit

A collection of useful python functions for looking up information and working with the Biolink Model

https://github.com/biolink/biolink-model-toolkit

Science Score: 36.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 12 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.2%) to scientific vocabulary

Keywords

biolink biolink-model ncats-translator

Keywords from Contributors

knowledge-graph rdf owl obofoundry ncats monarchinitiative json-api neo4j gene-ontology datamodel
Last synced: 11 months ago · JSON representation

Repository

A collection of useful python functions for looking up information and working with the Biolink Model

Basic Info
Statistics
  • Stars: 24
  • Watchers: 5
  • Forks: 11
  • Open Issues: 6
  • Releases: 50
Topics
biolink biolink-model ncats-translator
Created over 7 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

Python PyPI

Biolink Model Toolkit

Biolink Model Toolkit (BMT): A Python API for working with the Biolink Model.

BMT provides utility functions to look up Biolink Model for classes, relations, and properties based on Biolink CURIEs or external CURIEs that have been mapped to Biolink Model.

Note: Each release of BMT is pinned to a specific version of the Biolink Model to ensure consistency.

Usage

BMT provides convenience methods to operate on the Biolink Model.

Using this toolkit you can, - Get Biolink Model elements corresponding to a given Biolink class or slot name - Get Biolink Model elements corresponding to a given external CURIE/IRI - Get ancestors for a given Biolink Model element - Get descendants for a given Biolink Model element - Get parent for a given Biolink Model element - Get children for a given Biolink Model element - Check whether a given Biolink Model element is part of a specified subset

Owner

  • Name: biolink
  • Login: biolink
  • Kind: organization

GitHub Events

Total
  • Watch event: 3
  • Delete event: 2
  • Issue comment event: 7
  • Push event: 6
  • Pull request review event: 1
  • Pull request event: 4
  • Create event: 5
Last Year
  • Watch event: 3
  • Delete event: 2
  • Issue comment event: 7
  • Push event: 6
  • Pull request review event: 1
  • Pull request event: 4
  • Create event: 5

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 454
  • Total Committers: 12
  • Avg Commits per committer: 37.833
  • Development Distribution Score (DDS): 0.271
Past Year
  • Commits: 14
  • Committers: 3
  • Avg Commits per committer: 4.667
  • Development Distribution Score (DDS): 0.429
Top Committers
Name Email Commits
Sierra Taylor Moxon s****r@g****m 331
Deepak Unni d****3@g****m 46
richardbruskiewich r****h@d****m 39
dependabot[bot] 4****] 13
Richard Bruskiewich r****d@s****m 7
Lance Hannestad l****t@s****a 6
Patrick Wang p****g 5
hsolbrig s****g@j****u 2
Patrick Wang p****k@c****m 2
Nomi Harris n****s 1
Gaurav Vaidya g****v@r****g 1
Chris Bizon b****n@e****u 1
Committer Domains (Top 20 + Academic)
email.unc.edu: 1 renci.org: 1 covar.com: 1 jhu.edu: 1 sfu.ca: 1 starinformatics.com: 1 delphinai.com: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 57
  • Total pull requests: 97
  • Average time to close issues: 3 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 19
  • Total pull request authors: 8
  • Average comments per issue: 1.32
  • Average comments per pull request: 1.1
  • Merged pull requests: 91
  • Bot issues: 0
  • Bot pull requests: 15
Past Year
  • Issues: 0
  • Pull requests: 7
  • Average time to close issues: N/A
  • Average time to close pull requests: 15 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 1.14
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 3
View more stats
Top Authors
Issue Authors
  • sierra-moxon (18)
  • RichardBruskiewich (10)
  • patrickkwang (4)
  • YaphetKG (3)
  • GregHydeDartmouth (2)
  • colleenXu (2)
  • cbizon (2)
  • CaseyTa (2)
  • slobentanzer (2)
  • caufieldjh (1)
  • oew1v07 (1)
  • raven44099 (1)
  • cmungall (1)
  • andrewsu (1)
  • gaurav (1)
Pull Request Authors
  • sierra-moxon (64)
  • dependabot[bot] (19)
  • RichardBruskiewich (17)
  • patrickkwang (3)
  • deepakunni3 (3)
  • cbizon (1)
  • gaurav (1)
  • nlharris (1)
Top Labels
Issue Labels
bug (2) documentation (1) dependencies (1)
Pull Request Labels
dependencies (19) python (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 6,381 last-month
  • Total dependent packages: 5
  • Total dependent repositories: 37
  • Total versions: 69
  • Total maintainers: 3
pypi.org: bmt

Biolink Model Toolkit: A Python API for working with the Biolink Model

  • Versions: 69
  • Dependent Packages: 5
  • Dependent Repositories: 37
  • Downloads: 6,381 Last month
Rankings
Dependent packages count: 2.4%
Dependent repos count: 2.4%
Downloads: 6.2%
Average: 7.3%
Forks count: 11.4%
Stargazers count: 13.9%
Maintainers (3)
cmungall smoxon deepakunni3
Last synced: 12 months ago

Dependencies

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  • stringcase ^1.2.0
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.github/workflows/check-dependencies.yaml actions
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.github/workflows/initialize-toolkit-daily.yaml actions
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