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hetionet-analysis

Various data analysis performed using Hetionet, a hetnet of biomedical knowledge.

https://github.com/cu-dbmi/hetionet-analysis

Science Score: 75.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization cu-dbmi has institutional domain (medschool.cuanschutz.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.8%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Various data analysis performed using Hetionet, a hetnet of biomedical knowledge.

Basic Info
  • Host: GitHub
  • Owner: CU-DBMI
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 267 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 3
  • Releases: 1
Created over 1 year ago · Last pushed 7 months ago
Metadata Files
Readme License Code of conduct Citation

README.md

Hetionet Analysis

Software DOI badge

Various data analysis performed using Hetionet, a hetnet of biomedical knowledge.

Development

  1. Install uv.
  2. Install package locally (e.g. uv pip install -e ".[dev]").
  3. Run tests (e.g. uv run poe test, through poethepoet task).
  4. Run various tasks (e.g. uv run poe run_bioproc_gene_metapath_test)

Tasks

Poe the poet tasks may be run to help generate results without needing to run individual files or perform additional discovery within this project. You can show all available tasks with uv run poe.

  • Create Connectivity Search PathCount table: uv run poe run_pathcount_extract

Owner

  • Name: University of Colorado Department of Biomedical Informatics
  • Login: CU-DBMI
  • Kind: organization
  • Location: University of Colorado, School of Medicine, Anschutz Medical Campus

Citation (CITATION.cff) 

---
cff-version: 1.2.0
title: hetionet-analysis
message: >-
  If you use this software, please cite it using the
  metadata from the CITATION.cff file.
type: software
authors:
  - given-names: Sutanu
    family-names: Nandi
    orcid: "https://orcid.org/0009-0001-5887-999X"
  - given-names: Negar
    family-names: Janani
    orcid: 'https://orcid.org/0009-0000-7308-926X'
  - given-names: Dave
    family-names: Bunten
    orcid: "https://orcid.org/0000-0001-6041-3665"
  - given-names: Casey
    family-names: Greene
    orcid: 'https://orcid.org/0000-0001-8713-9213'
repository-code: "https://github.com/CU-DBMI/hetionet-analysis"
abstract: >-
  Various data analysis performed using Hetionet, a hetnet of biomedical knowledge.
keywords:
  - python
  - hetnets
  - hetionet
license: BSD-3-Clause
identifiers:
  - description: Software DOI
    type: doi
    value: "10.5281/zenodo.15597460"
references:
  - title: >-
      Node connectivity measurements for Hetionet v1.0 metapaths
    type: data
    version: v1.1
    languages:
      - en
    url: https://zenodo.org/record/1435833
    keywords:
      - dwpc
      - Hetionet
      - hetmat
      - hetnet
      - metapath
      - path counts
      - permutation
    authors:
      - family-names: Himmelstein
        given-names: Daniel
      - family-names: Zietz
        given-names: Michael
      - family-names: Kloster
        given-names: Kyle
      - family-names: Nagle
        given-names: Michael
      - family-names: Sullivan
        given-names: Blair
      - family-names: Greene
        given-names: Casey
    date-released: 2018-11-06
    date-published: 2018-11-06
    identifiers:
      - type: doi
        value: 10.5281/ZENODO.1435833
  - title: >-
      Systematic integration of biomedical knowledge prioritizes drugs for repurposing
    type: article
    issn: 2050-084X
    languages:
      - en
    pages: e26726
    volume: 6
    url: https://elifesciences.org/articles/26726
    authors:
      - family-names: Himmelstein
        given-names: Daniel Scott
      - family-names: Lizee
        given-names: Antoine
      - family-names: Hessler
        given-names: Christine
      - family-names: Brueggeman
        given-names: Leo
      - family-names: Chen
        given-names: Sabrina L
      - family-names: Hadley
        given-names: Dexter
      - family-names: Green
        given-names: Ari
      - family-names: Khankhanian
        given-names: Pouya
      - family-names: Baranzini
        given-names: Sergio E
    date-published: 2017-09-22
    identifiers:
      - type: doi
        value: 10.7554/eLife.26726

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 5
  • Delete event: 1
  • Issue comment event: 6
  • Push event: 10
  • Pull request review event: 2
  • Pull request review comment event: 1
  • Pull request event: 13
  • Fork event: 1
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 5
  • Delete event: 1
  • Issue comment event: 6
  • Push event: 10
  • Pull request review event: 2
  • Pull request review comment event: 1
  • Pull request event: 13
  • Fork event: 1

Dependencies

.github/workflows/run-tests.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pre-commit/action v3.0.1 composite
pyproject.toml pypi
  • black >=24.10
  • duckdb >=1.1.3
  • hetmatpy >=0.1
  • ipywidgets >=8.1.5
  • isort >=5.13.2
  • joblib >=1.4.2
  • jupyterlab >=4.3
  • jupyterlab-code-formatter >=3.0.2
  • jupytext >=1.16.4
  • lancedb >=0.15
  • neo4j >=5.26
  • requests >=2.32.3
uv.lock pypi
  • 141 dependencies