{"doi":"10.1093/database/bar003","title":"Quality assurance for the query and distribution systems of the RCSB Protein Data Bank","abstract":"The RCSB Protein Data Bank (RCSB PDB, www.pdb.org) is a key online resource for structural biology and related scientific disciplines. The website is used on average by 165,000 unique visitors per month, and more than 2000 other websites link to it. The amount and complexity of PDB data as well as the expectations on its usage are growing rapidly. Therefore, ensuring the reliability and robustness of the RCSB PDB query and distribution systems are crucially important and increasingly challenging. This article describes quality assurance for the RCSB PDB website at several distinct levels, including: (i) hardware redundancy and failover, (ii) testing protocols for weekly database updates, (iii) testing and release procedures for major software updates and (iv) miscellaneous monitoring and troubleshooting tools and practices. 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Rose","orcid":"0000-0001-9981-9750","position":18,"is_corresponding":false},{"id":58743,"name":"Chirag Shah","orcid":"0000-0002-3797-4293","position":19,"is_corresponding":false},{"id":23502,"name":"Jasmine Young","orcid":"0000-0001-8896-6878","position":20,"is_corresponding":false},{"id":45293,"name":"Benjamin T. Yukich","orcid":null,"position":21,"is_corresponding":false},{"id":2156,"name":"Helen M. Berman","orcid":"0000-0002-3337-0660","position":22,"is_corresponding":false},{"id":125,"name":"Philip  E. Bourne","orcid":"0000-0002-7618-7292","position":23,"is_corresponding":false}],"reference_count":19,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"21382834","pmcid":"PMC3056270","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":52.5,"fair_a":30.0,"fair_i":12.5,"fair_r":16.6667,"fair_zscore":-1.4441,"fair_rationale":{"fair_score":27.92,"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 basic metadata (DOI, abstract, authors) but lacks machine-readable metadata beyond standard journal formatting."}]},"A":{"name":"Accessible","score":30.0,"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":0.0,"signal":null,"rationale":"No data or code access protocol is described; the paper itself is accessible via the journal but no protocol for underlying data/code is given."}]},"I":{"name":"Interoperable","score":12.5,"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":0.25,"signal":null,"rationale":"The paper uses standard identifiers (DOI, PDB IDs) but does not employ standard formats or vocabularies for its own content."}]},"R":{"name":"Reusable","score":16.67,"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":0.167,"signal":null,"rationale":"The paper has a Creative Commons license (CC BY-NC 2.5) but lacks a data-availability statement and does not provide reproducible data or code."}]}},"suggestions":["Include a data-availability statement specifying where any underlying data or code can be accessed.","Deposit QA scripts or test suites in a public repository with a persistent identifier and license.","Add structured metadata (e.g., schema.org markup) to the paper to enhance machine-readability.","Provide a clear protocol for accessing any datasets or software used in the study."],"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":"2026-06-18T00:51:24.144478Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}