{"doi":"10.7717/peerj-cs.110","title":"Interoperability and FAIRness through a novel combination of Web technologies","abstract":"<jats:p>Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.</jats:p>","journal":"PeerJ Computer Science","year":2017,"id":2251,"datarank":4.614809387095637,"base_score":4.499809670330265,"endowment":4.499809670330265,"self_citation_contribution":0.6749714505495399,"citation_network_contribution":3.939837936546097,"self_endowment_contribution":0.6749714505495399,"citer_contribution":3.939837936546097,"corpus_percentile":70.8706265256306,"corpus_rank":359,"citation_count":90,"citer_count":76,"citers_with_citation_signal":57,"citers_with_endowment":57,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5092,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2017-04-24","fair_score":36.4583,"fair_percentile":18.315743183817062,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":791,"name":"Ruben Verborgh","orcid":"0000-0002-8596-222X","position":1,"is_corresponding":false},{"id":7089,"name":"Luiz Olavo Bonino da Silva Santos","orcid":"0000-0002-1164-1351","position":2,"is_corresponding":false},{"id":21832,"name":"Kathleen Stirrups","orcid":"0000-0002-6823-3252","position":4,"is_corresponding":false},{"id":19012,"name":"Erik M. van Mulligen","orcid":"0000-0003-1377-9386","position":8,"is_corresponding":false},{"id":27702,"name":"Paolo Ciccarese","orcid":"0000-0002-5156-2703","position":9,"is_corresponding":false},{"id":27703,"name":"Arnold Kuzniar","orcid":"0000-0003-1711-7961","position":10,"is_corresponding":false},{"id":27704,"name":"Anand Gavai","orcid":"0000-0002-4738-190X","position":11,"is_corresponding":false},{"id":19010,"name":"Mark Thompson","orcid":"0000-0002-7633-1442","position":12,"is_corresponding":false},{"id":7085,"name":"Rajaram Kaliyaperumal","orcid":"0000-0002-1215-167X","position":13,"is_corresponding":false},{"id":19090,"name":"Jerven T. Bolleman","orcid":"0000-0002-7449-1266","position":14,"is_corresponding":false},{"id":74,"name":"Michel J. Dumontier","orcid":"0000-0003-4727-9435","position":15,"is_corresponding":false},{"id":7430,"name":"Timothy Clark","orcid":"0000-0003-4060-7360","position":16,"is_corresponding":false},{"id":27705,"name":"Fleur Kelpin","orcid":"0000-0003-1527-5130","position":17,"is_corresponding":false},{"id":2495,"name":"Alasdair J. G. Gray","orcid":"0000-0002-5711-4872","position":18,"is_corresponding":false},{"id":105,"name":"Erik Anthony Schultes","orcid":"0000-0001-8888-635X","position":19,"is_corresponding":false},{"id":606,"name":"Mark D D. Wilkinson","orcid":"0000-0001-6960-357X","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"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":32.5,"fair_a":55.0,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":-0.7918,"fair_rationale":{"fair_score":36.46,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":32.5,"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":0.0,"signal":"datacite=0, pmcid=False, pmid=False","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 a DOI and basic bibliographic metadata, but no machine-readable metadata (e.g., RDFa, JSON-LD) within the text itself."}]},"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 paper is openly accessible under CC-BY 4.0 via a DOI, but no access protocol is provided for any underlying data or code."}]},"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":"The paper discusses standard formats and vocabularies (RDF, DCAT, etc.) but does not itself provide data in a standard machine-readable format."}]},"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 paper includes a data-availability statement and a clear license (CC-BY 4.0), but no actual data or code is provided for reuse."}]}},"suggestions":["Include machine-readable metadata (e.g., RDFa or JSON-LD) in the paper's HTML version to enhance findability.","Provide a link to a public repository containing the code and example data used in the demonstrations.","Add a formal data-availability statement that specifies a repository and persistent identifier for any supplementary materials.","Use standard formats (e.g., CSV, RDF) for any supplementary data files to improve interoperability."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:40:55.061363Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}