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hetionet

Hetionet: an integrative network of disease

https://github.com/hetio/hetionet

Science Score: 67.0%

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 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

data-integration drug-repurposing hetionet hetnet neo4j network rephetio

Keywords from Contributors

dwpcs hetnet-connectivity-search hetnets networks
Last synced: 6 months ago · JSON representation ·

Repository

Hetionet: an integrative network of disease

Basic Info
  • Host: GitHub
  • Owner: hetio
  • Language: HTML
  • Default Branch: main
  • Homepage: https://neo4j.het.io
  • Size: 380 MB
Statistics
  • Stars: 285
  • Watchers: 14
  • Forks: 69
  • Open Issues: 14
  • Releases: 1
Topics
data-integration drug-repurposing hetionet hetnet neo4j network rephetio
Created almost 10 years ago · Last pushed almost 3 years ago
Metadata Files
Readme Citation

README.md

Hetionet: an integrative network of disease

Hetionet is a hetnet — network with multiple node and edge (relationship) types — which encodes biology. The hetnet was designed for Project Rephetio, which aims to systematically identify why drugs work and predict new therapies for drugs. The research article describing Project Rephetio and Hetionet v1.0 is:

Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
eLife (2017-09-22) https://git.dhimmel.com/rephetio-manuscript/
DOI: 10.7554/elife.26726 · PMID: 28936969 · PMCID: PMC5640425

Version 1.0 contains 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. This repository is currently only a download location for Hetionet. The data integration and hetnet creation occurs in a separate repository (dhimmel/integrate) and is imported to this repository by import.ipynb.

Download Hetionet

Latest Zenodo DOI

The network is available in four formats:

The JSON and Neo4j formats contain node and edge properties, which are absent in the TSV and matrix formats, including licensing information. Therefore the recommended formats are JSON and Neo4j. Our hetio package in Python reads the JSON format, but it is otherwise a simple yet new format. The Neo4j graph database has an established and thriving ecosystem. However, if you would like to access Hetionet without Neo4j, then we suggest the JSON format. The matrix format refers to HetMat archives, which store edge adjacency matrices on disk. Additional usage information is available at the corresponding download locations.

Derivative Networks

This section contains networks that are derived, at least in part from Hetionet, but are not identical.

  • BEL: see pybel/hetionet-bel for Hetionet converted to Biological Expression Language (BEL). BEL expresses biological relationships in a machine-readable format. Changes or omission of certain nodes and edges were made to properly represent Hetionet in BEL, as documented in the hetionet-bel README. Currently, the repository contains exports of the BEL representation in multiple formats: as a BEL Script, as Nodelink JSON, and as GraphDati JSON. Contributed by Charles Tapley Hoyt.

Permuted Hetnets

We've created five permuted derivatives of Hetionet. The permutation randomizes edges while preserving node degree. Permuted hetnets are available in hetnet/permuted in JSON and Neo4j 2.3 formats. Relationship properties are omitted from the permuted hetnets.

Cloning

Large files in this repository are stored using Git LFS. If cloning this repository, please make sure that Git LFS is installed on your system. Otherwise, git will checkout text pointers for large files rather than the large files themselves!

Network Description

describe contains summary statistics on the hetnet. See describe/nodes/metanodes.tsv for details on the node types in the hetnet. See describe/edges/metaedges.tsv for details on the edge types. See describe/definitions.json for definitions of metanodes, metaedges, and node/edge properties. See describe/styles.json for the standard colors to be used for displaying metanodes.

Below, we provide two hetnet visualizations. Panel A shows the metagraph (graph of types) for Hetionet. Panel B shows the actual hetnet with nodes laid out in circles by type. Color denotes edge type.

Hetionet v1.0 visualizations

License

All original content in this repository is released as CC0. However, the hetnet integrates data from many resources and users should consider the licensing of each source (see this table). We apply a license attribute on a per node and per edge basis for sources with defined licenses. However, some resources don't provide any license, so for those we've requested permission. More information is available on Thinklab.

Owner

  • Name: Hetnets in Biomedicine
  • Login: hetio
  • Kind: organization

Repositories for hetnet-related research, tools, and datasets including Hetionet. By the teams of @dhimmel, @greenelab, & @sebaran

Citation (CITATION.cff) 

cff-version: 1.2.0
title: >-
  hetio/hetionet:
  Data repository containing Hetionet downloads
message: >-
  This citation is for the Hetionet data repository,
  which provides Hetionet in several formats including
  JSON, HetMatPy (matrix), Neo4j database, and TSV (tabular).
  For general citation of Hetionet v1.0, please cite Project Rephetio,
  the study that introduced Hetionet at <https://doi.org/10.7554/elife.26726>.
type: dataset
authors:
  - given-names: Daniel
    family-names: Himmelstein
    orcid: 'https://orcid.org/0000-0002-3012-7446'
  - given-names: Antoine
    family-names: Lizee
    orcid: 'https://orcid.org/0000-0002-1073-3190'
  - given-names: Faisal
    family-names: Alquaddoomi
    orcid: 'https://orcid.org/0000-0003-4297-8747'
  - given-names: Vincent
    family-names: Rubinetti
    orcid: 'https://orcid.org/0000-0002-4655-3773'
  - given-names: Dongbo
    family-names: Hu
    orcid: 'https://orcid.org/0000-0001-7870-8242'
  - given-names: Casey
    family-names: Greene
    orcid: 'https://orcid.org/0000-0001-8713-9213'
  - given-names: Sergio
    family-names: Baranzini
    orcid: 'https://orcid.org/0000-0003-0067-194X'
identifiers:
  - type: swh
    value: 'swh:1:dir:7a8ca59f120a90b86c31dc7be975f42ee0b4285e'
    description: Software Heritage Directory
  - type: swh
    value: 'swh:1:rev:af668689a81952058df8b1321cc6c744b93d83e2'
    description: Software Heritage Revision
repository-code: 'https://github.com/greenelab/connectivity-search-manuscript'
url: 'https://het.io/about/'
repository-artifact: 'https://zenodo.org/record/268568'
keywords:
  - neo4j
  - network
  - rephetio
  - hetionet
  - hetnet
  - drug-repurposing
  - data-integration
license: CC0-1.0

GitHub Events

Total
  • Watch event: 34
  • Fork event: 3
Last Year
  • Watch event: 34
  • Fork event: 3

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 87
  • Total Committers: 3
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.092
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Daniel Himmelstein d****n@g****m 79
dongbohu d****u@g****m 5
Vincent Rubinetti v****i@g****m 3

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 80
  • Total pull requests: 22
  • Average time to close issues: 8 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 35
  • Total pull request authors: 3
  • Average comments per issue: 4.25
  • Average comments per pull request: 2.32
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dhimmel (7)
  • ayujain04 (4)
  • cthoyt (3)
  • jromanowska (2)
  • victorconan (1)
  • DimitrisAlivas (1)
  • thomasleb0n (1)
  • rajarshd (1)
  • chhyunch (1)
  • LucaCappelletti94 (1)
  • jdauvill (1)
  • vincerubinetti (1)
  • wuyinjun-1993 (1)
  • schatzkara (1)
  • yingding (1)
Pull Request Authors
  • dongbohu (5)
  • dhimmel (4)
  • vincerubinetti (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
proxy.golang.org: github.com/hetio/hetionet
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 6.5%
Average: 6.7%
Dependent repos count: 6.9%
Last synced: 6 months ago

Dependencies

hetnet/neo4j/docker/Dockerfile docker
  • neo4j 3.5.12 build