{"doi":"10.1186/2047-217x-1-11","title":"GigaDB: announcing the GigaScience database","abstract":"With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience's goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond.","journal":"GigaScience","year":2012,"id":2670,"datarank":3.2634327199374145,"base_score":4.343805421853684,"endowment":4.343805421853684,"self_citation_contribution":0.6515708132780527,"citation_network_contribution":2.6118619066593616,"self_endowment_contribution":0.6515708132780527,"citer_contribution":2.6118619066593616,"corpus_percentile":68.42961757526444,"corpus_rank":389,"citation_count":76,"citer_count":72,"citers_with_citation_signal":64,"citers_with_endowment":64,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9518,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2012-07-12","fair_score":47.7083,"fair_percentile":44.415127528583994,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":23959,"name":"Peter Li","orcid":"0000-0001-9602-9550","position":1,"is_corresponding":false},{"id":46,"name":"Scott C. Edmunds","orcid":"0000-0001-6444-1436","position":2,"is_corresponding":false},{"id":31055,"name":"Tam P. Sneddon","orcid":"0000-0003-1137-8992","position":0,"is_corresponding":true}],"reference_count":11,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"23587345","pmcid":"PMC3626507","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":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":0.2259,"fair_rationale":{"fair_score":47.71,"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 mentions metadata capture and plans to use ISA-Tab for structured metadata, but does not describe rich, machine-readable metadata in practice beyond a DOIs and searchable metadata via DataCite."}]},"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 provides a clear protocol: data linked via DOI and available at gigadb.org, with data released under CC0 waiver, but no explicit mention of authentication/authorization or automated access mechanism like an API."}]},"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":"Use of standard identifiers (DOI, INSDC, Genbank, dbSNP, dbVar) and mention of ISA-Tab format for interoperability, but no evidence of widespread use of standard file formats or vocabularies beyond genomic data types."}]},"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":"Data released under CC0 waiver and includes supporting data for reproducibility, but no explicit data-availability statement in the paper and limited reproducibility details beyond the methylome example."}]}},"suggestions":["Add explicit data-availability statement in the paper with clear access instructions and license.","Implement automated machine-readable metadata (e.g., schema.org) for all datasets.","Provide API endpoint for programmatic data access.","Standardize all datasets using ISA-Tab format and deposit in public registries.","Include reproducibility test (e.g., containerized pipeline) for each dataset."],"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":"2026-06-18T00:41:18.689704Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}