{"apiVersion":"v1","directorySlug":"seqout-mcp-b171ae9874","title":"seqout","description":"Search millions of GEO, SRA, ENA, DRA, GEA, GSA & ArrayExpress datasets. Unified metadata, relevance-ranked results, and consolidated sample tables for research.","pageUrl":"https://www.mcpbundles.com/skills/seqout-mcp-b171ae9874","connectPath":"importable","connectAction":"import_server","catalogListing":false,"bundleSlug":null,"listingKind":"remote_mcp","kind":"provider","transportUrl":"https://seqout.org/api/mcp","hostedMcpUrl":null,"toolCount":109,"toolInventoryStatus":"observed","refreshedAt":"2026-11-03T13:26:00.516172+00:00","registryName":"org.seqout/seqout-mcp-b171ae9874","registryVersion":"2026.11.3","registryEligible":true,"tools":[{"name":"get_growth_stats","description":"Return monthly counts of projects, experiments, or data volume per database. modes: projects (studies/series count), experiments (samples count), bases (nucleotide bases for ENA, FASTQ/SRA bytes for SRA). Counts are per-month (not cumulative). Returns {mode, series: {db: [{month, count}]}, took_ms}.","inputSchema":{"type":"object","required":["mode"],"properties":{"db":{"anyOf":[{"type":"string","pattern":"^(geo|sra|arrayexpress|ena|gsa|dra|gea|sra_fastq_bytes|sra_sra_bytes)$"},{"type":"null"}]},"mode":{"type":"string","pattern":"^(projects|experiments|bases)$"}}},"title":"Get Growth Stats","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_growth_stats","displayName":"Get Growth Stats"},{"name":"get_organism_growth","description":"Return monthly and cumulative experiment/sample counts for a given organism across GEO, SRA, ArrayExpress, and ENA databases. The organism parameter should be a scientific name (e.g. 'Homo sapiens'). mode=absolute returns raw counts; mode=percentage returns the organism's share of total experiments per month per database. Returns {organism, mode, series: {db: [{month, count, cumulative}]}, took_ms}.","inputSchema":{"type":"object","required":["organism"],"properties":{"db":{"anyOf":[{"type":"string","pattern":"^(geo|sra|arrayexpress|ena|gsa|dra|gea)$"},{"type":"null"}]},"mode":{"type":"string","default":"absolute","pattern":"^(absolute|percentage)$"},"organism":{"type":"string","maxLength":200,"minLength":1}}},"title":"Get Organism Growth","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_organism_growth","displayName":"Get Organism Growth"},{"name":"get_organism_totals","description":"Return total experiment/sample counts per organism across GEO, SRA, ArrayExpress, and ENA. Optionally filter by publication year range. Returns {organisms: [{organism, geo, sra, arrayexpress, ena, total}], year_from, year_to, total_organisms, took_ms}.","inputSchema":{"type":"object","required":[],"properties":{"limit":{"anyOf":[{"type":"integer","maximum":10000.0,"minimum":1.0},{"type":"null"}]},"year_to":{"anyOf":[{"type":"integer","maximum":2100.0,"minimum":1900.0},{"type":"null"}]},"year_from":{"anyOf":[{"type":"integer","maximum":2100.0,"minimum":1900.0},{"type":"null"}]}}},"title":"Get Organism Totals","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_organism_totals","displayName":"Get Organism Totals"},{"name":"search_organisms","description":"Search for organisms by partial name match (case-insensitive). Returns up to `limit` organisms sorted by total experiment count. Use this for typeahead/autocomplete in organism selectors.","inputSchema":{"type":"object","required":["q"],"properties":{"q":{"type":"string","maxLength":200,"minLength":1},"limit":{"type":"integer","default":20,"maximum":100.0,"minimum":1.0}}},"title":"Search Organisms","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"search_organisms","displayName":"Search Organisms"},{"name":"get_global_contributions","description":"Return aggregated project/experiment/sample counts per geographic location (latitude/longitude rounded to 2 decimal places) from the unified_metadata table. Includes source breakdown (GEO/SRA/ArrayExpress/ENA), city, country, and top 5 organisms per location. Unfiltered and filtered results are cached for 7 days.","inputSchema":{"type":"object","required":[],"properties":{"assay_l1":{"anyOf":[{"type":"string"},{"type":"null"}]},"assay_l2":{"anyOf":[{"type":"string"},{"type":"null"}]},"organism":{"anyOf":[{"type":"string"},{"type":"null"}]},"place_type":{"anyOf":[{"type":"string"},{"type":"null"}]},"address_type":{"anyOf":[{"type":"string"},{"type":"null"}]}}},"title":"Get Global Contributions","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_global_contributions","displayName":"Get Global Contributions"},{"name":"get_global_contribution_filters","description":"Return distinct values for organism, assay_l1, and assay_l2 filters, ordered by count descending. When country is provided, counts are scoped to that country. Global and country-scoped results are cached for 7 days.","inputSchema":{"type":"object","required":[],"properties":{"country":{"anyOf":[{"type":"string"},{"type":"null"}]},"organism":{"anyOf":[{"type":"string"},{"type":"null"}]}}},"title":"Get Global Contribution Filters","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_global_contribution_filters","displayName":"Get Global Contribution Filters"},{"name":"get_country_accessions","description":"Return distinct project accessions from unified_metadata for a given country, optionally filtered by organism and assay. Returns a plain newline-separated text list of accessions.","inputSchema":{"type":"object","required":["country"],"properties":{"country":{"type":"string"},"assay_l2":{"anyOf":[{"type":"string"},{"type":"null"}]},"organism":{"anyOf":[{"type":"string"},{"type":"null"}]}}},"title":"Get Country Accessions","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_country_accessions","displayName":"Get Country Accessions"},{"name":"get_country_pis","description":"Return investigators for a whole country, ranked by project count descending. This is the map sidebar's ranking and takes no topic. For any question that names a research topic ('single cell', 'CRISPR'), use `get_search_investigators` instead; do NOT pull this unfiltered list and filter it yourself. An investigator is any author of a project's linked publication, or a GEO/ArrayExpress contributor when the project has no linked PMID. Returns {pis, covered_projects, total, took_ms}.","inputSchema":{"type":"object","required":["country"],"properties":{"country":{"type":"string"},"assay_l2":{"anyOf":[{"type":"string"},{"type":"null"}]},"organism":{"anyOf":[{"type":"string"},{"type":"null"}]}}},"title":"Get Country PIs","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_country_pis","displayName":"Get Country PIs"},{"name":"get_platform_totals","description":"Return total experiment counts per sequencing platform across databases. Also available at /platforms.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Platform Totals","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_platform_totals","displayName":"Get Platform Totals"},{"name":"get_platform_growth","description":"Return monthly experiment or project counts for a sequencing platform. Optionally filter by instrument_model. Returns {platform, mode, series: {db: [{month, count, cumulative}]}, took_ms}.","inputSchema":{"type":"object","required":["platform"],"properties":{"mode":{"type":"string","default":"experiments","pattern":"^(experiments|projects)$"},"assay":{"anyOf":[{"type":"string"},{"type":"null"}]},"country":{"anyOf":[{"type":"string"},{"type":"null"}]},"organism":{"anyOf":[{"type":"string"},{"type":"null"}]},"platform":{"type":"string"},"instrument_model":{"anyOf":[{"type":"string"},{"type":"null"}]}}},"title":"Get Platform Growth","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_platform_growth","displayName":"Get Platform Growth"},{"name":"get_platform_instruments","description":"Return instrument models for a platform with experiment counts.","inputSchema":{"type":"object","required":["platform"],"properties":{"platform":{"type":"string"}}},"title":"Get Platform Instruments","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_platform_instruments","displayName":"Get Platform Instruments"},{"name":"get_platform_filters","description":"Return available organisms, assays, and countries for a platform. Used to populate filter dropdowns in the sequencing technology stats card.","inputSchema":{"type":"object","required":["platform"],"properties":{"platform":{"type":"string"}}},"title":"Get Platform Filters","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_platform_filters","displayName":"Get Platform Filters"},{"name":"search_suggest","description":"Return spelling correction suggestions for a query. Useful when a search returns 0 results due to typos.","inputSchema":{"type":"object","required":["q"],"properties":{"q":{"type":"string","maxLength":500,"minLength":1}}},"title":"Search Suggest","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"search_suggest","displayName":"Search Suggest"},{"name":"ontology_term","description":"Look up one term in the ontology graph and return its source identifiers (xrefs), its MAPS_TO synonym cluster, and its hierarchy children. `max_hops` (default 2) bounds the synonym walk only — children are always the DIRECT children of the resulting synonym cluster, as the deep-dive explorer defines them. Set `children=false` to skip the children query entirely, which is much cheaper. xrefs are source CURIEs (UBERON:0002107, HGNC:5, MeSH:D008099, CVCL_0030) and are returned for the queried term,","inputSchema":{"type":"object","required":["term"],"properties":{"term":{"type":"string","maxLength":200,"minLength":1},"children":{"type":"boolean","default":true},"max_hops":{"type":"integer","default":2,"maximum":4.0,"minimum":1.0}}},"title":"Ontology Term","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"ontology_term","displayName":"Ontology Term"},{"name":"search_expansion","description":"Explain the synonym expansion that a plain-keyword search runs: per query term, the synonyms that actually reached the search, and how many that term has in total (they differ when the variant cap truncates the expansion). Structured/boolean queries are not expanded, so chunks is empty for them. Returns {query, structured, variants, variant_cap, chunks: [{term, synonyms, total}], took_ms}.","inputSchema":{"type":"object","required":["q"],"properties":{"q":{"type":"string","maxLength":500,"minLength":1},"exclude_ontology":{"anyOf":[{"type":"array","items":{"type":"string"}},{"type":"null"}]}}},"title":"Search Expansion","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"search_expansion","displayName":"Search Expansion"},{"name":"get_project","description":"Return a GEO series (GSE), SRA study (SRP/DRP/ERP), ENA project (PRJ*), or ArrayExpress project (E-*) record by accession.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Project","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project","displayName":"Get Project"},{"name":"get_project_metadata","description":"Return only title and description for a GEO series (GSE), SRA study (SRP/DRP/ERP), ENA project (PRJ*), or ArrayExpress experiment (E-*) accession.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Project Metadata","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_metadata","displayName":"Get Project Metadata"},{"name":"get_study_experiments","description":"List all experiments for a study accession (SRP/DRP/ERP/PRJ*). For ENA (PRJ*), returns one row per experiment_accession (first run only).","inputSchema":{"type":"object","required":["study"],"properties":{"limit":{"anyOf":[{"type":"integer","maximum":1000.0,"minimum":1.0},{"type":"null"}]},"study":{"type":"string","pattern":"^([SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[Gg][Ee][Aa][Dd]-)\\d+$"},"offset":{"type":"integer","default":0,"minimum":0.0}}},"title":"Get Study Experiments","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_study_experiments","displayName":"Get Study Experiments"},{"name":"find_study_experiments","description":"Look up one experiment accession across every experiment in a study, not just the page the grid has loaded. Backs the experiments grid's accession filter so it stays correct on large studies.","inputSchema":{"type":"object","required":["study"],"properties":{"study":{"type":"string","pattern":"^([SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[Gg][Ee][Aa][Dd]-)\\d+$"},"filters":{"type":"string","default":""}}},"title":"Find Study Experiments","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"find_study_experiments","displayName":"Find Study Experiments"},{"name":"get_study_samples","description":"Return distinct samples referenced by any experiment in an SRA study (SRP/DRP/ERP). PRJ accessions are resolved to their SRA study first.","inputSchema":{"type":"object","required":["study"],"properties":{"study":{"type":"string","pattern":"^([SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[Gg][Ee][Aa][Dd]-)\\d+$"}}},"title":"Get Study Samples","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_study_samples","displayName":"Get Study Samples"},{"name":"get_study_runs","description":"Return FASTQ/SRA download links for runs in an SRA/ENA study. Returns summary statistics plus a preview of up to 500 runs; pass full=true for every run instead (used by the UI's link export). FASTQ fields are semicolon-joined for paired-end runs. If a paired-layout run has one ENA FASTQ, fastq_is_interleaved is true and SRA/SRA Lite conversion should be used. For complete paginated per-file entries, use get_study_download_manifest.","inputSchema":{"type":"object","required":["study"],"properties":{"full":{"type":"boolean","default":false},"study":{"type":"string","pattern":"^([SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[Gg][Ee][Aa][Dd]-)\\d+$"}}},"title":"Get Study Runs","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_study_runs","displayName":"Get Study Runs"},{"name":"find_study_runs","description":"Resolve the runs grid's column filters against every run in a study, not just the 500-run preview, so the filters stay correct on large studies. Returns up to 500 matches; `capped` is true when more exist.","inputSchema":{"type":"object","required":["study"],"properties":{"study":{"type":"string","pattern":"^([SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[Gg][Ee][Aa][Dd]-)\\d+$"},"filters":{"type":"string","default":""}}},"title":"Find Study Runs","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"find_study_runs","displayName":"Find Study Runs"},{"name":"get_run","description":"Return FASTQ/SRA download links and layout for one run accession (SRR/ERR/DRR). fastq_ftp, fastq_bytes, and fastq_md5 are semicolon-joined for paired-end FASTQs. If a paired-layout run has one ENA FASTQ, fastq_is_interleaved is true and SRA/SRA Lite conversion should be used. Use get_run_checksums when you need parsed per-file FASTQ URLs, byte sizes, and MD5 checksums. Returns 404 if the run is unknown.","inputSchema":{"type":"object","required":["run"],"properties":{"run":{"type":"string","pattern":"^[SED]RR\\d+$"}}},"title":"Get Run","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_run","displayName":"Get Run"},{"name":"get_run_checksums","description":"Return per-file FASTQ and SRA download URLs with their byte size and MD5 checksum for a run accession (SRR/ERR/DRR), parsed into structured records so callers do not need to split semicolon-joined FASTQ fields. For paired-layout runs with one ENA FASTQ, flags indicate that SRA/SRA Lite conversion is required and which source should be used.","inputSchema":{"type":"object","required":["run"],"properties":{"run":{"type":"string","pattern":"^[SED]RR\\d+$"}}},"title":"Get Run Checksums","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_run_checksums","displayName":"Get Run Checksums"},{"name":"get_experiment","description":"Return experiment metadata (library, platform, instrument, parent study, linked samples) plus runs for an SRA or ENA experiment accession (SRX/ERX/DRX). Use /experiment/{accession}/runs to fetch just the runs.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^([SED]RX|CRX|HRX)\\d+$"}}},"title":"Get Experiment","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_experiment","displayName":"Get Experiment"},{"name":"get_experiment_runs","description":"Return run download links and layout for an SRX/ERX/DRX experiment.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^([SED]RX|CRX|HRX)\\d+$"}}},"title":"Get Experiment Runs","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_experiment_runs","displayName":"Get Experiment Runs"},{"name":"get_study_bams","description":"Return direct download links for original submitted BAM files in an SRA study. BAM files are extracted from the ncbi_files JSONB column where supertype is 'Original'. Not all studies have BAM files — returns total_bams=0 when none exist.","inputSchema":{"type":"object","required":["study"],"properties":{"study":{"type":"string","pattern":"^([SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[Gg][Ee][Aa][Dd]-)\\d+$"}}},"title":"Get Study BAMs","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_study_bams","displayName":"Get Study BAMs"},{"name":"get_project_metadata_rows","description":"Return paginated JSON metadata rows for a project. SRA/ENA studies return one row per run with experiment metadata, sample metadata, flattened sample_attribute:* columns, FASTQ/SRA download links, byte sizes, and MD5 fields. GEO and ArrayExpress projects return flattened sample rows. Prefer this structured JSON endpoint over CSV downloads for MCP use.","inputSchema":{"type":"object","required":["accession"],"properties":{"limit":{"type":"integer","default":500,"maximum":1000.0,"minimum":1.0},"cursor":{"type":"integer","default":0,"minimum":0.0},"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Project Metadata Rows","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_metadata_rows","displayName":"Get Project Metadata Rows"},{"name":"get_experiment_metadata_rows","description":"Return per-run JSON metadata rows for a single SRA/ENA experiment (SRX/ERX/DRX), in the same row format as /project/{accession}/metadata/rows but scoped to this experiment's runs.","inputSchema":{"type":"object","required":["accession"],"properties":{"limit":{"type":"integer","default":500,"maximum":1000.0,"minimum":1.0},"cursor":{"type":"integer","default":0,"minimum":0.0},"accession":{"type":"string","pattern":"^([SED]RX|CRX|HRX)\\d+$"}}},"title":"Get Experiment Metadata Rows","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_experiment_metadata_rows","displayName":"Get Experiment Metadata Rows"},{"name":"get_run_metadata_rows","description":"Return the single JSON metadata row for one run accession (SRR/ERR/DRR), in the same row format as /project/{accession}/metadata/rows.","inputSchema":{"type":"object","required":["run"],"properties":{"run":{"type":"string","pattern":"^[SED]RR\\d+$"}}},"title":"Get Run Metadata Rows","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_run_metadata_rows","displayName":"Get Run Metadata Rows"},{"name":"download_study_script","description":"Return a bash script to download all runs in a study using the specified source: fastq (EBI FASTQ via wget; paired single-FASTQ runs are converted from SRA/SRA Lite with sracha), sra (SRA normalized via wget), sra_lite (SRA Lite via wget), s3 (AWS S3 via aws cli), or gcs (Google Cloud via gsutil).","inputSchema":{"type":"object","required":["study","mode"],"properties":{"mode":{"type":"string","pattern":"fastq|sra|sra_lite|s3|gcs"},"study":{"type":"string","pattern":"^([SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[Gg][Ee][Aa][Dd]-)\\d+$"}}},"title":"Download Study Script","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"download_study_script","displayName":"Download Study Script"},{"name":"get_supplementary_files","description":"Return structured supplementary / processed data file links for a GEO (GSE) or ArrayExpress (E-*) project.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Supplementary Files","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_supplementary_files","displayName":"Get Supplementary Files"},{"name":"download_supplementary_script","description":"Return a bash script to download all supplementary / processed data files for a GEO (GSE) or ArrayExpress (E-MTAB) project using curl.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Download Supplementary Script","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"download_supplementary_script","displayName":"Download Supplementary Script"},{"name":"get_sample","description":"Return an SRA/ENA sample (SRS/DRS/ERS/SAM*) by accession.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^([SED]RS|SAM[A-Z]+|HRS)\\d+$"}}},"title":"Get Sample","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_sample","displayName":"Get Sample"},{"name":"get_sample_detail","description":"Return full metadata for a sample or experiment accession (GSM, SRX/DRX/ERX, SRS/DRS/ERS, SAM*). Includes parent project metadata, sample attributes, experiment info, and run download links.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^([SED]RX|[SED]RS|GSM|SAM[A-Z]+|CRX|HRX|HRS)\\d+$"}}},"title":"Get Sample Detail","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_sample_detail","displayName":"Get Sample Detail"},{"name":"get_common_name_by_scientific_name","description":"Return matching common names from the common_names table for a scientific name.","inputSchema":{"type":"object","required":["scientific_name"],"properties":{"scientific_name":{"type":"string","maxLength":255,"minLength":1}}},"title":"Get Common Name By Scientific Name","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_common_name_by_scientific_name","displayName":"Get Common Name By Scientific Name"},{"name":"get_common_names_by_scientific_names","description":"Batch variant of /common-name: pass scientific_name repeatedly to resolve a whole list in one request. Missing names are simply absent from the result (no 404).","inputSchema":{"type":"object","required":["scientific_name"],"properties":{"scientific_name":{"type":"array","items":{"type":"string"},"maxItems":200,"minItems":1}}},"title":"Get Common Names By Scientific Names","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_common_names_by_scientific_names","displayName":"Get Common Names By Scientific Names"},{"name":"get_geo_series_samples","description":"List all samples for a GEO series (GSE) or ArrayExpress experiment (E-XXXX-NNN).","inputSchema":{"type":"object","required":["accession"],"properties":{"limit":{"anyOf":[{"type":"integer","maximum":1000.0,"minimum":1.0},{"type":"null"}]},"offset":{"type":"integer","default":0,"minimum":0.0},"accession":{"type":"string"}}},"title":"Get GEO Series Samples","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_geo_series_samples","displayName":"Get GEO Series Samples"},{"name":"find_geo_series_samples","description":"Look up one sample accession across every sample in a GEO series or ArrayExpress/GEA experiment, not just the page the grid has loaded. Backs the samples grid's accession filter on large series.","inputSchema":{"type":"object","required":["accession"],"properties":{"filters":{"type":"string","default":""},"accession":{"type":"string"}}},"title":"Find GEO Series Samples","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"find_geo_series_samples","displayName":"Find GEO Series Samples"},{"name":"get_ae_experiment_samples","description":"List all samples for an ArrayExpress experiment accession (E-XXXX-NNN).","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^[Ee]-[A-Za-z]{4}-\\d+$"}}},"title":"Get ArrayExpress Experiment Samples","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_ae_experiment_samples","displayName":"Get ArrayExpress Experiment Samples"},{"name":"bulk_project_samples_metadata","description":"Return project title/description/overall_design/source plus flattened sample rows for project accessions (GSE, SRP, ERP, DRP).","inputSchema":{"type":"object","required":["accessions"],"properties":{"accessions":{"type":"array","items":{"type":"string"},"minItems":1}}},"title":"Bulk Project Samples Metadata","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"bulk_project_samples_metadata","displayName":"Bulk Project Samples Metadata"},{"name":"resolve_accession_project","description":"Resolve a sample/experiment/run accession (GSM/SRS/DRS/ERS/SRX/ERX/DRX/SRR/ERR/DRR) to its parent project accession (GSE or SRP/DRP/ERP). A run resolves via its experiment.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"(^[SED]RS\\d+$|^([SED]RX|CRX|HRX)\\d+$|^GSM\\d+$|^[SED]RR\\d+$)"}}},"title":"Resolve Accession Project","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"resolve_accession_project","displayName":"Resolve Accession Project"},{"name":"resolve_prj_project","description":"Resolve a PRJ accession to its project accession. PRJNA checks GEO series then SRA studies; PRJEB/PRJDA checks SRA only.","inputSchema":{"type":"object","required":["prj_accession"],"properties":{"prj_accession":{"type":"string","pattern":"^PRJ[A-Z]+\\d+$"}}},"title":"Resolve PRJ Project","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"resolve_prj_project","displayName":"Resolve PRJ Project"},{"name":"resolve_submission_studies","description":"List the SRA/ENA/DDBJ studies (SRP/ERP/DRP) filed under a submission accession (SRA######, ERA######, DRA######). Usually one, sometimes many.","inputSchema":{"type":"object","required":["submission"],"properties":{"submission":{"type":"string","pattern":"^[SED]RA\\d+$"}}},"title":"Resolve Submission Studies","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"resolve_submission_studies","displayName":"Resolve Submission Studies"},{"name":"classify_accession","description":"Pattern-match an accession and report which database family it belongs to and what entity it names (study/series/experiment/sample/run/bioproject). Format validation only — does not query the DB. Returns {valid: false} for unrecognized strings.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","maxLength":64,"minLength":2}}},"title":"Classify Accession","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"classify_accession","displayName":"Classify Accession"},{"name":"search_by_author","description":"Case-insensitive substring search across publication author lists, ranked by citation count. Each result is a publication (PMID, title, journal, DOI, authors, citation count) plus its linked dataset accessions across GEO, SRA, ArrayExpress, and ENA. Only studies with a linked PubMed publication are findable here.","inputSchema":{"type":"object","required":["q"],"properties":{"q":{"type":"string","maxLength":100,"minLength":2},"limit":{"type":"integer","default":20,"maximum":100.0,"minimum":1.0}}},"title":"Search By Author","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"search_by_author","displayName":"Search By Author"},{"name":"search_author_projects","description":"Given a person's name, find every dataset they authored across all four databases. Matches the name (first + last, tolerant of middle initials) against publication author lists, then resolves the linked studies. Returns project rows compatible with the search result cards. Only studies linked to a PubMed publication are findable.","inputSchema":{"type":"object","required":["q"],"properties":{"q":{"type":"string","maxLength":100,"minLength":3},"limit":{"type":"integer","default":200,"maximum":200.0,"minimum":1.0}}},"title":"Search Author Projects","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"search_author_projects","displayName":"Search Author Projects"},{"name":"find_publication","description":"Reverse lookup from a publication (PMID or DOI) to every project linked to it across GEO, SRA, ArrayExpress, ENA, DRA, and GEA. Provide either pmid or doi as a query parameter. Each project carries `via`, naming the table the link came from — the inverse of how a project page resolves its publication. Returns {..publication fields.., projects: [{accession, source, title, summary, published_at, via, center_name, country_code}], total_projects}.","inputSchema":{"type":"object","required":[],"properties":{"doi":{"anyOf":[{"type":"string","maxLength":200,"minLength":1},{"type":"null"}]},"pmid":{"anyOf":[{"type":"string","pattern":"^\\d+$"},{"type":"null"}]}}},"title":"Find Publication","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"find_publication","displayName":"Find Publication"},{"name":"get_project_xref","description":"Discover cross-references for a study across GEO, SRA, ArrayExpress and ENA by following cross-reference links, SRA aliases, and E-GEOD naming conventions. When a project has no direct link to a sequence-bearing study, this also resolves through its publication (PMID) and returns those with source='pmid' and a `via_pmid` field. Those are inferred from a shared paper, not declared cross-references, so present them as such -- a paper can cover several studies. Returns {accession: string, xref: [{a","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string"}}},"title":"Get Project Cross-References","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_xref","displayName":"Get Project Cross-References"},{"name":"convert_accession","description":"Resolve any accession (run/sample/experiment/project, any archive) to its canonical project, then list linked projects in the other archives (GEO/SRA/ENA/ArrayExpress/GSA). Cross-database links are project-level; to reach runs/experiments/samples in a target archive, call /project/{study}/runs|experiments|samples on a returned project. Pass db= to also get a flat `targets` list for that archive.","inputSchema":{"type":"object","required":["accession"],"properties":{"db":{"anyOf":[{"type":"string","pattern":"^(geo|sra|ena|dra|arrayexpress|gsa|gea|bioproject)$"},{"type":"null"}]},"accession":{"type":"string","maxLength":64,"minLength":2}}},"title":"Convert Accession","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"convert_accession","displayName":"Convert Accession"},{"name":"convert_accessions","description":"Batch form of /convert/{accession}. POST {\"accessions\": [...], \"db\": \"sra\"}. Each input resolves to its project plus linked projects in other archives. Max 200 accessions per request.","inputSchema":{"type":"object","required":["accessions"],"properties":{"db":{"anyOf":[{"type":"string","pattern":"^(geo|sra|ena|dra|arrayexpress|gsa|gea|bioproject)$"},{"type":"null"}]},"accessions":{"type":"array","items":{"type":"string"},"minItems":1}}},"title":"Convert Accessions","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"convert_accessions","displayName":"Convert Accessions"},{"name":"get_project_cite","description":"Return BibTeX citation(s) for a project accession. By default returns the original publication (smallest PMID). Use type=all to get BibTeX for every linked publication.","inputSchema":{"type":"object","required":["accession"],"properties":{"type":{"type":"string","default":"original","pattern":"^(original|all)$"},"format":{"type":"string","default":"json","pattern":"^(json|bibtex)$"},"accession":{"type":"string"}}},"title":"Get Project Cite","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_cite","displayName":"Get Project Cite"},{"name":"get_source_totals","description":"Return total project and sample counts for GEO, SRA, ArrayExpress, and ENA. Cached for 7 days. Returns {geo: {projects, samples}, sra: {...}, ...}.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Source Totals","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_source_totals","displayName":"Get Source Totals"},{"name":"get_single_cell_overview","description":"Study counts by type (fastq only, matrix only, fastq+matrix), total samples/cells, and top tissues/organisms across those studies.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Single Cell Overview","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_single_cell_overview","displayName":"Get Single Cell Overview"},{"name":"get_pentimento_overview","description":"Counts of samples scanned from the reads themselves: sex verdicts, assay calls, and validated microbial detections.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Pentimento Overview","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_pentimento_overview","displayName":"Get Pentimento Overview"},{"name":"get_tissue_microbes","description":"One cell per (tissue, organism): `positives` samples of `screened` carry that organism, over samples the Pentimento actually quantified. `positives_confirmed` is the high-breadth subset. Cells need 2 or more contributing studies and a tissue with 200 or more screened samples.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Tissue Microbes","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_tissue_microbes","displayName":"Get Tissue Microbes"},{"name":"get_sc_quality","description":"One point per (year, technology, evidence): the 25th, 50th and 75th percentile of per-matrix median UMI counts (`ncount`) and detected genes (`nfeature`) across single-cell matrices released that year.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get SC Quality","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_sc_quality","displayName":"Get SC Quality"},{"name":"get_sc_quality_samples","description":"One point per matrix, giving that matrix's median UMI count (`ncount`) and detected genes (`nfeature`), its release `year` and its `technology`.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get SC Quality Samples","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_sc_quality_samples","displayName":"Get SC Quality Samples"},{"name":"get_project_overlap","description":"Stats of how many projects each archive holds and how they intersect","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Project Overlap","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_overlap","displayName":"Get Project Overlap"},{"name":"get_last_updated","description":"Return the date of the newest record in the index. With ?db=<source> (geo|sra|arrayexpress|ena|gsa|dra|gea) returns that source's latest date; without it, the overall maximum. Cached for 7 days. Returns {db, last_updated, by_source}.","inputSchema":{"type":"object","required":[],"properties":{"db":{"anyOf":[{"type":"string","pattern":"^(geo|sra|arrayexpress|ena|gsa|dra|gea)$"},{"type":"null"}]}}},"title":"Get Last Updated","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_last_updated","displayName":"Get Last Updated"},{"name":"get_disease_summary","description":"Corpus-wide totals for studies with at least one sample annotated with a disease in this collection, resolved through MONDO ids and their descendants. `rare` is NIH GARD, matched by exact MONDO xref; `nord` is NORD, matched by name and so a looser set.","inputSchema":{"type":"object","required":["collection"],"properties":{"collection":{"type":"string"}}},"title":"Get Disease Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_disease_summary","displayName":"Get Disease Summary"},{"name":"get_disease_facets","description":"Study counts per disease category, clinical specialty and assay. Precomputed; the live join is ~80 s.","inputSchema":{"type":"object","required":["collection"],"properties":{"collection":{"type":"string"}}},"title":"Get Disease Facets","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_disease_facets","displayName":"Get Disease Facets"},{"name":"get_longread_summary","description":"Corpus-wide totals for studies with at least one PacBio or Oxford Nanopore experiment, across GEO, SRA, ENA, DDBJ DRA and GSA. A study mirrored in more than one archive counts once. `studies_hybrid` are studies that also sequenced on a short-read platform; `studies_long_read_only` had no other platform; the remainder have no experiment rows to judge by (GEO-only entries). `studies_exact_chemistry` had at least one run whose chemistry came from the submitted BAM's own header, not a model/date gue","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Long-Read Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_longread_summary","displayName":"Get Long-Read Summary"},{"name":"get_longread_facets","description":"Study counts per technology, platform, instrument model, library strategy, organism, archive, chemistry, has_exact_chemistry, assay category, year and long-read-only status. Values feed the filters of /longread/projects.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Long-Read Facets","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_longread_facets","displayName":"Get Long-Read Facets"},{"name":"get_singlecell_summary","description":"Corpus-wide totals for studies with matrix or read-derived single-cell evidence, or a declared single-cell classification (same population as /single-cell/projects). `cells` excludes studies whose only matrix is unfiltered (raw 10x barcodes, not real cells).","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Single-Cell Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_singlecell_summary","displayName":"Get Single-Cell Summary"},{"name":"get_singlecell_facets","description":"Study counts per chemistry, organism, tissue, modality, assay category, year, and has_matrix/has_fastq/is_long_read status. Values feed the filters of /single-cell/projects.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Single-Cell Facets","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_singlecell_facets","displayName":"Get Single-Cell Facets"},{"name":"get_perturbation_summary","description":"Corpus-wide totals for single-cell studies with genetic or chemical perturbation evidence (same population as /perturbation/projects). Detection is rule-based. `studies_high_medium` counts the studies whose evidence is strong enough to rely on.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Perturbation Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_perturbation_summary","displayName":"Get Perturbation Summary"},{"name":"get_perturbation_facets","description":"Study counts per perturbation type, confidence, data availability, genetic subtype, perturbation method, compound, organism, tissue, readout assay and year, top 100 values per facet. Values feed the filters of /perturbation/projects.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Perturbation Facets","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_perturbation_facets","displayName":"Get Perturbation Facets"},{"name":"get_spatial_summary","description":"Corpus-wide totals for studies flagged single-cell modality 'Spatial Transcriptomics' (same population as /spatial/projects). `studies_named_platform` counts studies whose own text names a specific platform (Visium, Xenium, MERFISH, ...); the rest only say 'spatial transcriptomics' generically.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Spatial Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_spatial_summary","displayName":"Get Spatial Summary"},{"name":"get_spatial_facets","description":"Study counts per platform, resolution, data availability, organism, tissue, readout assay, cell line, sample type and year, top 100 values per facet. Values feed the filters of /spatial/projects.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Spatial Facets","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_spatial_facets","displayName":"Get Spatial Facets"},{"name":"get_country_points","description":"Rounded lat/lng clusters with study counts for this country's submitting institutions, for map rendering (e.g. the OG image). Built by seqout-ingestion's sql/matviews/create_country_matview.sh.","inputSchema":{"type":"object","required":["code"],"properties":{"code":{"type":"string"}}},"title":"Get Country Points","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_country_points","displayName":"Get Country Points"},{"name":"get_country_summary","description":"Corpus-wide totals for studies submitted from one country (ISO-3166-1 alpha-2 code, e.g. IN, US), across every archive and technology.","inputSchema":{"type":"object","required":["code"],"properties":{"code":{"type":"string"}}},"title":"Get Country Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_country_summary","displayName":"Get Country Summary"},{"name":"get_country_facets","description":"Study counts per organism, assay category, archive, year and single-cell status for one country. Precomputed, capped to the top 40 values per facet. Values feed the filters of /country/{code}/projects.","inputSchema":{"type":"object","required":["code"],"properties":{"code":{"type":"string"}}},"title":"Get Country Facets","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_country_facets","displayName":"Get Country Facets"},{"name":"get_tissue_summary","description":"Corpus-wide totals for studies with at least one sample annotated with a tissue matching `term`, resolved through UBERON ids and their descendants (e.g. 'blood' also reaches 'whole blood', 'peripheral blood mononuclear cell', ...). `resolution` says whether the term matched an UBERON label exactly or only as a substring; `matched_labels` lists the matches. `matched_samples` counts samples resolved to one of the matched ids; `samples` is the matching studies' total across all annotations.","inputSchema":{"type":"object","required":["term"],"properties":{"term":{"type":"string"}}},"title":"Get Tissue Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_tissue_summary","displayName":"Get Tissue Summary"},{"name":"get_tissue_facets","description":"Study counts per organism, assay category, archive, journal, submitter country, year, FASTQ/single-cell/long-read status for studies matching `term`. Values feed the filters of /tissue/{term}/projects.","inputSchema":{"type":"object","required":["term"],"properties":{"term":{"type":"string"}}},"title":"Get Tissue Facets","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_tissue_facets","displayName":"Get Tissue Facets"},{"name":"get_disease_aliases","description":"GARD and NORD names","inputSchema":{"type":"object","required":["q"],"properties":{"q":{"type":"string","maxLength":200,"minLength":1},"limit":{"type":"integer","default":20,"maximum":100.0,"minimum":1.0}}},"title":"Get Disease Aliases","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_disease_aliases","displayName":"Get Disease Aliases"},{"name":"get_enriched_stats","description":"Return how many projects and samples have AI-enriched ontology metadata, plus per-column fill count and distinct-value count. Reads the enriched_summary materialized view.","inputSchema":{"type":"object","required":[],"properties":{}},"title":"Get Enriched Stats","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_enriched_stats","displayName":"Get Enriched Stats"},{"name":"get_enriched_crosstab","description":"Return counts of one standardised column (breakdown) within each value of another (group) — e.g. group=organism&breakdown=tissue gives the tissues seen per organism, with a distinct-tissue count per organism. Both axes must be in the curated crosstab column set. Reads the enriched_crosstab materialized view.","inputSchema":{"type":"object","required":["group","breakdown"],"properties":{"group":{"type":"string","pattern":"^[a-z_]+$"},"breakdown":{"type":"string","pattern":"^[a-z_]+$"}}},"title":"Get Enriched Crosstab","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_enriched_crosstab","displayName":"Get Enriched Crosstab"},{"name":"get_enriched_coverage","description":"Return how many projects and samples carry AI-enriched ontology metadata, split by archive (geo, sra, ena, arrayexpress, gsa, dra, gea), by organism, by assay and by assay_category. Archive totals are planner row estimates, so the percentages are approximate. A project with several organisms or assays counts under each, so those rows sum past the corpus total. The organism and assay lists are capped at limit; distinct_values carries the full counts. Reads the enriched_coverage materialized view.","inputSchema":{"type":"object","required":[],"properties":{"limit":{"type":"integer","default":50,"maximum":500.0,"minimum":1.0}}},"title":"Get Enriched Coverage","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_enriched_coverage","displayName":"Get Enriched Coverage"},{"name":"get_enriched_column","description":"Return the most common values (with counts) for one enriched column (e.g. tissue, cell_type, disease, assay). Reads the enriched_column_top_values materialized view.","inputSchema":{"type":"object","required":["column"],"properties":{"limit":{"type":"integer","default":50,"maximum":100.0,"minimum":1.0},"column":{"type":"string","pattern":"^[a-z_]+$"}}},"title":"Get Enriched Column","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_enriched_column","displayName":"Get Enriched Column"},{"name":"get_project_single_cell_status","description":"Resolves any GSE/SRP/ERP and reports the cached `single_cell_status` label.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Project Single Cell Status","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_single_cell_status","displayName":"Get Project Single Cell Status"},{"name":"get_project_single_cell_summary","description":"Summary of single cell projects at the sample level","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Project Single Cell Summary","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_single_cell_summary","displayName":"Get Project Single Cell Summary"},{"name":"list_single_cell_studies","description":"Studies carrying at least `min_evidence` of the three independent measurements (counted matrix, barcode-whitelist hit, R1 length structure).","inputSchema":{"type":"object","required":[],"properties":{"limit":{"type":"integer","default":200,"maximum":1000.0,"minimum":1.0},"offset":{"type":"integer","default":0,"minimum":0.0},"min_evidence":{"type":"integer","default":1,"maximum":3.0,"minimum":1.0},"require_matrix":{"type":"boolean","default":false}}},"title":"List Single Cell Studies","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"list_single_cell_studies","displayName":"List Single Cell Studies"},{"name":"get_project_longread_chemistry","description":"Every PacBio/Oxford Nanopore run in the study, independent of single-cell status and Pentimento linkage. `chemistry_confidence` is `exact` when read from the submitted BAM's own header, `declared` (ONT only) when parsed from the depositor's own protocol text, `bucket` when inferred from instrument_model alone (never publication date), `unknown` otherwise. `chemistry_confidence_label` spells the same tier for display (`bucket` -> \"estimated\"); sort or filter on the raw value instead. `runs` is `[","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Project Long-Read Chemistry","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_longread_chemistry","displayName":"Get Project Long-Read Chemistry"},{"name":"get_project_single_cell","description":"Per-sample cell/gene counts joined to read-derived (preflightx) species, sex and assay calls and to viral/microbial presence flags. 404s when the study is not in the Pentimento.","inputSchema":{"type":"object","required":["accession"],"properties":{"limit":{"type":"integer","default":200,"maximum":1000.0,"minimum":1.0},"offset":{"type":"integer","default":0,"minimum":0.0},"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Get Project Single Cell","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_single_cell","displayName":"Get Project Single Cell"},{"name":"download_pentimento_detections_csv","description":"One row per sample per organism, at full taxon resolution: class, kingdom, breadth tier, genome breadth, covered bases, reads, k-mer mass and unitigs. A screened sample with nothing found emits one row with an empty organism, so absence is distinguishable from never having been scanned.","inputSchema":{"type":"object","required":["accession"],"properties":{"all_rows":{"type":"boolean","default":false},"accession":{"type":"string","pattern":"^(GSE|[SED]RP|PRJ[A-Z]+|CRA|HRA|[Ee]-[A-Za-z]{4}-)\\d+$"}}},"title":"Download Pentimento Detections CSV","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"download_pentimento_detections_csv","displayName":"Download Pentimento Detections CSV"},{"name":"get_experiment_enriched","description":"Return the ontology-enriched sample record(s) for a single SRA/ENA experiment (SRX/ERX/DRX), scoped from the parent study's enriched metadata. Same fields as /project/{accession}/enriched.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^([SED]RX|CRX|HRX)\\d+$"},"human_readable_age":{"type":"boolean","default":true}}},"title":"Get Experiment Enriched","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_experiment_enriched","displayName":"Get Experiment Enriched"},{"name":"get_run_enriched","description":"Return the ontology-enriched sample record for a single run accession (SRR/ERR/DRR), resolved via run → experiment → sample. Same fields as /project/{accession}/enriched.","inputSchema":{"type":"object","required":["run"],"properties":{"run":{"type":"string","pattern":"^[SED]RR\\d+$"},"human_readable_age":{"type":"boolean","default":true}}},"title":"Get Run Enriched","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_run_enriched","displayName":"Get Run Enriched"},{"name":"get_project_similar","description":"Return the nearest studies to a project based on the precomputed 2D embedding (geo_series.neighbors / sra_studies.neighbors). Each result includes accession, distance, title, organisms, and source. Useful for 'find studies like X' / 'what else is similar to this dataset'.","inputSchema":{"type":"object","required":["accession"],"properties":{"limit":{"type":"integer","default":10,"maximum":100.0,"minimum":1.0},"accession":{"type":"string","pattern":"^(GSE|[SED]RP)\\d+$"}}},"title":"Get Project Similar","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_project_similar","displayName":"Get Project Similar"},{"name":"list_library_strategies","description":"Return every library_strategy seen in sra_experiments with a count, sorted by frequency. Use to populate filter dropdowns or to discover valid values for search_structured(library_strategy=...).","inputSchema":{"type":"object","required":[],"properties":{}},"title":"List Library Strategies","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"list_library_strategies","displayName":"List Library Strategies"},{"name":"list_instrument_models","description":"Return every instrument_model seen in sra_experiments with a count, sorted by frequency. Use to discover valid values for search_structured(instrument_model=...).","inputSchema":{"type":"object","required":[],"properties":{}},"title":"List Instrument Models","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"list_instrument_models","displayName":"List Instrument Models"},{"name":"list_journals","description":"Return the top journals appearing in linked publications, sorted by frequency. Use to discover valid values for search_structured(journal=...).","inputSchema":{"type":"object","required":[],"properties":{"limit":{"type":"integer","default":500,"maximum":5000.0,"minimum":1.0}}},"title":"List Journals","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"list_journals","displayName":"List Journals"},{"name":"list_centers","description":"Return the top submission centers from sra_submissions + ena_studies, sorted by frequency. Use to discover values for search_structured(center=...).","inputSchema":{"type":"object","required":[],"properties":{"limit":{"type":"integer","default":500,"maximum":5000.0,"minimum":1.0}}},"title":"List Centers","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"list_centers","displayName":"List Centers"},{"name":"get_sample_experiments","description":"Return the SRA/ENA experiment accession(s) that reference a sample (SRS/ERS/DRS/SAM*). Inverse of /experiment/{accession}'s samples list.","inputSchema":{"type":"object","required":["accession"],"properties":{"accession":{"type":"string","pattern":"^([SED]RS|SAM[A-Z]+|HRS)\\d+$"}}},"title":"Get Sample Experiments","annotations":{"readOnlyHint":true,"untrustedContentHint":true},"logicalName":"get_sample_experiments","displayName":"Get Sample Experiments"}],"toolSource":"directory_preview","agentAction":"both","installLinks":[{"id":"cursor","label":"Cursor","href":"cursor://anysphere.cursor-deeplink/mcp/install?name=seqout&config=eyJ1cmwiOiAiaHR0cHM6Ly9zZXFvdXQub3JnL2FwaS9tY3AifQ%3D%3D"},{"id":"vscode","label":"VS Code","href":"vscode:mcp/install?%7B%22name%22%3A%22seqout%22%2C%22type%22%3A%22http%22%2C%22url%22%3A%22https%3A%2F%2Fseqout.org%2Fapi%2Fmcp%22%7D"},{"id":"vscode-insiders","label":"VS Code Insiders","href":"vscode-insiders:mcp/install?%7B%22name%22%3A%22seqout%22%2C%22type%22%3A%22http%22%2C%22url%22%3A%22https%3A%2F%2Fseqout.org%2Fapi%2Fmcp%22%7D"},{"id":"claude-web","label":"Claude.ai","href":"https://claude.ai/customize/connectors?modal=add-custom-connector&connectorName=seqout&connectorUrl=https%3A%2F%2Fseqout.org%2Fapi%2Fmcp"},{"id":"codex","label":"Codex","copyText":"codex mcp add \"seqout\" --url \"https://seqout.org/api/mcp\""},{"id":"chatgpt","label":"ChatGPT","href":"https://www.mcpbundles.com/docs/integrations/chatgpt"}],"catalogUrl":"https://www.mcpbundles.com/api/directory/v1/servers/seqout-mcp-b171ae9874","callUrl":"https://www.mcpbundles.com/api/directory/v1/servers/seqout-mcp-b171ae9874/tools/{tool}","mcpServerUrl":"https://seqout.org/api/mcp","liveCatalogUrl":"https://www.mcpbundles.com/api/directory/v1/servers/seqout-mcp-b171ae9874?live=1"}