{"doi":"10.1007/s11306-012-0462-0","title":"MetaboLights: towards a new COSMOS of metabolomics data management","abstract":"Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.","journal":"Metabolomics","year":2012,"id":1955,"datarank":3.205232205176456,"base_score":4.465908118654584,"endowment":4.465908118654584,"self_citation_contribution":0.6698862177981877,"citation_network_contribution":2.5353459873782684,"self_endowment_contribution":0.6698862177981877,"citer_contribution":2.5353459873782684,"corpus_percentile":68.26688364524003,"corpus_rank":391,"citation_count":86,"citer_count":67,"citers_with_citation_signal":63,"citers_with_endowment":63,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9428,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2012-09-25","fair_score":50.8333,"fair_percentile":78.6499560246262,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":22181,"name":"Pablo Conesa","orcid":"0000-0003-0575-7718","position":1,"is_corresponding":false},{"id":7597,"name":"Kenneth Haug","orcid":"0000-0003-3168-4145","position":2,"is_corresponding":false},{"id":22182,"name":"Tejasvi Mahendraker","orcid":null,"position":3,"is_corresponding":false},{"id":22183,"name":"Mark Williams","orcid":"0000-0002-1294-1110","position":4,"is_corresponding":false},{"id":284,"name":"Eamonn Maguire","orcid":"0000-0002-7277-7834","position":5,"is_corresponding":false},{"id":5765,"name":"Philippe Rocca-Serra","orcid":null,"position":6,"is_corresponding":false},{"id":22184,"name":"Reza M. Salek","orcid":"0000-0001-8604-1732","position":8,"is_corresponding":false},{"id":83646,"name":"Kelliane A. Medeiros","orcid":"0000-0003-0141-5788","position":9,"is_corresponding":false},{"id":289,"name":"Rocca-Serra, Philippe","orcid":"0000-0001-9853-5668","position":10,"is_corresponding":false},{"id":290,"name":"Susanna‐Assunta Sansone","orcid":"0000-0001-5306-5690","position":11,"is_corresponding":false},{"id":73,"name":"Christoph Steinbeck","orcid":"0000-0001-6966-0814","position":0,"is_corresponding":true}],"reference_count":8,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"23060735","pmcid":"PMC3465651","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":37.5,"fair_r":33.3333,"fair_zscore":0.5085,"fair_rationale":{"fair_score":50.83,"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 mentions metadata and the use of ISA-Tab and MIBBI checklists, but does not provide evidence of machine-readable metadata or detailed metadata schema."}]},"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 states that MetaboLights is open access and provides a URL for data submission, but does not specify a clear, step-by-step access protocol for data retrieval."}]},"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 paper references open standards like mzML, nmrML, ISA-Tab, and MIBBI, but does not demonstrate their actual use in the paper's own data or provide specific identifiers."}]},"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 Creative Commons Attribution License and mentions stable identifiers (MTBLS), but lacks a data-availability statement for the paper itself and does not detail reproducibility measures."}]}},"suggestions":["Include a machine-readable metadata file (e.g., ISA-Tab) as supplementary material for the paper.","Provide a direct link to the deposited dataset with a clear access protocol (e.g., 'Data available at http://www.ebi.ac.uk/metabolights/MTBLSxxx').","Add a formal data-availability statement specifying the license and conditions for reuse of the paper's data.","Use persistent identifiers (e.g., DOIs) for all referenced datasets and software.","Describe the specific standard formats and vocabularies used in the paper's own data (e.g., mzML for MS data)."],"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":"2026-06-18T00:40:28.089120Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}