{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:44:11Z","timestamp":1760708651923,"version":"3.37.3"},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,1]]},"DOI":"10.1186\/1471-2105-15-s1-s11","type":"journal-article","created":{"date-parts":[[2014,1,10]],"date-time":"2014-01-10T08:59:04Z","timestamp":1389344344000},"source":"Crossref","is-referenced-by-count":18,"title":["The Risa R\/Bioconductor package: integrative data analysis from experimental metadata and back again"],"prefix":"10.1186","volume":"15","author":[{"given":"Alejandra","family":"Gonz\u00e1lez-Beltr\u00e1n","sequence":"first","affiliation":[]},{"given":"Steffen","family":"Neumann","sequence":"additional","affiliation":[]},{"given":"Eamonn","family":"Maguire","sequence":"additional","affiliation":[]},{"given":"Susanna-Assunta","family":"Sansone","sequence":"additional","affiliation":[]},{"given":"Philippe","family":"Rocca-Serra","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,1,10]]},"reference":[{"key":"6254_CR1","unstructured":"BioSharing. [\n                    http:\/\/biosharing.org\n                    \n                  ]"},{"issue":"18","key":"6254_CR2","doi-asserted-by":"publisher","first-page":"2354","DOI":"10.1093\/bioinformatics\/btq415","volume":"26","author":"P Rocca-Serra","year":"2010","unstructured":"Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA: ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010, 26 (18): 2354-2356. 10.1093\/bioinformatics\/btq415.","journal-title":"Bioinformatics"},{"key":"6254_CR3","unstructured":"GitHub ISA-Tools. [\n                    https:\/\/github.com\/ISA-tools\n                    \n                  ]"},{"key":"6254_CR4","unstructured":"MIBBI. [\n                    http:\/\/biosharing.org\/mibbi\n                    \n                  ]"},{"issue":"4","key":"6254_CR5","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1093\/bioinformatics\/bts718","volume":"29","author":"E Maguire","year":"2013","unstructured":"Maguire E, Gonz\u00e1lez-Beltr\u00e1n A, Whetzel PL, Sansone SA, Rocca-Serra P: OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets. Bioinformatics. 2013, 29 (4): 525-527. 10.1093\/bioinformatics\/bts718.","journal-title":"Bioinformatics"},{"issue":"Web Server","key":"6254_CR6","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1093\/nar\/gkr469","volume":"39","author":"PL Whetzel","year":"2011","unstructured":"Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA: BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011, 39 (Web Server): 541-545.","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"6254_CR7","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1093\/nar\/gks1174","volume":"41","author":"G Rustici","year":"2013","unstructured":"Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U: ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res. 2013, 41 (Database): 987-990.","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"6254_CR8","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1093\/nar\/gkq967","volume":"39","author":"R Leinonen","year":"2011","unstructured":"Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-T\u00e1rraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G: The European Nucleotide Archive. Nucleic Acids Res. 2011, 39 (Database): 28-31. 10.1093\/nar\/gkq967.","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"6254_CR9","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1093\/nar\/gks1262","volume":"41","author":"JA Vizca\u00edno","year":"2013","unstructured":"Vizca\u00edno JA, C\u00f4t\u00e9 RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, P\u00e9rez-Riverol Y, Reisinger F, R\u00edos D, Wang R, Hermjakob H: The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41 (Database): 1063-1069.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"6254_CR10","doi-asserted-by":"publisher","first-page":"781","DOI":"10.1093\/nar\/gks1004","volume":"41","author":"K Haug","year":"2013","unstructured":"Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, Gonz\u00e1lez-Beltr\u00e1n A, Sansone SA, Griffin JL, Steinbeck C: MetaboLights-an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res. 2013, 41 (D1): 781-786. 10.1093\/nar\/gks1004.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"6254_CR11","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/ng.1054","volume":"44","author":"SA Sansone","year":"2012","unstructured":"Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D: Toward interoperable bioscience data. Nat Genet. 2012, 44 (2): 121-126. 10.1038\/ng.1054.","journal-title":"Nat Genet"},{"key":"6254_CR12","unstructured":"ISA commons. [\n                    http:\/\/isacommons.org\n                    \n                  ]"},{"key":"6254_CR13","unstructured":"GigaScience Journal. [\n                    http:\/\/www.gigasciencejournal.com\/\n                    \n                  ]"},{"key":"6254_CR14","unstructured":"Scientific Data. [\n                    http:\/\/www.nature.com\/scientificdata\/\n                    \n                  ]"},{"key":"6254_CR15","unstructured":"R project. [\n                    http:\/\/www.r-project.org\n                    \n                  ]"},{"issue":"10","key":"6254_CR16","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5 (10): R80-10.1186\/gb-2004-5-10-r80.","journal-title":"Genome Biol"},{"issue":"B","key":"6254_CR17","doi-asserted-by":"publisher","first-page":"35","DOI":"10.14806\/ej.18.B.542","volume":"18","author":"A Gonz\u00e1lez-Beltr\u00e1n","year":"2012","unstructured":"Gonz\u00e1lez-Beltr\u00e1n A, Maguire E, Rocca-Serra P, Sansone SA: The open source ISA software suite and its international user community: knowledge management of experimental data. EMBnet. journal. 2012, 18 (B): 35-37. 10.14806\/ej.18.B.542.","journal-title":"EMBnet. journal"},{"key":"6254_CR18","unstructured":"Oligo-arrays. [\n                    http:\/\/www.bioconductor.org\/help\/workflows\/oligo-arrays\/\n                    \n                  ]"},{"key":"6254_CR19","unstructured":"High-throughput sequencing. [\n                    http:\/\/www.bioconductor.org\/help\/workflows\/high-throughput-sequencing\/\n                    \n                  ]"},{"key":"6254_CR20","unstructured":"High-throughput assays. [\n                    http:\/\/www.bioconductor.org\/help\/workflows\/high-throughput-assays\/\n                    \n                  ]"},{"key":"6254_CR21","unstructured":"Risa 1.0.0. [\n                    http:\/\/www.bioconductor.org\/packages\/2.11\/bioc\/html\/Risa.html\n                    \n                  ]"},{"key":"6254_CR22","unstructured":"Risa 1.2.1. [\n                    http:\/\/www.bioconductor.org\/packages\/2.12\/bioc\/html\/Risa.html\n                    \n                  ]"},{"key":"6254_CR23","unstructured":"faahKO BioC package. [\n                    http:\/\/www.bioconductor.org\/packages\/release\/data\/experiment\/html\/faahKO.html\n                    \n                  ]"},{"key":"6254_CR24","volume-title":"faahKO: Saghatelian et al. (2004) FAAH knockout LC\/MS data","author":"CA Smith","year":"2012","unstructured":"Smith CA: faahKO: Saghatelian et al. (2004) FAAH knockout LC\/MS data. 2012, [R package version 1.2.13], [\n                    http:\/\/dx.doi.org\/10.1021\/bi0480335\n                    \n                  ]"},{"issue":"45","key":"6254_CR25","doi-asserted-by":"publisher","first-page":"14332","DOI":"10.1021\/bi0480335","volume":"43","author":"A Saghatelian","year":"2004","unstructured":"Saghatelian A, Trauger SA, Want EJ, Hawkins EG, Siuzdak G, Cravatt BF: Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry. 2004, 43 (45): 14332-14339. 10.1021\/bi0480335.","journal-title":"Biochemistry"},{"key":"6254_CR26","unstructured":"ARMSTRONG-S-3. [\n                    http:\/\/discovery.hsci.harvard.edu\/bioinvindex\/study.seam?studyId=ARMSTRONG-S-3\n                    \n                  ]"},{"issue":"5973","key":"6254_CR27","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1126\/science.1186624","volume":"327","author":"Y Wang","year":"2010","unstructured":"Wang Y, Krivtsov AV, Sinha AU, North TE, Goessling W, Feng Z, Zon LI, Armstrong SA: The Wnt\/beta-catenin pathway is required for the development of leukemia stem cells in AML. Science. 2010, 327 (5973): 1650-1653. 10.1126\/science.1186624.","journal-title":"Science"},{"issue":"Database","key":"6254_CR28","doi-asserted-by":"publisher","first-page":"984","DOI":"10.1093\/nar\/gkr1051","volume":"40","author":"SJ Ho Sui","year":"2012","unstructured":"Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TA, Sompallae R, Krivtsov A, Shivdasani RA, Armstrong SA, Culhane AC, Correll M, Sansone SA, Hofmann O, Hide W: The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res. 2012, 40 (Database): 984-991.","journal-title":"Nucleic Acids Res"},{"key":"6254_CR29","unstructured":"MTBLS2. [\n                    http:\/\/www.ebi.ac.uk\/metabolights\/MTBLS2\n                    \n                  ]"},{"key":"6254_CR30","volume-title":"The design of experiments - Statistical principles for practical application","author":"R Mead","year":"1988","unstructured":"Mead R: The design of experiments - Statistical principles for practical application. 1988, Cambridge University Press"},{"key":"6254_CR31","unstructured":"ISA Configuration Files. [\n                    https:\/\/github.com\/ISA-tools\/Configuration-Files\n                    \n                  ]"},{"issue":"3","key":"6254_CR32","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1021\/ac051437y","volume":"78","author":"CA Smith","year":"2006","unstructured":"Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G: XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 2006, 78 (3): 779-787. 10.1021\/ac051437y.","journal-title":"Anal Chem"},{"key":"6254_CR33","volume-title":"Mol Cell Proteomics","author":"L Martens","year":"2011","unstructured":"Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, R\u00f6mpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW: mzML-a community standard for mass spectrometry data. Mol Cell Proteomics. 2011, 10: R110.000133"},{"key":"6254_CR34","unstructured":"MetaboLights. [\n                    http:\/\/www.ebi.ac.uk\/metabolights\/\n                    \n                  ]"},{"key":"6254_CR35","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1007\/s11306-012-0401-0","volume":"9","author":"S Neumann","year":"2013","unstructured":"Neumann S, Thum A, B\u00f6ttcher C: Nearline acquisition and processing of liquid chromatography-tandem mass spectrometry data. Metabolomics. 2013, 9: 84-91. 10.1007\/s11306-012-0401-0.","journal-title":"Metabolomics"},{"key":"6254_CR36","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1021\/ac202450g","volume":"84","author":"C Kuhl","year":"2012","unstructured":"Kuhl C, Tautenhahn R, B\u00f6ttcher C, Larson TR, Neumann S: CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography\/mass spectrometry data sets. Anal Chem. 2012, 84: 283-289. 10.1021\/ac202450g.","journal-title":"Anal Chem"},{"issue":"4","key":"6254_CR37","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001, 29 (4): 365-371. 10.1038\/ng1201-365.","journal-title":"Nat Genet"},{"issue":"3","key":"6254_CR38","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","volume":"20","author":"L Gautier","year":"2004","unstructured":"Gautier L, Cope L, Bolstad BM, Irizarry RA: affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004, 20 (3): 307-315. 10.1093\/bioinformatics\/btg405.","journal-title":"Bioinformatics"},{"key":"6254_CR39","volume-title":"biocViews: Categorized views of R package repositories","author":"V Carey","year":"2012","unstructured":"Carey V, Harshfield B, Falcon S: biocViews: Categorized views of R package repositories. 2012"},{"key":"6254_CR40","unstructured":"Ellis B, Haaland P, Hahne F, Meur NL, Gopalakrishnan N: flowCore: flowCore: Basic structures for flow cytometry data. [R package version 1.24.2]"},{"issue":"15","key":"6254_CR41","doi-asserted-by":"publisher","first-page":"2088","DOI":"10.1093\/bioinformatics\/bts308","volume":"28","author":"J Hao","year":"2012","unstructured":"Hao J, Astle W, De Iorio M, Ebbels TM: BATMAN-an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model. Bioinformatics. 2012, 28 (15): 2088-2090. 10.1093\/bioinformatics\/bts308.","journal-title":"Bioinformatics"},{"issue":"10","key":"6254_CR42","doi-asserted-by":"publisher","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","volume":"11","author":"S Anders","year":"2010","unstructured":"Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol. 2010, 11 (10): R106-10.1186\/gb-2010-11-10-r106.","journal-title":"Genome Biol"},{"key":"6254_CR43","volume-title":"Modeling biomedical experimental processes with OBI","author":"RR Brinkman","year":"2010","unstructured":"Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, Zheng J, OBI consortium: Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010, 1 (Suppl 1): (S7)"},{"key":"6254_CR44","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1186\/1471-2105-7-489","volume":"7","author":"TF Rayner","year":"2006","unstructured":"Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006, 7: 489-489. 10.1186\/1471-2105-7-489.","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"6254_CR45","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1093\/bioinformatics\/btl005","volume":"22","author":"PL Whetzel","year":"2006","unstructured":"Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006, 22 (7): 866-873. 10.1093\/bioinformatics\/btl005.","journal-title":"Bioinformatics"},{"issue":"Database","key":"6254_CR46","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1093\/nar\/gks1193","volume":"41","author":"T Barrett","year":"2013","unstructured":"Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A: NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 2013, 41 (Database): 991-995.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"6254_CR47","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nbt.1823","volume":"29","author":"P Yilmaz","year":"2011","unstructured":"Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011, 29 (5): 415-420. 10.1038\/nbt.1823.","journal-title":"Nat Biotechnol"},{"issue":"8","key":"6254_CR48","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1038\/nbt1329","volume":"25","author":"CF Taylor","year":"2007","unstructured":"Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, Hermjakob H: The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007, 25 (8): 887-893. 10.1038\/nbt1329.","journal-title":"Nat Biotechnol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S1-S11.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T20:28:42Z","timestamp":1548188922000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S1-S11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1]]},"references-count":48,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2014,1]]}},"alternative-id":["6254"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s1-s11","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2014,1]]},"article-number":"S11"}}