{"id":22396770,"url":"https://github.com/skyeav/tablassert","last_synced_at":"2026-07-10T01:31:38.718Z","repository":{"id":277062788,"uuid":"931215299","full_name":"SkyeAv/Tablassert","owner":"SkyeAv","description":"Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.","archived":false,"fork":false,"pushed_at":"2026-06-26T21:03:53.000Z","size":9166,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-06-29T09:36:39.573Z","etag":null,"topics":["bioinformatics","data-quality-control","declarative-pipeline","entity-resolution","kgx","knowledge-graph","ncats-translator","ner","tablassert","table-mining","yaml-configuration"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SkyeAv.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","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":"AGENTS.md","dco":null,"cla":null}},"created_at":"2025-02-11T22:46:45.000Z","updated_at":"2026-05-30T00:16:06.000Z","dependencies_parsed_at":null,"dependency_job_id":"c7994d3c-4b0d-4599-9e71-2b08638a1bd5","html_url":"https://github.com/SkyeAv/Tablassert","commit_stats":null,"previous_names":["skyeav/tablassert-3.0.0-","skyeav/tablassert","skyeav/tablassert3.0.0"],"tags_count":21,"template":false,"template_full_name":null,"purl":"pkg:github/SkyeAv/Tablassert","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SkyeAv%2FTablassert","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SkyeAv%2FTablassert/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SkyeAv%2FTablassert/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SkyeAv%2FTablassert/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SkyeAv","download_url":"https://codeload.github.com/SkyeAv/Tablassert/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SkyeAv%2FTablassert/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35317805,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-09T02:00:07.329Z","response_time":57,"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":["bioinformatics","data-quality-control","declarative-pipeline","entity-resolution","kgx","knowledge-graph","ncats-translator","ner","tablassert","table-mining","yaml-configuration"],"created_at":"2024-12-05T06:09:17.818Z","updated_at":"2026-07-10T01:31:38.713Z","avatar_url":"https://github.com/SkyeAv.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Tablassert\n\n[![PyPI](https://img.shields.io/pypi/v/tablassert.svg)](https://pypi.org/project/tablassert/)\n[![Python](https://img.shields.io/pypi/pyversions/tablassert.svg)](https://pypi.org/project/tablassert/)\n[![License](https://img.shields.io/pypi/l/tablassert.svg)](https://github.com/SkyeAv/Tablassert/blob/main/LICENSE)\n[![Docs](https://img.shields.io/github/deployments/SkyeAv/Tablassert/github-pages?label=docs)](https://skyeav.github.io/Tablassert/)\n\nExtract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution built in and optional quality control.\n\n```bash\npip install tablassert\ntablassert build config.yaml\n```\n\n**[Full Documentation](https://skyeav.github.io/Tablassert/)** — installation guides, tutorials, configuration reference, and API docs.\n\n## Installation\n\n```bash\npip install tablassert\n```\n\nBase install includes web and Excel support. Optional extras are available for CPU compatibility and QC runtime selection:\n\n```bash\npip install \"tablassert[rt]\"       # Polars build for CPUs without required instructions\npip install \"tablassert[qc]\"       # Enable QC with CPU ONNX Runtime\npip install \"tablassert[qc-cuda]\"  # Enable QC with CUDA ONNX Runtime on GPU 0\n```\n\nQC is disabled by default at the graph level. Set `qc: true` in a graph config to enable the audit stage.\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cstrong\u003eDocker\u003c/strong\u003e\u003c/summary\u003e\n\n```bash\ndocker pull ghcr.io/skyeav/tablassert:latest\n\ndocker run --rm \\\n  -v /path/to/config:/data \\\n  -v /path/to/datassert:/datassert \\\n  ghcr.io/skyeav/tablassert:latest \\\n  build /data/graph-config.yaml\n```\n\n\u003c/details\u003e\n\n## Quick Demo\n\n```python\nfrom pathlib import Path\nfrom tablassert.lib import resolve_many\n\n# Resolve gene names to CURIEs against a datassert database\nresults = resolve_many(\n    col=\"gene\",\n    entities=[\"TP53\", \"BRCA1\", \"EGFR\"],\n    datassert=Path(\"/path/to/datassert\"),\n    taxon=\"9606\",\n)\n\nfor row in results:\n    print(f\"{row['original gene']} → {row['gene']} ({row['gene name']})\")\n# TP53 → HGNC:11998 (TP53)\n# BRCA1 → HGNC:1100 (BRCA1)\n# EGFR → HGNC:3236 (EGFR)\n```\n\nPoint `resolve_many()` at a datassert database and resolve any iterable of entity strings to CURIEs — no LazyFrame setup, NLP preprocessing, or DuckDB connection management required. For full pipeline builds with YAML configuration, use `tablassert build config.yaml`.\n\n## Key Features\n\n- **Declarative Configuration** — YAML-based, no code required\n- **Entity Resolution** — Maps text to biological entities (genes, diseases, chemicals)\n- **Quality Control** — Optional three-stage validation (exact → fuzzy → BERT embeddings)\n- **KGX Compliance** — NCATS Translator-compatible NDJSON output\n- **Performance** — Lazy evaluation pipelines with Polars and DuckDB-accelerated entity resolution\n\n## Contributing\n\nSee **[CONTRIBUTING.md](CONTRIBUTING.md)** for development setup, code style, and pull request guidelines.\n\n## License\n\n[Apache License 2.0](LICENSE)\n\n## Contributors\n\n[Skye Lane Goetz](mailto:sgoetz@isbscience.org) — Institute for Systems Biology, CalPoly SLO\n\n[Gwênlyn Glusman](mailto:gglusman@isbscience.org) — Institute for Systems Biology\n\nJared C. Roach — Institute for Systems Biology\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fskyeav%2Ftablassert","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fskyeav%2Ftablassert","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fskyeav%2Ftablassert/lists"}