{"doi":"10.1093/database/bau101","title":"A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools","abstract":"The publicly available online database MelGene provides a comprehensive, regularly updated, collection of data from genetic association studies in cutaneous melanoma (CM), including random-effects meta-analysis results of all eligible polymorphisms. The updated database version includes data from 192 publications with information on 1114 significantly associated polymorphisms across 280 genes, along with new front-end and back-end capabilities. Various types of relationships between data are calculated and visualized as networks. We constructed 13 different networks containing the polymorphisms and the genes included in MelGene. We explored the derived network representations under the following questions: (i) are there nodes that deserve consideration regarding their network connectivity characteristics? (ii) What is the relation of either the genome-wide or nominally significant CM polymorphisms/genes with the ones highlighted by the network representation? We show that our network approach using the MelGene data reveals connections between statistically significant genes/ polymorphisms and other genes/polymorphisms acting as 'hubs' in the reconstructed networks. To the best of our knowledge, this is the first database containing data from a comprehensive field synopsis and systematic meta-analyses of genetic polymorphisms in CM that provides user-friendly tools for in-depth molecular network visualization and exploration. The proposed network connections highlight potentially new loci requiring further investigation of their relation to melanoma risk. Database URL: http://www.melgene.org.","journal":"Database","year":2014,"id":8971,"datarank":0.5193292539205986,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.14659325645239843,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.14659325645239843,"corpus_percentile":51.74938974776241,"corpus_rank":594,"citation_count":11,"citer_count":5,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9543,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2014-11-07","fair_score":44.5833,"fair_percentile":43.007915567282325,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":77417,"name":"M. M. Bourdakou","orcid":null,"position":4,"is_corresponding":false},{"id":77418,"name":"A. Sakellariou","orcid":null,"position":5,"is_corresponding":false},{"id":70572,"name":"Katerina P. Kypreou","orcid":null,"position":6,"is_corresponding":false},{"id":18031,"name":"A. J. Stratigos","orcid":null,"position":11,"is_corresponding":false},{"id":70574,"name":"Emmanouil Athanasiadis","orcid":"0000-0002-2771-5562","position":13,"is_corresponding":false},{"id":70571,"name":"Kyriaki Antonopoulou","orcid":"0000-0002-9212-737X","position":14,"is_corresponding":false},{"id":18032,"name":"Foteini Chatzinasiou","orcid":null,"position":15,"is_corresponding":false},{"id":7730,"name":"Christina M. Lill","orcid":"0000-0002-1903-6762","position":16,"is_corresponding":false},{"id":77420,"name":"Marilena M. Bourdakou","orcid":"0000-0001-8075-0634","position":17,"is_corresponding":false},{"id":77421,"name":"Αλέξανδρος Σακελλαρίου","orcid":"0000-0002-5427-933X","position":18,"is_corresponding":false},{"id":18033,"name":"Katerina Kypreou","orcid":null,"position":19,"is_corresponding":false},{"id":18034,"name":"Irene Stefanaki","orcid":"0000-0002-2964-370X","position":20,"is_corresponding":false},{"id":2427,"name":"Evangelos Evangelou","orcid":"0000-0002-5488-2999","position":21,"is_corresponding":false},{"id":148,"name":"John P. A. Ioannidis","orcid":"0000-0003-3118-6859","position":22,"is_corresponding":false},{"id":526,"name":"Muin J. Khoury","orcid":"0000-0002-9887-443X","position":23,"is_corresponding":false},{"id":70576,"name":"Alexander Stratigos","orcid":"0000-0002-6088-5694","position":24,"is_corresponding":false},{"id":18035,"name":"George M. Spyrou","orcid":"0000-0002-2470-3363","position":25,"is_corresponding":false}],"reference_count":20,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"25380778","pmcid":"PMC4224266","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":55.0,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":-0.0568,"fair_rationale":{"fair_score":44.58,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"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":0.5,"signal":null,"rationale":"The paper describes a structured database schema with fields like gene symbol and rs identifiers, but does not mention machine-readable metadata standards or formats."}]},"A":{"name":"Accessible","score":55.0,"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":0.5,"signal":null,"rationale":"The database is publicly accessible via a web URL, but no API or programmatic access protocol is described."}]},"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":"Standard identifiers (e.g., NCBI rs IDs) are used, but the paper does not specify standard data formats for exchange or download."}]},"R":{"name":"Reusable","score":33.33,"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":0.5,"signal":null,"rationale":"The article is under CC BY license and the database is publicly available, but there is no explicit data license for the database content or a data availability statement for the underlying dataset."}]}},"suggestions":["Provide a machine-readable metadata file (e.g., JSON-LD) describing the database schema and content.","Offer an API for programmatic access to the database.","Use standard data formats (e.g., CSV, VCF) for bulk download of the dataset.","Include a clear data license (e.g., CC0) for the database content in the paper.","Add a data availability statement explicitly stating how to access and reuse the data."],"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":"2026-06-18T00:50:03.345599Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}