{"doi":"10.1093/gigascience/giaa041","title":"Community standards for open cell migration data","abstract":"Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.","journal":"GigaScience","year":2020,"id":4292,"datarank":1.1728676925088912,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"self_citation_contribution":0.515098080672772,"citation_network_contribution":0.6577696118361192,"self_endowment_contribution":0.515098080672772,"citer_contribution":0.6577696118361192,"corpus_percentile":59.39788445890968,"corpus_rank":500,"citation_count":31,"citer_count":16,"citers_with_citation_signal":15,"citers_with_endowment":15,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8129,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-05-01","fair_score":61.25,"fair_percentile":92.70008795074759,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":44541,"name":"Paola Masuzzo","orcid":"0000-0003-3699-1195","position":1,"is_corresponding":false},{"id":44542,"name":"Christophe Ampe","orcid":"0000-0002-8554-3594","position":2,"is_corresponding":false},{"id":44543,"name":"Gert-Jan Bakker","orcid":"0000-0003-3602-0014","position":3,"is_corresponding":false},{"id":44544,"name":"Sébastien Besson","orcid":"0000-0001-8783-1429","position":4,"is_corresponding":false},{"id":44545,"name":"Robert H. Eibl","orcid":"0000-0002-6687-5286","position":5,"is_corresponding":false},{"id":44546,"name":"Peter Friedl","orcid":"0000-0002-0119-4041","position":6,"is_corresponding":false},{"id":44547,"name":"Matthias Gunzer","orcid":"0000-0002-5534-6055","position":7,"is_corresponding":false},{"id":44548,"name":"Mark Kittisopikul","orcid":"0000-0002-9558-6248","position":8,"is_corresponding":false},{"id":44549,"name":"Sylvia E. Le Dévédec","orcid":"0000-0002-0615-9616","position":9,"is_corresponding":false},{"id":44550,"name":"Simone Leo","orcid":"0000-0001-8271-5429","position":10,"is_corresponding":false},{"id":39835,"name":"Josh Moore","orcid":"0000-0003-4028-811X","position":11,"is_corresponding":false},{"id":44551,"name":"Yael Paran","orcid":"0000-0001-9544-6213","position":12,"is_corresponding":false},{"id":44552,"name":"Jaime Prilusky","orcid":"0000-0002-7019-0191","position":13,"is_corresponding":false},{"id":289,"name":"Rocca-Serra, Philippe","orcid":"0000-0001-9853-5668","position":14,"is_corresponding":false},{"id":44553,"name":"Philippe Roudot","orcid":"0000-0001-6632-8728","position":15,"is_corresponding":false},{"id":44554,"name":"Marc Schuster","orcid":"0000-0002-7751-7708","position":16,"is_corresponding":false},{"id":44555,"name":"Gwendolien Sergeant","orcid":"0000-0001-9869-3826","position":17,"is_corresponding":false},{"id":44556,"name":"Staffan Strömblad","orcid":"0000-0002-1236-6339","position":18,"is_corresponding":false},{"id":37917,"name":"Jason R. Swedlow","orcid":"0000-0002-2198-1958","position":19,"is_corresponding":false},{"id":44557,"name":"Merijn van Erp","orcid":"0000-0002-9642-9789","position":20,"is_corresponding":false},{"id":44558,"name":"Marleen Van Troys","orcid":"0000-0003-4283-8103","position":21,"is_corresponding":false},{"id":44559,"name":"Assaf Zaritsky","orcid":"0000-0002-1477-5478","position":22,"is_corresponding":false},{"id":290,"name":"Susanna‐Assunta Sansone","orcid":"0000-0001-5306-5690","position":23,"is_corresponding":false},{"id":44560,"name":"Lennart Martens","orcid":"0000-0003-4277-658X","position":24,"is_corresponding":false},{"id":286,"name":"Alejandra Noemí González Beltrán","orcid":"0000-0003-3499-8262","position":0,"is_corresponding":true}],"reference_count":81,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"32396199","pmcid":"PMC7317087","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":67.5,"fair_i":50.0,"fair_r":50.0,"fair_zscore":1.4508,"fair_rationale":{"fair_score":61.25,"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 paper describes rich metadata via MIACME, ISA-Tab, and JSON schemas, but does not provide evidence of persistent identifiers or machine-actionable metadata in use for its own presented dataset."}]},"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":"Data and code are deposited in GitHub and GigaDB with open access, but the paper does not specify an explicit access protocol (e.g., authentication steps or a formal API endpoint) for the repository."}]},"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 explicitly uses standard formats (ISA-Tab, OME, biotracks, CSV, JSON), controlled vocabularies, and ontologies, achieving full interoperability within its domain."}]},"R":{"name":"Reusable","score":50.0,"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":0.833,"signal":null,"rationale":"A clear data-availability statement, CC-BY license, and supporting data in GigaDB plus GitHub repositories are provided, and reproducibility notebooks are offered, though formal versioning of datasets is not explicitly highlighted."}]}},"suggestions":["Assign persistent identifiers (e.g., DOIs) to all dataset snapshots and reference them prominently in the paper.","Provide a step-by-step access protocol (e.g., how to call the repository API) for both human and machine users.","Include explicit version numbers and release dates for the example datasets used in the paper.","Add a machine-readable license file (e.g., LICENSE.txt) directly in every example code repository.","Publish a formal data management plan or usage guide for the cell migration repository to enhance reusability."],"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":"2026-06-18T00:44:53.965222Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}