{"doi":"10.1093/database/bax105","title":"FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability","abstract":"The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.","journal":"Database","year":2018,"id":8099,"datarank":1.3013965292128922,"base_score":3.6888794541139363,"endowment":3.6888794541139363,"self_citation_contribution":0.5533319181170905,"citation_network_contribution":0.7480646110958018,"self_endowment_contribution":0.5533319181170905,"citer_contribution":0.7480646110958018,"corpus_percentile":84.14171888295814,"corpus_rank":2051,"citation_count":39,"citer_count":33,"citers_with_citation_signal":22,"citers_with_endowment":22,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9367,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2018-01-01","fair_score":52.9167,"fair_percentile":55.629139072847686,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":72076,"name":"James A. Overton","orcid":"0000-0001-5139-5557","position":1,"is_corresponding":false},{"id":6476,"name":"Christopher J. Mungall","orcid":"0000-0002-6601-2165","position":2,"is_corresponding":false},{"id":55670,"name":"Alessandro Sette","orcid":"0000-0001-7013-2250","position":3,"is_corresponding":false},{"id":34766,"name":"Bjoern Peters","orcid":"0000-0002-8457-6693","position":4,"is_corresponding":false},{"id":55655,"name":"Randi Vita","orcid":"0000-0001-8957-7612","position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"29688354","pmcid":"PMC5819722","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":77.5,"fair_a":55.0,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":0.1022,"fair_rationale":{"fair_score":52.92,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":77.5,"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":0.75,"signal":null,"rationale":"The IEDB provides rich metadata with up to 400 attributes per assay, but the paper acknowledges that not all metadata is consistently linked to external vocabularies or machine-readable."}]},"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":"Data is accessible via HTTP without authentication, but the paper notes that the primary HTML interface is not optimally machine-actionable, requiring screen scraping, and alternative machine-readable formats are not automatically discoverable."}]},"I":{"name":"Interoperable","score":37.5,"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":0.75,"signal":null,"rationale":"The IEDB uses OBO Foundry ontologies and standard formats like JSON-LD, but the paper states that not all fields use external vocabularies and links to vocabularies are not consistently explicit."}]},"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 IEDB has added a CC BY 4.0 license and provenance information, but the paper indicates that machine-readable licensing and provenance are still being implemented, and community standards for epitope data are not formally established."}]}},"suggestions":["Make all metadata values linkable to external vocabularies with explicit URLs, as planned for I2.","Provide a machine-readable representation (e.g., RDF/OWL) for all assay records, as outlined in the long-term vision.","Add machine-readable licensing information to individual assay and reference pages using Dublin Core 'license' predicate.","Complete the standardization of journal article location fields (F3) with structured vocabularies or ontology terms.","Ensure that alternative machine-readable formats (XML, SQL dump) are discoverable from the HTML pages via links or content negotiation."],"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":"2026-06-18T00:43:50.518968Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}