{"doi":"10.1093/nar/gkv1310","title":"The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases","abstract":"The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.","journal":"Nucleic Acids Research","year":2015,"id":3890,"datarank":3.4837450331885282,"base_score":4.248495242049359,"endowment":4.248495242049359,"self_citation_contribution":0.637274286307404,"citation_network_contribution":2.846470746881124,"self_endowment_contribution":0.637274286307404,"citer_contribution":2.846470746881124,"corpus_percentile":68.67371847030105,"corpus_rank":386,"citation_count":71,"citer_count":71,"citers_with_citation_signal":56,"citers_with_endowment":56,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9375,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-11-28","fair_score":56.0417,"fair_percentile":91.38082673702726,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":39676,"name":"Palagi, Patricia M","orcid":null,"position":1,"is_corresponding":false},{"id":39677,"name":"Durinx, Christine","orcid":null,"position":2,"is_corresponding":false},{"id":39678,"name":"Baudis, Michael","orcid":null,"position":3,"is_corresponding":false},{"id":39679,"name":"von Mering, Christian","orcid":null,"position":4,"is_corresponding":false},{"id":39680,"name":"Szövenyi, Peter","orcid":null,"position":5,"is_corresponding":false},{"id":39681,"name":"et al","orcid":null,"position":6,"is_corresponding":false},{"id":39675,"name":"Stockinger, Heinz","orcid":null,"position":0,"is_corresponding":false}],"reference_count":74,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"26615188","pmcid":"PMC4702916","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"other-oa","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":50.0,"fair_r":41.6667,"fair_zscore":0.9797,"fair_rationale":{"fair_score":56.04,"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 many databases (e.g., UniProtKB/Swiss-Prot, STRING, SWISS-MODEL) and mentions identifiers and ontologies (e.g., GO, ChEBI), but does not provide any machine-readable metadata or structured data descriptions; only human-readable narrative is given."}]},"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 lists specific URLs (e.g., www.uniprot.org, www.expasy.org, www.string-db.org) and mentions some APIs (e.g., neXtProt API, arrayMap HTTP-based data API), but does not describe detailed access protocols, authentication, or formal access procedures for all resources."}]},"I":{"name":"Interoperable","score":50.0,"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":1.0,"signal":null,"rationale":"The paper extensively references standard formats, ontologies (GO, ChEBI, Uberon), and identifiers (e.g., UniProt accession numbers, cross-references), indicating strong use of interoperability standards across its resources."}]},"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 is published under a Creative Commons Attribution License, mentions user support and training, and describes resource availability (e.g., downloadable flat files), but lacks explicit data-availability statements for the underlying code or reproducibility details for the paper itself."}]}},"suggestions":["Include explicit machine-readable metadata (e.g., schema.org markup or JSON-LD) for each resource described in the paper.","Provide a formal data-availability statement for the paper, specifying where to find the exact data/code used for the review or analysis.","Add a clear license statement for each individual database or tool, not just the paper, to clarify reuse conditions.","Describe standardized access protocols (e.g., REST API documentation, authentication methods, and usage policies) for all listed resources.","Include a reproducibility section detailing how to replicate any analyses or figures in the paper, linking to deposited code."],"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":"2026-06-18T00:41:45.700028Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}