{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T16:56:38Z","timestamp":1753894598362,"version":"3.41.2"},"reference-count":50,"publisher":"Ubiquity Press, Ltd.","license":[{"start":{"date-parts":[[2017,3,23]],"date-time":"2017-03-23T00:00:00Z","timestamp":1490227200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,23]]},"DOI":"10.5334\/dsj-2017-011","type":"journal-article","created":{"date-parts":[[2017,3,23]],"date-time":"2017-03-23T12:49:11Z","timestamp":1490273351000},"source":"Crossref","is-referenced-by-count":0,"title":["A FAIR-Based Approach to Enhancing the Discovery and Re-Use of Transcriptomic Data Assets for Nuclear Receptor Signaling Pathways"],"prefix":"10.5334","volume":"16","author":[{"given":"Scott A.","family":"Ochsner","sequence":"first","affiliation":[]},{"given":"Yolanda F.","family":"Darlington","sequence":"additional","affiliation":[]},{"given":"Apollo","family":"McOwiti","sequence":"additional","affiliation":[]},{"given":"Wasula H.","family":"Kankanamge","sequence":"additional","affiliation":[]},{"given":"Alexey","family":"Naumov","sequence":"additional","affiliation":[]},{"given":"Lauren B.","family":"Becnel","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6689-0104","authenticated-orcid":false,"given":"Neil J.","family":"McKenna","sequence":"additional","affiliation":[]}],"member":"3285","reference":[{"issue":"W1","key":"key20170323084810_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"},{"issue":"4","key":"key20170323084810_B2","doi-asserted-by":"crossref","first-page":"e61758","DOI":"10.1371\/journal.pone.0061758","article-title":"An alkylphenol mix promotes seminoma derived cell proliferation through an ERalpha36-mediated mechanism","volume":"8","author":"Ajj","year":"2013","journal-title":"PLoS One"},{"issue":"Database issue","key":"key20170323084810_B3","doi-asserted-by":"crossref","first-page":"D885","DOI":"10.1093\/nar\/gkn764","article-title":"NCBI GEO: archive for high-throughput functional genomic data","volume":"37","author":"Barrett","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"key20170323084810_B4","doi-asserted-by":"crossref","first-page":"e0135615","DOI":"10.1371\/journal.pone.0135615","article-title":"Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways","volume":"10","author":"Becnel","year":"2015","journal-title":"PLoS One"},{"key":"key20170323084810_B5","article-title":"Hierarchical pathway and biosource mapping support visualization of nuclear receptor signaling transcriptional networks in Transcriptomine","author":"Becnel","year":"2016","journal-title":"Science Signaling"},{"key":"key20170323084810_B6","article-title":"Pathway and biosample mapping support hypothesis generation through visualization of nuclear receptor signaling networks in Transcriptomine","author":"Becnel","year":"2017","journal-title":"Science Signaling"},{"key":"key20170323084810_B7","unstructured":"BorgmanC L Why are the attribution and citation of scientific data important?2011[Online]. Available at: http:\/\/sites.nationalacademies.org\/PGA\/brdi\/PGA_064019 (Accessed May 21, 2015)."},{"issue":"6","key":"key20170323084810_B8","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.cell.2005.08.020","article-title":"Core transcriptional regulatory circuitry in human embryonic stem cells","volume":"122","author":"Boyer","year":"2005","journal-title":"Cell"},{"issue":"Database issue","key":"key20170323084810_B9","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","article-title":"Pathway Commons, a web resource for biological pathway data","volume":"39","author":"Cerami","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"key20170323084810_B10","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1016\/j.steroids.2013.05.001","article-title":"Androgens inhibit adipogenesis during human adipose stem cell commitment to preadipocyte formation","volume":"78","author":"Chazenbalk","year":"2013","journal-title":"Steroids"},{"key":"key20170323084810_B11","article-title":"Analysis of the receptor-interacting protein-140 (RIP140\/Nrip1)-dependent transcriptome in the mouse adipogenic program","author":"Christian","year":"2005","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"key":"key20170323084810_B12","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1046\/j.1365-2575.1998.00040.x","article-title":"Successfully completing case study research: combining rigour, relevance and pragmatism","volume":"8","author":"Darke","year":"1998","journal-title":"Information Systems Journal"},{"key":"key20170323084810_B13","doi-asserted-by":"crossref","DOI":"10.1093\/jamia\/ocw096","article-title":"Improving the discoverability, accessibility, and citability of omics datasets: a case report","author":"Darlington","year":"2016","journal-title":"J Am Med Inform Assoc"},{"key":"key20170323084810_B14","unstructured":"DataCite Cite Your Data2015[Online]. Available at: https:\/\/www.datacite.org\/services\/cite-your-data.html (Accessed 21 May, 2015)"},{"issue":"D1","key":"key20170323084810_B15","doi-asserted-by":"crossref","first-page":"D481","DOI":"10.1093\/nar\/gkv1351","article-title":"The Reactome pathway Knowledgebase","volume":"44","author":"Fabregat","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"key20170323084810_B16","unstructured":"FDA Providing Regulatory Submissions in Electronic Format \u2014 Submissions Under Section 745A(a) of the Federal Food, Drug, and Cosmetic Act2014[Online]. Available at: http:\/\/www.fda.gov\/downloads\/Drugs\/Guidances\/UCM384686.pdf"},{"key":"key20170323084810_B17","article-title":"Analysis of the peroxisome proliferator activated receptor-\u03b1 (PPAR\u03b1\/Ppara)-regulated transcriptome in mouse skeletal muscle","author":"Finck","year":"2005","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"issue":"7429","key":"key20170323084810_B18","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/492356d","article-title":"Data-set visibility: Cite links to data in reference lists","volume":"492","author":"Goodman","year":"2012","journal-title":"Nature"},{"key":"key20170323084810_B19","article-title":"Time course analysis of the methylprednisolone (MePred)-regulated transcriptome in rat kidney","author":"Hoffman","year":"2005","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"issue":"7","key":"key20170323084810_B20","doi-asserted-by":"crossref","first-page":"e41333","DOI":"10.1371\/journal.pone.0041333","article-title":"Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data","volume":"7","author":"Huber-Keener","year":"2012","journal-title":"PLoS One"},{"key":"key20170323084810_B21","article-title":"Time course transcriptomic analysis of dexamethasone (Dex)-treated mouse chondroctyes","author":"James","year":"2007","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"key":"key20170323084810_B22","article-title":"Analysis of the dihydrotestosterone (DHT)- and RTI 6413-018-dependent transcriptomes in LNCaP prostate cancer cells","author":"Kazmin","year":"2006","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"issue":"Database issue","key":"key20170323084810_B23","doi-asserted-by":"crossref","first-page":"D1113","DOI":"10.1093\/nar\/gku1057","article-title":"ArrayExpress update\u2014simplifying data submissions","volume":"43","author":"Kolesnikov","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"key20170323084810_B24","article-title":"Analysis of the androgen receptor (AR)-dependent transcriptome in PC3 prostatic carcinoma cells","author":"Lin","year":"2009","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"issue":"5","key":"key20170323084810_B25","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1016\/j.cell.2015.05.011","article-title":"Treatment of obesity with celastrol","volume":"161","author":"Liu","year":"2015","journal-title":"Cell"},{"key":"key20170323084810_B26","doi-asserted-by":"crossref","first-page":"e10084","DOI":"10.7554\/eLife.10084","article-title":"Correction: Nuclear receptor LRH-1\/NR5A2 is required and targetable for liver endoplasmic reticulum stress resolution","volume":"4","author":"Mamrosh","year":"2015","journal-title":"Elife"},{"issue":"6","key":"key20170323084810_B27","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/0092-8674(95)90199-X","article-title":"The nuclear receptor superfamily: the second decade","volume":"83","author":"Mangelsdorf","year":"1995","journal-title":"Cell"},{"issue":"6","key":"key20170323084810_B28","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1136\/amiajnl-2014-002974","article-title":"The National Institutes of Health\u2019s Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data","volume":"21","author":"Margolis","year":"2014","journal-title":"J Am Med Inform Assoc"},{"key":"key20170323084810_B29","unstructured":"MartoneM E Data Citation Synthesis Group: Joint Declaration of Data Citation Principles. San Diego, FORCE112014[Online]. Available at: https:\/\/www.force11.org\/datacitation"},{"issue":"4","key":"key20170323084810_B30","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/S0092-8674(02)00641-4","article-title":"Combinatorial control of gene expression by nuclear receptors and coregulators","volume":"108","author":"McKenna","year":"2002","journal-title":"Cell"},{"key":"key20170323084810_B31","unstructured":"NCBI GEO2R2016[Online]. Available at: https:\/\/www.ncbi.nlm.nih.gov\/geo\/geo2r\/"},{"key":"key20170323084810_B32","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bas026","article-title":"Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE","author":"Neveol","year":"2012","journal-title":"Database (Oxford) (bas026)"},{"key":"key20170323084810_B33","unstructured":"NIH NIH Genomic Data Sharing Policy2016[Online]. Available at: https:\/\/gds.nih.gov\/03policy2.html"},{"issue":"8\u20139","key":"key20170323084810_B34","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.steroids.2009.10.004","article-title":"Conjugated and non-conjugated androgens differentially modulate specific early gene transcription in breast cancer in a cell-specific manner","volume":"75","author":"Notas","year":"2010","journal-title":"Steroids"},{"key":"key20170323084810_B35","unstructured":"OAI The Open Archives Initiative Protocol for Metadata Harvesting2016[Online]. Available at: http:\/\/www.openarchives.org\/OAI\/openarchivesprotocol.html"},{"key":"key20170323084810_B36","article-title":"Analysis of the peroxisome proliferator-activated receptor-\u03b3 (PPAR\u03b3\/Pparg)-regulated transcriptome during adipogenesis in mouse 3T3-L1 adipocytes","author":"Ochsner","year":"2009","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"issue":"12","key":"key20170323084810_B37","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/nmeth1208-991","article-title":"Much room for improvement in deposition rates of expression microarray datasets","volume":"5","author":"Ochsner","year":"2008","journal-title":"Nat Methods"},{"key":"key20170323084810_B38","unstructured":"PillerC Law ignored, patients at risk2015[Online]. Available at: https:\/\/www.statnews.com\/2015\/12\/13\/clinical-trials-investigation\/"},{"issue":"9","key":"key20170323084810_B39","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1373\/clinchem.2014.226100","article-title":"Registering diagnostic and prognostic trials of tests: is it the right thing to do?","volume":"60","author":"Rifai","year":"2014","journal-title":"Clin Chem"},{"issue":"10","key":"key20170323084810_B40","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.1089\/scd.2011.0040","article-title":"Current methods of adipogenic differentiation of mesenchymal stem cells","volume":"20","author":"Scott","year":"2011","journal-title":"Stem Cells Dev"},{"issue":"2","key":"key20170323084810_B41","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1016\/j.ydbio.2007.05.004","article-title":"Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains","volume":"307","author":"Sharova","year":"2007","journal-title":"Dev Biol"},{"issue":"1","key":"key20170323084810_B42","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1210\/en.2004-1649","article-title":"Testosterone inhibits adipogenic differentiation in 3T3-L1 cells: nuclear translocation of androgen receptor complex with beta-catenin and T-cell factor 4 may bypass canonical Wnt signaling to down-regulate adipogenic transcription factors","volume":"147","author":"Singh","year":"2006","journal-title":"Endocrinology"},{"key":"key20170323084810_B43","article-title":"Early tissue responses to etanercept in psoriasis lesions","author":"Swindell","year":"2014","journal-title":"Gene Expression Omnibus"},{"key":"key20170323084810_B44","article-title":"Time course- and dose-dependent analysis of the rosiglitazone (Rosi)-dependent and peroxisome proliferator-activated receptor-\u03b3 (PPAR\u03b3\/Pparg) DNA-binding domain-dependent transcriptomes in dendritic cells","author":"Szatmari","year":"2007","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"key":"key20170323084810_B45","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/978-1-62703-435-7_20","article-title":"PharmGKB: the Pharmacogenomics Knowledge Base","volume":"1015","author":"Thorn","year":"2013","journal-title":"Methods Mol Biol"},{"key":"key20170323084810_B46","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci Data"},{"issue":"2","key":"key20170323084810_B47","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1373\/clinchem.2012.193813","article-title":"Data submission and quality in microarray-based microRNA profiling","volume":"59","author":"Witwer","year":"2013","journal-title":"Clin Chem"},{"key":"key20170323084810_B48","article-title":"Comparative transcriptomic analysis of white, brown and beige fat cell lines","author":"Wu","year":"2012","journal-title":"Nuclear Receptor Signaling Atlas Datasets"},{"volume-title":"Case Study Research: Design and Methods","year":"2013","author":"Yin","key":"key20170323084810_B49"},{"key":"key20170323084810_B50","article-title":"Acute and chronic time course analysis of the WY14643-regulated transcriptome in Female ovariectomized C57BL\/6 mouse liver","author":"Zacharewski","year":"2013","journal-title":"Nuclear Receptor Signaling Atlas Datasets"}],"container-title":["Data Science Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/doi.org\/10.5334\/dsj-2017-011","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,11]],"date-time":"2022-07-11T09:19:09Z","timestamp":1657531149000},"score":1,"resource":{"primary":{"URL":"http:\/\/datascience.codata.org\/articles\/10.5334\/dsj-2017-011\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,23]]},"references-count":50,"alternative-id":["10.5334\/dsj-2017-011"],"URL":"https:\/\/doi.org\/10.5334\/dsj-2017-011","relation":{},"ISSN":["1683-1470"],"issn-type":[{"type":"electronic","value":"1683-1470"}],"subject":[],"published":{"date-parts":[[2017,3,23]]},"article-number":"11"}}