Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-seq/microarray datasets by organism/tissue/condition, comparing across studies (case-control, time-series, dose-response), and assessing dataset suitabili

Gene Expression & Omics Data Retrieval Retrieve gene expression experiments and multi omics datasets with disambiguation and quality assessment. IMPORTANT : Always use English terms in tool calls. Respond in the user's language. LOOK UP DON'T GUESS : Never assume which datasets exist or their accessions. Always search to confirm. Domain Reasoning Before retrieving, determine: organism, tissue, experimental design (case control/time series/dose response). These affect which database to search and how to interpret results. RNA seq provides wider dynamic range; microarray has extensive legacy data. Prioritize experiments with =3 biological replicates, complete annotations, and both raw+processed data. Workflow Phase 0: Clarification (When Needed) Ask ONLY if: gene name ambiguous, tissue/condition unclear, organism not specified. Skip for: specific accessions (E MTAB , E GEOD , S BSST ), clear disease/tissue+organism, explicit platform requests. Phase 1: Query Disambiguation Resolve official gene symbol (HGNC for human, MGI for mouse). Note common aliases for search expansion. User Query Type Search Strategy Specific accession Direct retrieval Gene + condition "[gene] [condition]" + species filter Disease only "[disease]" + species filter Technology specific Add platform keywords Phase 2: Data Retrieval (Internal) Search silently. Do NOT narrate the process. Fallback Chains Primary Fallback ArrayExpress search BioStudies search arrayexpress get experiment biostudies get study arrayexpress get experiment files Note "Files unavailable" Phase 3: Report Dataset Profile Present as a Dataset Search Report . Hide search process. Include: 1. Search Summary : query, databases searched, result count 2. Top Experiments (per experiment): Accession, organism, type (RNA seq/microarray), platform, sample count, date Description, experimental design (conditions, replicates, tissue) Sample groups table, data files table Quality assessment (●●●/●●○/●○○) 3. Multi Omics Studies (from BioStudies): accession, type, data types included 4. Summary Table : all experiments ranked 5. Recommendations : best dataset for user's purpose, integration notes 6. Data Access : download links, database URLs Data Quality Tiers Tier Symbol Criteria High ●●● =3 bio replicates, complete metadata, processed data available Medium ●●○ 2 3 replicates OR some metadata gaps Low ●○○ No replicates, sparse metadata, or access issues Caution ○○○ Single sample, no replication, outdated platform Reasoning Framework Dataset quality : Prioritize =3 biological replicates, complete annotations, both raw+processed data. Single replicate experiments can inform but not be sole evidence. Platform comparison : RNA seq = wider dynamic range, novel transcripts. Microarray = probe limited but extensive legacy data. Cross platform combining requires batch correction. Metadata scoring : Rate 0 5 on: (1) sample annotations, (2) design documented, (3) pipeline described, (4) raw data deposited, (5) publication linked. Score <=2 warrants caution. GEO vs ArrayExpress : GEO has broader coverage (older studies); ArrayExpress enforces stricter metadata. BioStudies captures multi omics. Search both. Synthesis Questions 1. Does the dataset have sufficient replication and metadata for the intended analysis? 2. Are there batch effects or confounding variables? 3. Do multiple datasets show concordant patterns, and can they be integrated? Error Handling Error Response "No experiments found" Broaden keywords, remove species filter, try synonyms "Accession not found" Verify format, check if withdrawn "Files not available" Note: "Data files restricted by submitter" "API timeout" Retry once, note "(metadata retrieval incomplete)" Tool Reference ArrayExpress : arrayexpress search experiments (search), arrayexpress get experiment (metadata), arrayexpress get experiment files (downloads), arrayexpress get experiment samples (annotations) BioStudies : biostudies search (search), biostudies get study (metadata+sections), biostudies get study files (files) Additional Sources : GEO search rnaseq datasets / geo search datasets GEO (largest RNA seq repo) OmicsDI search datasets cross repository aggregation (GEO+ArrayExpress+PRIDE+MassIVE) GTEx get expression summary baseline tissue expression (54 normal tissues, param: gene symbol ) ENAPortal search studies sequencing studies (param: query with description="..." ) CxGDisc search datasets single cell datasets (needs exact disease ontology terms) GxA list experiments / GxA get experiment info / GxA get experiment expression EBI Gene Expression Atlas: curated baseline (tissue) and differential (condition comparison) bulk RNA seq/microarray experiments. Filter GxA list experiments by species and experiment type ("baseline" vs "differential") first; GxA get experiment expression needs a specific experiment accession (e.g. E MTAB 2836 ) plus gene id . ARCHS4 get gene expression / ARCHS4 get gene correlations ARCHS4: box plot expression statistics (min/Q1/median/Q3/max, log2) across human/mouse tissues and cell lines, and top co expressed genes by Pearson correlation across 300K+ uniformly reprocessed RNA seq samples. Good for a quick baseline expression sanity check or finding candidate co regulated genes without running a full differential expression pipeline. Bgee search genes / Bgee get gene expression / Bgee list species Bgee: curated baseline expression by tissue calls across 29+ animal species (vs. ARCHS4's human/mouse only reprocessed RNA seq, or GxA's curated but narrower experiment set). Bgee get gene expression needs BOTH an Ensembl gene ID and an NCBI taxonomy ID (e.g. gene id="ENSG00000141510" , species id="9606" for human TP53) resolve the gene ID with Bgee search genes first if you only have a symbol. Use Bgee list species to confirm a species is covered before assuming Bgee has it. Best for cross species comparison questions ("is gene X expressed in the same tissues in mouse and zebrafish?"), not for finding raw sequencing datasets to download. PubMed search articles dataset discovery via publications Search Parameters ArrayExpress : keywords (free text), species (scientific name), array (platform filter), limit BioStudies : query (free text), limit

tooluniverse-expression-data-retrieval