{"doi":"10.3390/cancers17091595","title":"Natural Language Processing of Radiology Reports to Assess Survival in Patients with Advanced Melanoma","abstract":"Background/Objectives: To use natural language processing (NLP) to extract large-scale data from the CT radiology reports of patients with advanced melanoma treated with immunotherapy and to determine whether liver metastases affect survival. Methods: Patient criteria (M1 disease subclassified into M1a, M1b, or M1c) as well as alternative criteria (M1 with advanced melanoma, imaged with CT chest, abdomen, and pelvis from July 2014–March 2019) were included retrospectively. NLP was used to identify metastases from CT reports, and then patients were classified according to American Joint Committee on Cancer (AJCC) staging disease subclassified into M1L+ or M1L−, indicating whether liver metastases were present or not). Statistical analysis included constructing Kaplan–Meier survival curves and calculating hazard ratios (HRs). Results: 2239 patients were included (mean age, 63 years). Whether using AJCC or alternative criteria, overall survival (OS) was poorest for M1L+ (entire cohort median OS, 0.69 years [95% CI: 0.60–0.82]; immunotherapy cohort median OS, 1.4 years [95% CI: 0.92–2.0]) compared to M1L− (entire cohort median OS, 1.8 years [95% CI: 1.4–2.2]; immunotherapy cohort median OS; M1L−, 2.9 years [95% CI: 2.3–3.9]). The median HR for M1L+ (median HR, 5.35 [95% CI: 4.59–6.24]) was higher than that for M0 (p < 0.001). The median HR for M1L+ (median HR, 2.13 [95% CI: 1.65–2.64]) was higher than that for M0 (p < 0.01). Conclusions: Patients with advanced melanoma, particularly those with liver metastases, demonstrated inferior survival, even when treated with immunotherapy.","journal":"Cancers","year":2025,"id":565459,"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":10324,"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":0.626,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":4.1667,"fair_percentile":4.891470498318557,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":867932,"name":"Jordan Eichholz","orcid":null,"position":1,"is_corresponding":false},{"id":353291,"name":"Varadan Sevilimedu","orcid":"0000-0002-0938-9396","position":2,"is_corresponding":false},{"id":615169,"name":"Natalie Gangai","orcid":"0000-0003-0603-7165","position":3,"is_corresponding":false},{"id":242191,"name":"Danny N. Khalil","orcid":"0000-0003-4688-0958","position":4,"is_corresponding":false},{"id":68931,"name":"Michael A. Postow","orcid":"0000-0002-3367-7961","position":5,"is_corresponding":false},{"id":402908,"name":"Richard Kinh Gian","orcid":"0000-0002-6554-0310","position":6,"is_corresponding":false},{"id":717695,"name":"Jeeban Paul Das","orcid":"0000-0001-7619-4241","position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:56:28.709936Z","pmid":"40361518","pmcid":"PMC12071518","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":11.1111,"fair_a":18.75,"fair_i":0.0,"fair_r":16.6667,"fair_zscore":-1.1986,"fair_rationale":{"fair_score":4.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":11.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"Data generated or analyzed during the study are available from the corresponding author by request.","grounded":true,"rationale":"No persistent identifier string (DOI, Handle, ARK, URN, or repository accession) is given for the data.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"Data generated or analyzed during the study are available from the corresponding author by request.","grounded":true,"rationale":"The data are held by the corresponding author, not a named repository.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data generated or analyzed during the study are available from the corresponding author by request.","grounded":true,"rationale":"The statement points to the corresponding author, matching Colavizza category 1 (data available on request).","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide an itemised inventory of the dataset (no section, table, or list of files/variables). 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A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Data generated or analyzed during the study are available from the corresponding author by request.","why":"No persistent identifier string (DOI, Handle, ARK, URN, or repository accession) is given for the data.","gain":16.67,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. 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For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Data generated or analyzed during the study are available from the corresponding author by request.","why":"The access route is a discretionary request to a person, which is not an unconditional or followable route per the definition.","gain":16.67,"priority":"essential","scored":true},{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 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A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier (DOI, accession, RRID) for any external resource (source data, code, database) is given in the text.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence in the paper states when the data become available or how long they persist.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:53:14.686350Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}