{"doi":"10.5281/zenodo.3560778","title":"RDF Linked Data representation of GC-MS data from the 'Rose Genome' article published in Nature genetics, June, 2018","abstract":"This dataset corresponds to the RDF Linked Data representation of the measurements of 61 known metabolites (all annotated with resolvable CHEBI identifiers and InChi strings), measured by gas chromatography mass-spectrometry (GC-MS) in 6 different Rose cultivars (all annotated with resolvable NCBITaxonomy Identifiers) and 3 organism parts (all annotated with resolvable Plant Ontology identifiers). The quantitation types are annotated with resolvable STATO terms. Most of the semantics resources belong to the OBO foundry. The transformation to RDF was performed on a Frictionless Tabular Data Package (https://frictionlessdata.io/specs/tabular-data-package/), holding the data extracted from a supplementary material table, available from https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-018-0110-3/MediaObjects/41588_2018_110_MOESM3_ESM.zip and published alongside the Nature Genetics manuscript identified by the following doi: https://doi.org/10.1038/s41588-018-0110-3, published in June 2018. This supplementary material table was deposited to Zenodo and is identified by the following doi: https://doi.org/10.5281/zenodo.2598799 This dataset is used to demonstrate how to make data Findable, Accessible, Discoverable and Interoperable (FAIR) and how Frictionless Tabular Data Package representations can be easily mobilised for reanalysis and data science. It is associated to the following project: https://github.com/proccaserra/rose2018ng-notebook with all the necessary information, executable code and tutorials in the form of Jupyter notebooks.","journal":"OPAL (Open@LaTrobe) (La Trobe University)","year":2019,"id":176,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":37.91700569568755,"corpus_rank":716,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9537,"is_oa":true,"file_count":1,"downloads":95,"has_version_chain":false,"published_date":"2019-12-03","fair_score":44.5833,"fair_percentile":43.007915567282325,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":290,"name":"Susanna‐Assunta Sansone","orcid":"0000-0001-5306-5690","position":1,"is_corresponding":false},{"id":289,"name":"Rocca-Serra, Philippe","orcid":"0000-0001-9853-5668","position":0,"is_corresponding":false}],"reference_count":0,"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":"green","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":47.0,"fair_a":68.0,"fair_i":20.0,"fair_r":43.3333,"fair_zscore":-0.0568,"fair_rationale":{"fair_score":44.58,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":47.0,"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":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":0.75,"signal":null,"rationale":"The paper provides rich metadata including resolvable identifiers (CHEBI, NCBITaxonomy, Plant Ontology, STATO) and references to OBO foundry, but does not describe machine-readable metadata beyond the RDF representation itself."}]},"A":{"name":"Accessible","score":68.0,"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":1.0,"signal":null,"rationale":"The paper clearly states the data is accessible via Zenodo (DOI: 10.5281/zenodo.3560778) and provides direct links to the supplementary material and GitHub repository with executable code."}]},"I":{"name":"Interoperable","score":20.0,"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 data uses standard RDF Linked Data format, resolvable identifiers from OBO foundry, and Frictionless Tabular Data Package specification, ensuring interoperability."}]},"R":{"name":"Reusable","score":43.33,"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":1.0,"signal":"downloads=95","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":0.833,"signal":null,"rationale":"The paper includes a data-availability statement, a Zenodo DOI, a GitHub repository with Jupyter notebooks, and uses standard vocabularies, but does not explicitly mention a license for reuse."}]}},"suggestions":["Add a clear license (e.g., CC0 or CC-BY) to the dataset to explicitly state reuse permissions.","Include a formal data-availability statement in the paper text that mentions the license and conditions for reuse.","Provide a machine-readable metadata file (e.g., JSON-LD or schema.org) alongside the RDF data to enhance findability.","Ensure all identifiers are resolvable via persistent URIs and document the resolution mechanism.","Add versioning information and a changelog to the GitHub repository to track updates and improve reproducibility."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-18T04:56:44.009943Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}