{"id":49165208,"url":"https://github.com/scriptogre/biomedical-data","last_synced_at":"2026-05-01T07:01:28.918Z","repository":{"id":353108979,"uuid":"1218005294","full_name":"scriptogre/biomedical-data","owner":"scriptogre","description":"Biomedical databases as Parquet files (DrugCentral, Pharos, Open Targets, AACT Clinical Trials, MONDO, STRING, CORUM)","archived":false,"fork":false,"pushed_at":"2026-04-22T13:46:45.000Z","size":16,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-04-22T15:03:33.251Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scriptogre.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-04-22T12:45:52.000Z","updated_at":"2026-04-22T13:41:29.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/scriptogre/biomedical-data","commit_stats":null,"previous_names":["scriptogre/biomedical-data"],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/scriptogre/biomedical-data","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scriptogre%2Fbiomedical-data","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scriptogre%2Fbiomedical-data/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scriptogre%2Fbiomedical-data/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scriptogre%2Fbiomedical-data/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scriptogre","download_url":"https://codeload.github.com/scriptogre/biomedical-data/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scriptogre%2Fbiomedical-data/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32487739,"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":"online","status_checked_at":"2026-05-01T02:00:05.856Z","response_time":64,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2026-04-22T15:00:27.056Z","updated_at":"2026-05-01T07:01:28.907Z","avatar_url":"https://github.com/scriptogre.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Biomedical Data (Parquet)\n\nZstd-compressed Parquet exports of biomedical databases for use with [DuckDB](https://duckdb.org/). These are **curated subsets** tailored for pharmacology research (not full database mirrors).\n\nAutomated monthly via GitHub Actions. Download from [Releases](https://github.com/scriptogre/biomedical-data/releases).\n\n## Databases\n\n| Database | What's included | Source |\n|---|---|---|\n| **DrugCentral** | All tables from the official schema | [Public PostgreSQL](https://unmtid-dbs.net/) |\n| **Pharos/TCRD** | All tables from the MySQL dump | [FigShare](https://figshare.com/search?q=pharos+database+mysql) |\n| **Open Targets** | Selected datasets (targets, diseases, drugs, associations, mechanisms, indications) | [EBI FTP](https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/latest/) |\n| **Clinical Trials (AACT)** | All tables from the daily flat file export | [AACT](https://aact.ctti-clinicaltrials.org/downloads) |\n| **MONDO** | Full ontology (nodes + edges) | [GitHub releases](https://github.com/monarch-initiative/mondo/releases) |\n| **STRING** | Human (taxon 9606) only: protein info, aliases, physical interactions | [StringDB](https://string-db.org/) |\n| **CORUM** | Full complex dataset | [Helmholtz Munich](https://mips.helmholtz-muenchen.de/corum/) |\n\n## Usage\n\n```bash\n# Download a database\ngh release download drugcentral/latest -R scriptogre/biomedical-data\ntar xzf drugcentral.tar.gz -C data/drugcentral/\n```\n\n```python\nimport duckdb\nconn = duckdb.connect()\nconn.execute(\"SELECT * FROM read_parquet('data/drugcentral/structures.parquet') LIMIT 10\")\n```\n\n## License\n\nEach database retains its original license. This repository only provides format conversion.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscriptogre%2Fbiomedical-data","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscriptogre%2Fbiomedical-data","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscriptogre%2Fbiomedical-data/lists"}