{"id":51669420,"url":"https://github.com/lieberinstitute/nda-dbgap","last_synced_at":"2026-07-14T23:01:54.927Z","repository":{"id":368703770,"uuid":"1286373120","full_name":"LieberInstitute/nda-dbgap","owner":"LieberInstitute","description":"establishing NDA and dbGaP data submission protocols","archived":false,"fork":false,"pushed_at":"2026-07-06T00:43:56.000Z","size":604,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"devel","last_synced_at":"2026-07-12T04:41:51.646Z","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/LieberInstitute.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":"AGENTS.md","dco":null,"cla":null}},"created_at":"2026-07-01T18:01:22.000Z","updated_at":"2026-07-06T00:43:59.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/LieberInstitute/nda-dbgap","commit_stats":null,"previous_names":["gpertea/nra-dbgap","lieberinstitute/nda-dbgap"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LieberInstitute/nda-dbgap","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fnda-dbgap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fnda-dbgap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fnda-dbgap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fnda-dbgap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LieberInstitute","download_url":"https://codeload.github.com/LieberInstitute/nda-dbgap/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fnda-dbgap/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35482263,"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":"2026-07-14T02:00:06.603Z","response_time":114,"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":"2026-07-14T23:01:50.124Z","updated_at":"2026-07-14T23:01:54.918Z","avatar_url":"https://github.com/LieberInstitute.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NDA and dbGaP data submission SOP\n\nThis repository documents and develops a reproducible workflow for preparing LIBD controlled-access data submissions to the NIMH Data Archive (NDA), with dbGaP registration/linkage tracked where required for human genomic data.\n\nThe first worked example is SNP-array genotype data preparation for the union of:\n\n- SCZ-PNN donors represented by NDA Study `3054`\n- MBv donors represented by Ryan's `119`-row MBv donor/sample list\n- overlapping donors/controls deduplicated before packaging\n\n## Current goal\n\nPrepare, validate, and submit a genotype data package to NDA collection `C5229`, while documenting the process well enough to become a reusable SOP.\n\nParallel discovery work:\n\n- understand Ryan Miller's existing NDA data packaging work for collection `C5229`\n- inspect whether MBv Visium prep exists on JHPCE for experiment `2863`\n- prepare genotype inputs on `srv16` from the documented genotype locations\n- determine how the NDA genotype submission should link to NDA Studies, Experiments, Submissions, and the dbGaP record\n\n## Documentation map\n\n- `docs/NDA-collection-info.md` - current interpretation of collection `C5229`, including Studies, Experiments, Submissions, counts, and open mapping questions.\n- `docs/workstreams.md` - live tracker for active workstreams, blockers, evidence, and next actions.\n- `docs/sop-nda-genotype-submission.md` - discovery-stage SOP for NDA genotype package preparation, validation, and submission.\n- `docs/sop-nda-genotype-data-package.md` - neutral command-level guide for preparing an NDA genotype package from VCF inputs and donor/GUID metadata.\n- `docs/handoffs/jhpce-srv16-nda-genotype-handoff.md` - handoff for JHPCE Ryan/MBv package discovery and srv16 genotype package preparation.\n\n## Controlled data rules\n\nDo not commit controlled donor-level or genotype data.\n\nDo not commit:\n\n- donor rows\n- BrNum row lists, unless explicitly approved\n- GUID or pseudo-GUID crosswalks\n- NDA downloads\n- genotype files\n- local validation outputs containing donor identifiers\n- archive files or package payloads\n\nSafe to commit:\n\n- SOP documentation\n- aggregate counts\n- non-sensitive command patterns\n- high-level path references needed for reproducibility\n- notes that explicitly avoid donor rows and GUID mappings\n\nBrNums may be used in local work or chat when needed.\n\nGenerated local working directories for controlled files should stay untracked.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fnda-dbgap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flieberinstitute%2Fnda-dbgap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fnda-dbgap/lists"}