{"doi":"10.1093/database/baaf086","title":"Panorama: a database for the oncogenic evaluation of somatic mutations in pan-cancer","abstract":"Somatic mutations, key alterations in cancer development, exert differential effects across tissues and biological layers, such as transcriptomes, proteomes, and post-translational modifications (PTMs). Although previous pan-cancer studies have characterized the molecular landscape of cancer, the effects of individual somatic mutations across different tissues remain insufficiently explored. Here, we developed Panorama to evaluate the oncogenic potential of single somatic mutations across all cancer types. We collected cancer proteogenomics or multiomics data from over 10 000 individuals across 19 cancer types. Based on five evaluation criteria, we assessed whether a specific mutation affects the abundance of a particular gene's transcriptome, proteome, or phosphoproteome; the tumor microenvironment; specific RNA- or protein-based signaling pathways; and outlier-level overexpression of PTMs, aiding in potential drug target identification. By leveraging five oncogenic metrics, Panorama quantifies the oncogenic potential of individual somatic mutations and provides a framework for identifying driver mutations by incorporating their downstream effects. With Panorama, researchers can integrate cancer proteogenomics data, providing a comprehensive approach that enhances our understanding of single somatic mutations in specific tissues. Finally, Panorama was developed as a web-based database to ensure easy access for researchers and is freely available at http://139.150.65.64:8080/or https://github.com/prosium/panorama.","journal":"Database","year":2026,"id":1045,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":765,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9216,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2026-01-01","fair_score":46.6667,"fair_percentile":43.733509234828496,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":14579,"name":"Seon-Young Kim","orcid":"0000-0002-1030-7730","position":1,"is_corresponding":false},{"id":14578,"name":"Seung-Jin Park","orcid":null,"position":0,"is_corresponding":true}],"reference_count":81,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"41540913","pmcid":"PMC12808847","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":67.5,"fair_i":25.0,"fair_r":41.6667,"fair_zscore":0.1316,"fair_rationale":{"fair_score":46.67,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper provides only minimal metadata (title, authors, abstract, DOI) in human-readable form and does not offer structured, machine-readable metadata (e.g., JSON-LD, RDF) or formal schema/ontology annotations."}]},"A":{"name":"Accessible","score":67.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The paper clearly states that the database is freely available via a web interface and GitHub, but does not specify a formal authentication or standardized access protocol (e.g., API, SPARQL endpoint) beyond basic web browsing."}]},"I":{"name":"Interoperable","score":25.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper uses standard file formats (Parquet) and common tools (xCell, CIBERSORT, GSVA), but does not employ formal community vocabularies, ontologies, or persistent identifiers (e.g., for genes, mutations, or data elements)."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"The paper includes a data availability statement, provides data and code on GitHub with a CC-BY license, and describes analysis steps, but lacks a formal software license, version archive, or detailed provenance metadata for full reproducibility."}]}},"suggestions":["Add structured, machine-readable metadata (e.g., JSON-LD schema.org annotations) to the paper and database landing page.","Provide a persistent identifier (e.g., DOI) for the database version and code repository.","Adopt community-standard ontologies (e.g., OBO Foundry terms for cancer types, genes, mutations) in the database schema.","Publish a stable API with documentation to enable programmatic access.","Include a formal software license (e.g., MIT, Apache 2.0) and a CONTRIBUTING guide on GitHub, plus archived releases on Zenodo."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T06:56:07.327138Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}