{"id":17099073,"url":"https://github.com/dhimmel/hgnc","last_synced_at":"2026-05-01T01:32:20.718Z","repository":{"id":82487633,"uuid":"80041649","full_name":"dhimmel/hgnc","owner":"dhimmel","description":"Extracting human gene families from HGNC","archived":false,"fork":false,"pushed_at":"2017-01-26T19:38:34.000Z","size":3853,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-23T18:12:45.217Z","etag":null,"topics":["data","gene-families","genes","hgnc","hugo","human"],"latest_commit_sha":null,"homepage":"https://thinklab.com/d/34#13","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dhimmel.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-01-25T18:05:54.000Z","updated_at":"2017-01-26T19:37:11.000Z","dependencies_parsed_at":null,"dependency_job_id":"19088340-0e8e-4ea1-8869-defe1201047b","html_url":"https://github.com/dhimmel/hgnc","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/dhimmel/hgnc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fhgnc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fhgnc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fhgnc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fhgnc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dhimmel","download_url":"https://codeload.github.com/dhimmel/hgnc/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fhgnc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32482460,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-30T13:12:12.517Z","status":"ssl_error","status_checked_at":"2026-04-30T13:12:06.837Z","response_time":57,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["data","gene-families","genes","hgnc","hugo","human"],"created_at":"2024-10-14T15:08:55.679Z","updated_at":"2026-05-01T01:32:20.700Z","avatar_url":"https://github.com/dhimmel.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Extracting human gene families from HGNC\n\nThis repository processes the [gene family data](https://doi.org/10.1186/s40246-016-0062-6 \"Gray et al (2016) A review of the new HGNC gene family resource. Human Genomics\") from HGNC. In the future, the repository may expand its scope to process other types of HGNC data.\n\n## Notebooks\n\n+ [`1.download.ipynb`](1.download.ipynb) downloads HGNC data. Check this notebook to see the last modified dates of downloaded files.\n+ [`2.families.ipynb`](2.families.ipynb) constructs the gene family ontology in `networkx`. Annotates gene families with their corresponding Entrez Gene IDs. Gene membership in a family is propagated, e.g. genes belonging to the \"[Glutamate metabotropic receptors](http://www.genenames.org/cgi-bin/genefamilies/set/281)\" family also belong to the \"Glutamate receptors\" family.\n\n## Files \u0026 Directories\n\n+ [`download`](download) contains unmodified downloads from the EBI FTP site.\n+ [`data`](data) contains generated datasets. [`families.graphml`](data/families.graphml) contains a GraphML-formatted network of the HGNC gene family ontology. [`gene-families.tsv`](data/gene-families.tsv) contains the mapping between gene families and Entrez genes.\n\n## Questions\n\nHave a question? Submit all feedback or questions via [GitHub issues](https://github.com/dhimmel/hgnc/issues)!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fhgnc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdhimmel%2Fhgnc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fhgnc/lists"}