{"doi":"10.3390/life11010042","title":"Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases","abstract":"There has long been an interest in understanding how the hazards from spaceflight may trigger or exacerbate human diseases. With the goal of advancing our knowledge on physiological changes during space travel, NASA GeneLab provides an open-source repository of multi-omics data from real and simulated spaceflight studies. Alone, this data enables identification of biological changes during spaceflight, but cannot infer how that may impact an astronaut at the phenotypic level. To bridge this gap, Scalable Precision Medicine Oriented Knowledge Engine (SPOKE), a heterogeneous knowledge graph connecting biological and clinical data from over 30 databases, was used in combination with GeneLab transcriptomic data from six studies. This integration identified critical symptoms and physiological changes incurred during spaceflight.","journal":"Life","year":2021,"id":5563,"datarank":1.045101445603787,"base_score":2.995732273553991,"endowment":2.995732273553991,"self_citation_contribution":0.4493598410330987,"citation_network_contribution":0.5957416045706884,"self_endowment_contribution":0.4493598410330987,"citer_contribution":0.5957416045706884,"corpus_percentile":58.584214808787635,"corpus_rank":510,"citation_count":20,"citer_count":8,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6838,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-12","fair_score":39.375,"fair_percentile":20.030782761653473,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":54518,"name":"Ana Uriarte Acuna","orcid":null,"position":1,"is_corresponding":false},{"id":54519,"name":"Amber M. Paul","orcid":"0000-0002-1657-3618","position":2,"is_corresponding":false},{"id":37836,"name":"Ryan T. Scott","orcid":"0000-0003-0654-5661","position":3,"is_corresponding":false},{"id":51,"name":"Atul Janardhan Butte","orcid":"0000-0002-7433-2740","position":4,"is_corresponding":false},{"id":54520,"name":"Egle Cekanaviciute","orcid":"0000-0003-3306-1806","position":5,"is_corresponding":false},{"id":1310,"name":"Sergio E. Baranzini","orcid":"0000-0003-0067-194X","position":6,"is_corresponding":false},{"id":37877,"name":"Sylvain V. Costes","orcid":"0000-0002-8542-2389","position":7,"is_corresponding":false},{"id":1311,"name":"Charlotte A. Nelson","orcid":"0000-0002-3687-1102","position":0,"is_corresponding":true}],"reference_count":37,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"33445483","pmcid":"PMC7828077","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":25.0,"fair_r":25.0,"fair_zscore":-0.5279,"fair_rationale":{"fair_score":39.38,"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 metadata only in the abstract and tables, but lacks machine-readable metadata or structured data citation."}]},"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 data are available via NASA GeneLab and code via Zenodo, but no access protocol (e.g., API or authentication details) is described."}]},"I":{"name":"Interoperable","score":25.0,"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":0.5,"signal":null,"rationale":"The study uses standard formats (FASTQ, CEL) and common identifiers (e.g., HomoloGene IDs, GO), but does not declare use of controlled vocabularies or persistent identifiers for all entities."}]},"R":{"name":"Reusable","score":25.0,"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":0.333,"signal":null,"rationale":"The paper states 'Data Availability Statement: Not applicable' and provides code with a DOI, but lacks a license for the data, missing details on provenance and reproducibility steps."}]}},"suggestions":["Include a machine-readable metadata file (e.g., ISA-Tab or JSON-LD) with the paper submission.","Specify an explicit data access protocol with a persistent identifier and authentication method if applicable.","Use standard data formats and controlled vocabularies (e.g., NCBI Taxonomy, Gene Ontology) consistently in supplementary files.","Add a proper data availability statement with a license (e.g., CC0) and a link to archived, versioned data.","Document all preprocessing and analysis steps in a reproducible workflow (e.g., Jupyter notebooks or Docker container) and cite it."],"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":"2026-06-18T00:47:52.785591Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}