[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6CZ575855JF8CNC2XJQDFVZ":3,"skill-same:01M6CZ575855JF8CNC2XJQDFVZ":63},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":18,"publishedAt":23,"linkOnly":24,"markdownContent":25,"markdownBody":26,"frontMatter":27,"refName":28,"commitSha":29,"skillDirectory":30,"forksCount":31,"repositoryHtmlUrl":32,"repositoryHomepageUrl":6,"ownerHtmlUrl":33,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":34,"install":35,"resources":48},"01M6CZ575855JF8CNC2XJQDFVZ","search-gsa",null,"Search CNCB Genome Sequence Archive (GSA) for sequencing runs, experiments, studies, and samples deposited at the China National Center for Bioinformation.","Scientific-Tooling\u002Fstructured-intelligence","Scientific-Tooling","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F267453265?v=4","01M6CZ1SE6GGD4F67EAQ0PVX38","Scientific Tooling","01M6CZ1SJKCFVGH10Z3A152K02",4,"MIT","https:\u002F\u002Fgithub.com\u002FScientific-Tooling\u002Fstructured-intelligence\u002Fblob\u002Fmain\u002Fskills\u002Fsearch-gsa\u002FSKILL.md",[],[19,20,21,22],"search","search gsa","experiments","archive","2026-11-10 10:12:30",false,"---\nname: search-gsa\ndescription: Search CNCB Genome Sequence Archive (GSA) for sequencing runs, experiments, studies, and samples deposited at the China National Center for Bioinformation.\n---\n\n# Skill: Search GSA\n\n## Use When\n\n- A user wants to find sequencing data deposited in the CNCB Genome Sequence Archive (GSA) at ngdc.cncb.ac.cn.\n- A user needs to look up GSA accessions: CRA (project), CRX (experiment), CRR (run), CRS (sample), or SAMC (biosample).\n- A user wants to retrieve run-level metadata (read count, file size, platform, library strategy) for data in GSA.\n- A user wants to search GSA by organism, tissue, disease, keyword, or data type.\n- A user wants to list all runs belonging to a GSA project (CRA accession).\n- A user needs the download URL or FASP path for CRR files from CNCB.\n\n## Inputs\n\n- Required:\n  - one of: free-text search query, GSA accession (CRA\u002FCRX\u002FCRR\u002FCRS\u002FSAMC), organism name, or NCBI taxonomy ID\n- Optional:\n  - data type filter: `Genome`, `Transcriptome`, `Metagenome`, `Epigenome`, `Variation`, `Proteome`\n  - library strategy filter (e.g., `RNA-Seq`, `WGS`, `ChIP-Seq`, `ATAC-Seq`)\n  - sequencing platform (e.g., `Illumina`, `PacBio`, `ONT`)\n  - organism filter (scientific name or taxonomy ID)\n  - output format: `json` or `tsv`\n  - maximum results (`size`, default 20)\n  - output directory\n\n## Workflow\n\n1. Determine the access method:\n   - **Direct accession lookup**: construct the CNCB accession detail URL:\n     - `https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fbrowse\u002F\u003CCRA-accession>` for projects\n     - `https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Frun\u002F\u003CCRR-accession>` for individual runs\n   - **Keyword search**: use the GSA search API endpoint:\n     ```\n     GET https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fsearch?searchTerm=\u003Cquery>&page=1&pageSize=20\n     ```\n   - **Programmatic metadata fetch**: use the GSA data API:\n     ```\n     GET https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fapi\u002Fv1\u002Fproject\u002F\u003CCRA>\n     GET https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fapi\u002Fv1\u002Frun\u002F\u003CCRR>\n     ```\n2. Parse the response to extract: accession, title, organism, submission date, run count, total bases, platform, and library strategy.\n3. For project-level queries, enumerate all CRR runs and collect per-run metadata.\n4. Construct download URLs for CRR files:\n   - FTP: `ftp:\u002F\u002Fdownload.cncb.ac.cn\u002Fgsa\u002F\u003CCRA>\u002F\u003CCRX>\u002F\u003CCRR>\u002F`\n   - HTTPS: `https:\u002F\u002Fdownload.cncb.ac.cn\u002Fgsa\u002F\u003CCRA>\u002F\u003CCRX>\u002F\u003CCRR>\u002F`\n5. Report a summary table and the accession list.\n\n## Output Contract\n\n- Search or fetch request URL used\n- Number of matching projects or runs\n- Summary table with columns: Accession (CRR\u002FCRA), Title, Organism, Platform, Strategy, Spots, Bases, Size, Submission Date\n- Download URL(s) for CRR files\n- Accession list saved to `accessions.txt` when an output directory is provided\n- Optional `metadata.json` or `metadata.tsv` with full per-run fields\n\n## Limits\n\n- GSA web API is subject to change; confirm endpoint availability with a test request if needed.\n- Some datasets in GSA are access-controlled and require registration at ngdc.cncb.ac.cn before download.\n- GSA accessions follow CNCB conventions (CRA\u002FCRX\u002FCRR\u002FCRS) distinct from NCBI (SRP\u002FSRX\u002FSRR\u002FSRS); do not mix them.\n- CNSA (China National Sequence Archive, for assembled genomes) is a separate archive also at CNCB; GSA is specifically for raw sequencing data.\n- The FTP server may be slow for users outside mainland China; HTTPS is generally preferred.\n- Common failure cases:\n  - confusing CRA (project) with CRR (run) accession types\n  - attempting to use NCBI E-utilities with GSA accessions (they are not indexed by NCBI)\n  - missing authentication cookie when accessing controlled-access datasets\n  - constructing download paths without the correct CRA\u002FCRX\u002FCRR hierarchy\n","# Skill: Search GSA\n\n## Use When\n\n- A user wants to find sequencing data deposited in the CNCB Genome Sequence Archive (GSA) at ngdc.cncb.ac.cn.\n- A user needs to look up GSA accessions: CRA (project), CRX (experiment), CRR (run), CRS (sample), or SAMC (biosample).\n- A user wants to retrieve run-level metadata (read count, file size, platform, library strategy) for data in GSA.\n- A user wants to search GSA by organism, tissue, disease, keyword, or data type.\n- A user wants to list all runs belonging to a GSA project (CRA accession).\n- A user needs the download URL or FASP path for CRR files from CNCB.\n\n## Inputs\n\n- Required:\n  - one of: free-text search query, GSA accession (CRA\u002FCRX\u002FCRR\u002FCRS\u002FSAMC), organism name, or NCBI taxonomy ID\n- Optional:\n  - data type filter: `Genome`, `Transcriptome`, `Metagenome`, `Epigenome`, `Variation`, `Proteome`\n  - library strategy filter (e.g., `RNA-Seq`, `WGS`, `ChIP-Seq`, `ATAC-Seq`)\n  - sequencing platform (e.g., `Illumina`, `PacBio`, `ONT`)\n  - organism filter (scientific name or taxonomy ID)\n  - output format: `json` or `tsv`\n  - maximum results (`size`, default 20)\n  - output directory\n\n## Workflow\n\n1. Determine the access method:\n   - **Direct accession lookup**: construct the CNCB accession detail URL:\n     - `https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fbrowse\u002F\u003CCRA-accession>` for projects\n     - `https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Frun\u002F\u003CCRR-accession>` for individual runs\n   - **Keyword search**: use the GSA search API endpoint:\n     ```\n     GET https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fsearch?searchTerm=\u003Cquery>&page=1&pageSize=20\n     ```\n   - **Programmatic metadata fetch**: use the GSA data API:\n     ```\n     GET https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fapi\u002Fv1\u002Fproject\u002F\u003CCRA>\n     GET https:\u002F\u002Fngdc.cncb.ac.cn\u002Fgsa\u002Fapi\u002Fv1\u002Frun\u002F\u003CCRR>\n     ```\n2. Parse the response to extract: accession, title, organism, submission date, run count, total bases, platform, and library strategy.\n3. For project-level queries, enumerate all CRR runs and collect per-run metadata.\n4. Construct download URLs for CRR files:\n   - FTP: `ftp:\u002F\u002Fdownload.cncb.ac.cn\u002Fgsa\u002F\u003CCRA>\u002F\u003CCRX>\u002F\u003CCRR>\u002F`\n   - HTTPS: `https:\u002F\u002Fdownload.cncb.ac.cn\u002Fgsa\u002F\u003CCRA>\u002F\u003CCRX>\u002F\u003CCRR>\u002F`\n5. Report a summary table and the accession list.\n\n## Output Contract\n\n- Search or fetch request URL used\n- Number of matching projects or runs\n- Summary table with columns: Accession (CRR\u002FCRA), Title, Organism, Platform, Strategy, Spots, Bases, Size, Submission Date\n- Download URL(s) for CRR files\n- Accession list saved to `accessions.txt` when an output directory is provided\n- Optional `metadata.json` or `metadata.tsv` with full per-run fields\n\n## Limits\n\n- GSA web API is subject to change; confirm endpoint availability with a test request if needed.\n- Some datasets in GSA are access-controlled and require registration at ngdc.cncb.ac.cn before download.\n- GSA accessions follow CNCB conventions (CRA\u002FCRX\u002FCRR\u002FCRS) distinct from NCBI (SRP\u002FSRX\u002FSRR\u002FSRS); do not mix them.\n- CNSA (China National Sequence Archive, for assembled genomes) is a separate archive also at CNCB; GSA is specifically for raw sequencing data.\n- The FTP server may be 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