{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T02:56:52Z","timestamp":1767927412303,"version":"3.49.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"10","funder":[{"name":"GeneLab Project"},{"DOI":"10.13039\/100000104","name":"National Aeronautics and Space Administration","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000104","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000104","name":"NASA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000104","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006195","name":"Ames Research Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006195","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NASA\u2019s Space Biology Program"},{"name":"Division of Space Life and Physical Sciences Research and Applications"},{"name":"SLPSRA"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated \u2018omics\u2019 (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms. GLDS is supported by an integrated data system allowing federated search across several public bioinformatics repositories. Archived datasets can be queried using full-text search (e.g. keywords, Boolean and wildcards) and results can be sorted in multifactorial manner using assistive filters. GLDS also provides a collaborative platform built on GenomeSpace for sharing files and analyses with collaborators. It currently houses 172 datasets and supports standard guidelines for submission of datasets, MIAME (for microarray), ENCODE Consortium Guidelines (for RNA-seq) and MIAPE Guidelines (for proteomics).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/genelab.nasa.gov\/<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty884","type":"journal-article","created":{"date-parts":[[2018,10,16]],"date-time":"2018-10-16T11:11:36Z","timestamp":1539688296000},"page":"1753-1759","source":"Crossref","is-referenced-by-count":90,"title":["GeneLab: Omics database for spaceflight experiments"],"prefix":"10.1093","volume":"35","author":[{"given":"Shayoni","family":"Ray","sequence":"first","affiliation":[{"name":"Space Biosciences Division, USRA\/NASA Ames Research Center, Moffett Field, CA, USA"}]},{"given":"Samrawit","family":"Gebre","sequence":"additional","affiliation":[{"name":"Space Biosciences Division, KBRwyle\/NASA Ames Research Center, Moffett Field, CA, USA"}]},{"given":"Homer","family":"Fogle","sequence":"additional","affiliation":[{"name":"Space Biosciences Division, KBRwyle\/NASA Ames Research Center, Moffett Field, CA, USA"}]},{"given":"Daniel C","family":"Berrios","sequence":"additional","affiliation":[{"name":"Space Biosciences Division, USRA\/NASA Ames Research Center, Moffett Field, CA, USA"}]},{"given":"Peter B","family":"Tran","sequence":"additional","affiliation":[{"name":"Intelligent Systems Division, NASA Ames Research Center, Moffett Field, CA, USA"}]},{"given":"Jonathan M","family":"Galazka","sequence":"additional","affiliation":[{"name":"Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA"}]},{"given":"Sylvain V","family":"Costes","sequence":"additional","affiliation":[{"name":"Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,10,17]]},"reference":[{"key":"2023013107484028400_bty884-B1","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","volume":"44","author":"Afgan","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013107484028400_bty884-B2","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1152\/japplphysiol.90780.2008","article-title":"Effects of spaceflight on murine skeletal muscle gene expression","volume":"106","author":"Allen","year":"2009","journal-title":"J. Appl. Physiol"},{"key":"2023013107484028400_bty884-B3","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1016\/j.ijrobp.2010.11.058","article-title":"Lack of radiation dose or quality dependence of epithelial-to-mesenchymal transition (EMT) mediated by transforming growth factor beta","volume":"79","author":"Andarawewa","year":"2011","journal-title":"Int. J. Radiat. Oncol. Biol. Phys"},{"key":"2023013107484028400_bty884-B4","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.lssr.2015.07.006","article-title":"Concepts and challenges in cancer risk prediction for the space radiation environment","volume":"6","author":"Barcellos-Hoff","year":"2015","journal-title":"Life Sci. Space Res"},{"key":"2023013107484028400_bty884-B5","first-page":"1254","article-title":"Irradiated mammary gland stroma promotes the expression of tumorigenic potential by unirradiated epithelial cells","volume":"60","author":"Barcellos-Hoff","year":"2000","journal-title":"Cancer Res"},{"key":"2023013107484028400_bty884-B6","doi-asserted-by":"crossref","first-page":"4191","DOI":"10.1038\/s41598-018-22613-1","article-title":"Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: a systems biology GeneLab case study","volume":"8","author":"Beheshti","year":"2018","journal-title":"Sci. Rep"},{"key":"2023013107484028400_bty884-B7","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1667\/RR15062.1","article-title":"NASA GeneLab Project: bridging Space Radiation Omics with Ground Studies","volume":"189","author":"Beheshti","year":"2018","journal-title":"Radiat. Res"},{"key":"2023013107484028400_bty884-B8","doi-asserted-by":"crossref","first-page":"e0199621.","DOI":"10.1371\/journal.pone.0199621","article-title":"A microRNA signature and TGF-\u03b21 response were identified as the key master regulators for spaceflight response","volume":"13","author":"Beheshti","year":"2018","journal-title":"PLoS One"},{"key":"2023013107484028400_bty884-B9","doi-asserted-by":"crossref","first-page":"e61372.","DOI":"10.1371\/journal.pone.0061372","article-title":"Microgravity induces pelvic bone loss through osteoclastic activity, osteocytic osteolysis, and osteoblastic cell cycle inhibition by CDKN1a\/p21","volume":"8","author":"Blaber","year":"2013","journal-title":"PLoS One"},{"key":"2023013107484028400_bty884-B10","doi-asserted-by":"crossref","first-page":"491","DOI":"10.3390\/life4030491","article-title":"Space radiation: the number one risk to astronaut health beyond low earth orbit","volume":"4","author":"Chancellor","year":"2014","journal-title":"Life"},{"key":"2023013107484028400_bty884-B11","doi-asserted-by":"crossref","first-page":"e0169314.","DOI":"10.1371\/journal.pone.0169314","article-title":"Gene expression profiling in slow-type calf soleus muscle of 30 days space-flown mice","volume":"12","author":"Gambara","year":"2017","journal-title":"PLoS One"},{"key":"2023013107484028400_bty884-B12","doi-asserted-by":"crossref","first-page":"i17.","DOI":"10.1093\/jrr\/rrt170","article-title":"Mitochondrial damage and radiation carcinogenesis","volume":"55","author":"Hei","year":"2014","journal-title":"J. Radiat. Res"},{"key":"2023013107484028400_bty884-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1089\/ast.2012.0876","article-title":"Ground-based facilities for simulation of microgravity: organism-specific recommendations for their use, and recommended terminology","volume":"13","author":"Herranz","year":"2013","journal-title":"Astrobiology"},{"key":"2023013107484028400_bty884-B14","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1667\/RR14338.1","article-title":"Simulating space radiation-induced breast tumor incidence using automata","volume":"186","author":"Heuskin","year":"2016","journal-title":"Radiat. Res"},{"key":"2023013107484028400_bty884-B15","doi-asserted-by":"crossref","first-page":"e0152877.","DOI":"10.1371\/journal.pone.0152877","article-title":"Spaceflight activates lipotoxic pathways in mouse liver","volume":"11","author":"Jonscher","year":"2016","journal-title":"PLoS One"},{"key":"2023013107484028400_bty884-B16","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.actaastro.2004.05.068","article-title":"Effects of HZE particle on the nigrostriatal dopaminergic system in a future Mars mission","volume":"56","author":"Koike","year":"2005","journal-title":"Acta Astronaut"},{"key":"2023013107484028400_bty884-B17","doi-asserted-by":"crossref","first-page":"21","DOI":"10.3732\/ajb.1400458","article-title":"Transcriptional response of Arabidopsis seedlings during spaceflight reveals peroxidase and cell wall remodeling genes associated with root hair development","volume":"102","author":"Kwon","year":"2015","journal-title":"Am. J. Bot"},{"key":"2023013107484028400_bty884-B18","doi-asserted-by":"crossref","first-page":"8304","DOI":"10.1158\/0008-5472.CAN-08-1212","article-title":"Targeted and nontargeted effects of ionizing radiation that impact genomic instability","volume":"68","author":"Maxwell","year":"2008","journal-title":"Cancer Res"},{"key":"2023013107484028400_bty884-B19","doi-asserted-by":"crossref","first-page":"608.","DOI":"10.5114\/aoms.2016.59894","article-title":"Effects of single and combined low frequency electromagnetic fields and simulated microgravity on gene expression of human mesenchymal stem cells during chondrogenesis","volume":"14","author":"Mayer-Wagner","year":"2018","journal-title":"Arch. Med. Sci"},{"key":"2023013107484028400_bty884-B20","doi-asserted-by":"crossref","first-page":"364","DOI":"10.3389\/fpls.2014.00364","article-title":"High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core \u201cDSB\u201d response specific to clastogenic treatments","volume":"5","author":"Missirian","year":"2014","journal-title":"Front. Plant Sci"},{"key":"2023013107484028400_bty884-B21","doi-asserted-by":"crossref","first-page":"5125","DOI":"10.1038\/ncomms6125","article-title":"Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures","volume":"5","author":"Munro","year":"2014","journal-title":"Nat. Commun"},{"key":"2023013107484028400_bty884-B22","doi-asserted-by":"crossref","first-page":"pe22.","DOI":"10.1126\/stke.2832005pe22","article-title":"A life science Semantic Web: are we there yet?","volume":"2005","author":"Neumann","year":"2005","journal-title":"Sci. STKE"},{"key":"2023013107484028400_bty884-B23","doi-asserted-by":"crossref","first-page":"e0174174.","DOI":"10.1371\/journal.pone.0174174","article-title":"Is spaceflight-induced immune dysfunction linked to systemic changes in metabolism?","volume":"12","author":"Pecaut","year":"2017","journal-title":"PLoS One"},{"key":"2023013107484028400_bty884-B24","doi-asserted-by":"crossref","first-page":"245.","DOI":"10.1038\/nmeth.3732","article-title":"Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace","volume":"13","author":"Qu","year":"2016","journal-title":"Nat. Methods"},{"key":"2023013107484028400_bty884-B25","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1016\/j.asr.2009.01.015","article-title":"Effects of heavy particle irradiation and diet on object recognition memory in rats","volume":"43","author":"Rabin","year":"2009","journal-title":"Adv. Space Res"},{"key":"2023013107484028400_bty884-B26","doi-asserted-by":"crossref","first-page":"121.","DOI":"10.1038\/ng.1054","article-title":"Toward interoperable bioscience data","volume":"44","author":"Sansone","year":"2012","journal-title":"Nat. Genet"},{"key":"2023013107484028400_bty884-B27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1667\/RR13804.1","article-title":"Understanding cancer development processes after HZE-particle exposure: roles of ROS, DNA damage repair and inflammation","volume":"183","author":"Sridharan","year":"2015","journal-title":"Radiat. Res"},{"key":"2023013107484028400_bty884-B28","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/978-3-319-12136-9_4","volume-title":"Genomic Instability and Cancer Metastasis","author":"Tang","year":"2015"},{"key":"2023013107484028400_bty884-B29","first-page":"A68","article-title":"The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge","volume":"19","author":"Tomczak","year":"2015","journal-title":"Contemp. Oncol. (Pozn)"},{"key":"2023013107484028400_bty884-B30","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1016\/j.jacc.2009.11.053","article-title":"Understanding radiation-induced vascular disease","volume":"55","author":"Weintraub","year":"2010","journal-title":"J. Am. Coll. Cardiol"},{"key":"2023013107484028400_bty884-B31","doi-asserted-by":"crossref","first-page":"16299","DOI":"10.1073\/pnas.0707155104","article-title":"Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq","volume":"104","author":"Wilson","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013107484028400_bty884-B32","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1016\/j.imbio.2012.06.009","article-title":"Regulation of TGF\u03b2 in the immune system: an emerging role for integrins and dendritic cells","volume":"217","author":"Worthington","year":"2012","journal-title":"Immunobiology"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/10\/1753\/48969335\/bioinformatics_35_10_1753.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/10\/1753\/48969335\/bioinformatics_35_10_1753.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:50:58Z","timestamp":1675162258000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/10\/1753\/5134065"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,10,17]]},"references-count":32,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2019,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty884","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,5,15]]},"published":{"date-parts":[[2018,10,17]]}}}