{"doi":"10.1107/s1600577525005272","title":"Towards a new vision of PaNET: enhancing reasoning capabilities for better photon and neutron data discovery","abstract":"The Photon and Neutron Experimental Techniques (PaNET) ontology was released in 2021 as an ontology for two major European research infrastructure communities. It provides a standardized taxonomy of experimental techniques employed across the photon and neutron scientific domain, and is part of a wider effort to apply the FAIR (findable, accessible, interoperable, reusable) principles within the community. Specifically, it is used to enhance the quality of metadata in photon and neutron data catalogue services. However, PaNET currently relies on a manual definition approach, which is time consuming and incomplete. A new structure of PaNET is proposed to address this by including logical frameworks that enable automatic reasoning as opposed to the manual approach in the original ontology, resulting in over a hundred new technique subclass relationships that are currently missing in PaNET. These new relationships, which are evaluated by the PaNET working group and other domain experts, will improve data catalogue searches by connecting users to more relevant datasets, thereby enhancing data discoverability. In addition, the results of this work serve as a validation mechanism for PaNET, as the very process of building the logical frameworks, as well as any incorrect inferences made by the reasoner, has exposed existing issues within the original ontology.","journal":"Journal of Synchrotron Radiation","year":2025,"id":9960,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":42.961757526444266,"corpus_rank":695,"citation_count":2,"citer_count":2,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7408,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-07-30","fair_score":49.7917,"fair_percentile":77.9023746701847,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":85212,"name":"Balázs Bagó","orcid":"0009-0004-9707-6825","position":1,"is_corresponding":false},{"id":85213,"name":"Sebastian Busch","orcid":"0000-0002-9815-909X","position":2,"is_corresponding":false},{"id":85214,"name":"Renaud Duyme","orcid":null,"position":3,"is_corresponding":false},{"id":85215,"name":"Guillaume Gaisné","orcid":"0000-0002-3401-7930","position":4,"is_corresponding":false},{"id":286,"name":"Alejandra Noemí González Beltrán","orcid":"0000-0003-3499-8262","position":5,"is_corresponding":false},{"id":85216,"name":"Heike Görzig","orcid":"0000-0001-9121-8643","position":6,"is_corresponding":false},{"id":85217,"name":"Giannis Koumoutsos","orcid":"0009-0000-6215-8493","position":7,"is_corresponding":false},{"id":85218,"name":"Rolf Krahl","orcid":"0000-0002-1266-3819","position":8,"is_corresponding":false},{"id":85219,"name":"Paul Millar","orcid":"0000-0002-3957-1279","position":9,"is_corresponding":false},{"id":85220,"name":"Carlo Minotti","orcid":"0000-0002-2739-966X","position":10,"is_corresponding":false},{"id":85221,"name":"Melanie Nentwich","orcid":"0000-0002-5850-4469","position":11,"is_corresponding":false},{"id":85222,"name":"Lajos Schrettner","orcid":null,"position":12,"is_corresponding":false},{"id":85223,"name":"Kirsty Syder","orcid":"0009-0008-2130-7155","position":13,"is_corresponding":false},{"id":289,"name":"Rocca-Serra, Philippe","orcid":"0000-0001-9853-5668","position":14,"is_corresponding":false},{"id":290,"name":"Susanna‐Assunta Sansone","orcid":"0000-0001-5306-5690","position":15,"is_corresponding":false},{"id":85224,"name":"Stephen P. Collins","orcid":"0000-0001-5120-0764","position":16,"is_corresponding":false},{"id":11702,"name":"Tin Wee Tan","orcid":"0009-0008-7829-3647","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"40737182","pmcid":"PMC12416419","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":55.0,"fair_i":50.0,"fair_r":41.6667,"fair_zscore":0.4143,"fair_rationale":{"fair_score":49.79,"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 (title, authors, abstract, keywords) but lacks machine-readable structured metadata such as RDFa or JSON-LD."}]},"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 mentions a GitHub repository fork and a data availability section, but the full access protocol (e.g., direct links, license for code) is not explicitly stated in the provided text."}]},"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 uses standard formats (OWL, CSV, ROBOT), standard identifiers (IRIs), and references established vocabularies, demonstrating strong interoperability."}]},"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 open access (CC-BY), provides a detailed methodology for reproducibility, and references a public repository, but the data availability statement is incomplete in the provided text."}]}},"suggestions":["Include machine-readable metadata (e.g., schema.org JSON-LD) in the paper's HTML version to enhance findability.","Provide explicit, direct links to the ontology repository and any associated data/code in the abstract or introduction.","Add a formal data availability statement that specifies the license for the ontology and any supplementary materials.","Register the ontology in a community registry (e.g., BioPortal, OBO Foundry) to improve discoverability and reuse.","Ensure all external resources (e.g., GitHub repository) use persistent identifiers and are versioned for long-term access."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v1","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v1","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-17T23:00:09.734368Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}