Q (haiku): what's the best way to put clinical data into cbioportal? ▶ list_guides {} ◀ result {"result":[{"uri":"cbioportal://mutation-frequency-guide","description":"Comprehensive guide for calculating gene mutation frequencies with gene-specific profiling denominators"},{"uri":"cbioportal://clinical-data-guide","description":"Guide for querying clinical data including patient vs sample level considerations"},{"uri":"cbioportal://sample-filtering-guide","description":"Guide for filtering samples and studies in cBioPortal queries"},{"uri":"cbioportal://common-pitfalls","description":"Guide to avoid common mistakes when querying cBioPortal data. If you already know which numbered pitfall applies, fetch just that section via read_guide(\"cbioportal://common-pitfalls#\") (e.g. #16) instead of the full guide"},{"uri":"cbioportal://treatment-guide","description":"Guide for querying treatment/clinical event data including drug agents, timelines, and linking to genomic data"},{"uri":"cbioportal://faq-guide","description":"General cBioPortal FAQ: history, how to cite, data types, reference genome, abbreviations, GISTIC thresholds, API access"},{"uri":"cbioportal://statistical-tests-guide","description":"Statistical test selection guide — decision matrix for choosing Fisher's exact, Wilcoxon, chi-squared, t-test, ANOVA, etc. based on data type and group count"},{"uri":"cbioportal://gene-expression-guide","description":"Gene expression / copy-number / methylation analysis. Covers genetic_alteration_derived, profile_type discovery, and the gene_pair_coexpression view for Spearman correlation between two genes"},{"uri":"cbioportal://external-resources-guide","description":"Guide for finding external linked resources such as imaging, pathology, Minerva, HTAN, or other resource_* table links before declaring data unavailable"},{"uri":"cbioportal://gene-resolution-guide","description":"Guide for resolving ambiguous gene symbols, aliases, gene families, and shorthand such as CD3 before querying expression or alteration data"},{"uri":"cbioportal://study-resolution-guide","description":"Guide for resolving requested studies, avoiding silent substitute cohorts, and redirecting to known external cBioPortal instances when data is not in this deployment"},{"uri":"cbioportal://germline-guide","description":"Guide for querying germline variant data — storage columns, study discovery, query patterns, and somatic vs germline considerations"},{"uri":"cbioportal://study-guide/{study_id}","description":"Dynamic study-specific guide - use get_study_guide(study_id) tool to generate"}]} ▶ read_guide { "uri": "cbioportal://faq-guide" } ◀ result # cBioPortal FAQ Guide Curated answers to frequently asked general questions about cBioPortal. Source: [cBioPortal FAQ](https://docs.cbioportal.org/user-guide/faq/). ## What is cBioPortal? cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. It was originally developed at Memorial Sloan Kettering Cancer Center (MSK) and is now maintained by a multi-institutional team. ## History - **2008**: cBioPortal first became available online. - **2012**: First major publication — Cerami et al., *Cancer Discovery*. - **2013**: Second major publication — Gao et al., *Science Signaling*. - **2023**: Third major publication — de Bruijn et al., *Cancer Research*. ## How to Cite cBioPortal When using cBioPortal in publications, cite these three papers: 1. Cerami et al. "The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data." *Cancer Discovery* 2, 401–404 (2012). doi:10.1158/2159-8290.CD-12-0095 2. Gao et al. "Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal." *Science Signaling* 6, pl1 (2013). doi:10.1126/scisignal.2004088 3. de Bruijn et al. "Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal." *Cancer Research* 83, 3861–3867 (2023). doi:10.1158/0008-5472.CAN-23-0816 Also cite the specific study publication(s) whose data you used. ## What Data Types Does cBioPortal Contain? - **Mutations** (non-synonymous somatic mutations) - **DNA copy-number alterations** (CNA) from GISTIC or other methods - **mRNA expression** data (RNA-seq, microarray) - **Protein/phosphoprotein** levels (RPPA, mass spectrometry) - **DNA methylation** data - **Structural variants** (gene fusions, rearrangements) - **Clinical data** (demographics, diagnosis, treatment, outcomes) Note: Synonymous mutations are not included in cBioPortal. ## Data Types Usually Not Stored Directly cBioPortal generally does not store: - raw CT, MRI, pathology-slide, or histology image files - raw sequencing files such as BAM, CRAM, or FASTQ - polygenic risk scores as a standard data type - full external clinical-trial databases However, this deployment may contain links to external viewers or portals through `resource_*` tables. For imaging, pathology, Minerva, HTAN, or viewer questions, read `cbioportal://external-resources-guide` and check those tables before saying the data is absent. ## What the MCP Agent Can and Cannot Produce The MCP agent can: - query cBioPortal data and return tables in text/JSON/Markdown - summarize counts, frequencies, and available attributes - provide cBioPortal study links and DataHub download links when applicable - provide SQL snippets or handoff instructions for R/Python/cBioPortal tools The MCP agent should not promise to: - render Kaplan-Meier plots or other visual figures directly - export large … (6558 more chars) ═ answer (success) Based on the FAQ and cBioPortal documentation, here's the best way to load clinical data into cBioPortal: ## For the Public cBioPortal If you want to **contribute to the public cBioPortal**, follow these steps: 1. **Prepare your data in cBioPortal format** — cBioPortal has a standardized data submission format. Visit the [cBioPortal Data Curation Guide](https://docs.cbioportal.org/file-formats-and-structure/) for detailed file format specifications. 2. **Key files you'll need:** - **Study metadata** (`meta_*.txt` files) - **Clinical data file** (e.g., `data_clinical_patient.txt`, `data_clinical_sample.txt`) - **Genomic data files** (mutation, CNA, mRNA, etc.) - **Sample map** linking samples to patients 3. **Submit to the cBioPortal DataHub** — Once your data is properly formatted, you can contribute it to the public repository following their submission process outlined in the documentation. ## For a Private cBioPortal Instance If you're running a **private cBioPortal deployment** (like an institutional instance): 1. **Package your study** in the standard cBioPortal format (same structure as above) 2. **Place the study folder** in the deployment's data directory 3. **Restart the application** or run the import script to load the study into the database 4. The ClickHouse backend will parse the clinical and genomic files and make them queryable ## For Quick Visualization Without Full Submission cBioPortal provides **standalone tools** (e.g., Mutation Mapper, OncoPrint) for visualizing your own data without full study submission. --- **Which scenario applies to you?** If you clarify whether you're submitting to the public portal, running a private instance, or just visualizing data temporarily, I can provide more specific guidance on file format and submission steps.