Nanopublications for exposing experimental data in the life-sciences: a Huntington’s Disease case study

Journal of Biomedical Semantics

Marco Roos¹  Barend Mons¹  Erik A Schultes¹  Kristina M Hettne¹  Zuotian Tatum¹  van Eelke der Horst¹  Jun Zhao²  Rajaram Kaliyaperumal¹  Mark Thompson¹  Eleni Mina¹ 

[1] Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands;Department of Zoology, University of Oxford, Oxford, UK

关键词: Data integration;    Interoperability;    Workflows;    Research object;    Provenance;    Nanopublication;    Huntington’s disease;   

Others  :  1221436
DOI  :  10.1186/2041-1480-6-5

 received in 2014-05-31, accepted in 2015-02-09,  发布年份 2015

【 摘 要 】

Data from high throughput experiments often produce far more results than can ever appear in the main text or tables of a single research article. In these cases, the majority of new associations are often archived either as supplemental information in an arbitrary format or in publisher-independent databases that can be difficult to find. These data are not only lost from scientific discourse, but are also elusive to automated search, retrieval and processing. Here, we use the nanopublication model to make scientific assertions that were concluded from a workflow analysis of Huntington’s Disease data machine-readable, interoperable, and citable. We followed the nanopublication guidelines to semantically model our assertions as well as their provenance metadata and authorship. We demonstrate interoperability by linking nanopublication provenance to the Research Object model. These results indicate that nanopublications can provide an incentive for researchers to expose data that is interoperable and machine-readable for future use and preservation for which they can get credits for their effort. Nanopublications can have a leading role into hypotheses generation offering opportunities to produce large-scale data integration.

【 授权许可】

   
2015 Mina et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, et al.: The STRING, database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2010, 39(Database):D561-D568. http://www.nar.oxfordjournals.org/cgi/doi/10.1093/nar/gkq973 webcite
• [2]Jelier R, Schuemie MJ, Roes PJ, van Mulligen EM, Kors JA: Literature-based concept profiles for gene annotation: The issue of weighting. Int J Med Inform 2008, 77(5):354-362. http://www.sciencedirect.com/science/article/pii/S1386505607001372 webcite
• [3]van Haagen HHHBM, ’t Hoen PAC, Botelho Bovo A, de Morrée A, van Mulligen EM, Chichester C, et al.: Novel protein-protein interactions inferred from literature context. PLoS ONE 2009, 4(11):e7894. http://dx.plos.org/10.1371/journal.pone.0007894 webcite
• [4]Yepes AJ, Verspoor K: Towards automatic large-scale curation of genomic variation: improving coverage based on supplementary material. In BioLINK SIG 2013. Berlin, Germany; 2013.
• [5]Guidelines for Nanopublication http://nanopub.org/guidelines/working_draft/ webcite
• [6]Beck T, Free RC, Thorisson GA, Brookes AJ: Semantically enabling a genome-wide association study database. 3:9. http://www.jbiomedsem.com/content/3/1/9/abstract webcite
• [7]Landles C, Bates GP: Huntingtin and the molecular pathogenesis of Huntington’s disease. EMBO reports 2004, 5(10):958-963. http://www.nature.com/doifinder/10.1038/sj.embor.7400250 webcite
• [8]Cha JHJ: Transcriptional dysregulation in Huntington’s disease. Trends Neurosci 2000, 23(9):387-392. http://www.sciencedirect.com/science/article/pii/S016622360001609X webcite
• [9]Thomas EA, Coppola G, Desplats PA, Tang B, Soragni E, Burnett R, et al.: The HDAC inhibitor 4b ameliorates the disease phenotype and transcriptional abnormalities in Huntington’s disease transgenic mice. Proc Nat Acad Sci 2008, 105(40):15564. http://www.pnas.org/content/105/40/15564.short webcite
• [10]Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol 1987, 196(2):261-282. [PMID: 3656447]
• [11]Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB,: Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473(7345):43-49. http://www.nature.com/doifinder/10.1038/nature09906 webcite
• [12]Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P Oinn: Taverna: a tool for building and running workflows of services. Nucleic Acids Res 2006, 34(Web Server issue):W729-732. [PMID: 16845108]
• [13]Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S,: The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res 2013. [PMID: 23640334]
• [14]Hodges A: Regional and cellular gene expression changes in human Huntington’s disease brain. Hum Mol Genet 2006, 15(6):965-977. http://www.hmg.oxfordjournals.org/cgi/doi/10.1093/hmg/ddl013 webcite
• [15]UCSC genome browser home http://genome.ucsc.edu/ webcite,
• [16]Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al.: The human genome browser at UCSC. 12(6):996-1006. http://genome.cshlp.org/content/12/6/996 webcite
• [17]Kaltenbach LS, Romero E, Becklin RR, Chettier R, Bell R, Phansalkar A,: Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet 2007, 3(5):e82. http://dx.plos.org/10.1371/journal.pgen.0030082 webcite
• [18]AllegroGraph RDFStore Web 3.0’s Database http://www.franz.com/agraph/allegrograph/ webcite
• [19]Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J: Bio2RDF towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008, 41(5):706-716. [PMID: 18472304]
• [20]SIO - semanticscience - the semanticscience integrated ontology (SIO) - scientific knowledge discovery - google project hosting https://code.google.com/p/semanticscience/wiki/SIO webcite
• [21]Ioannidis JPA, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, et al.: Repeatability of published microarray gene expression analyses. Nat Genet 2008, 41(2):149-155. http://www.nature.com/doifinder/10.1038/ng.295 webcite
• [22]Taverna workflow provenance http://www.w3.org/2011/prov/wiki/TavernaProvenance webcite
• [23]Belhajjame K, Corcho O, Garijo D, Zhao J, Missier P, Newman D, et al.: Workflow-centric research objects: first class citizens in scholarly discourse. In Proc. Workshop on the Semantic Publishing (SePublica). Proc. Workshop on the Semantic Publishing (SePublica), Crete, Greece; 2012. http://users.ox.ac.uk/~oerc0033/preprints/sepublica2012.pdf webcite
• [24]Zhao J, Klyne G, Holubowicz P, Palma R, Soiland-Reyes S, Hettne K, et al.: RO-Manager: a tool for creating and manipulating research objects to support reproducibility and reuse in sciences. Proceedings of the 2nd International Workshop on Linked Science, 2012. https://www.escholar.manchester.ac.uk/uk-ac-man-scw:192016 webcite
• [25]OWL-S: Semantic markup for web services http://www.w3.org/Submission/2004/SUBM-OWL-S-20041122/ webcite
• [26]Imarisio S, Carmichael J, Korolchuk V, Chen CW, Saiki S, Rose C, et al.: Huntington’s disease: from pathology and genetics to potential therapies. 412(2):191-209. [PMID: 18466116]
• [27]Jenny Carmichael DCR: Huntington’s disease: molecular basis of neurodegeneration. Expert Rev Mol Med 2003, 5(20):1-21.
• [28]Pajouhesh H, Lenz GR: Medicinal chemical properties of successful central nervous system drugs. 2(4):541-553. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201314/ webcite. [PMID: 16489364 PMCID: PMC1201314]
• [29]Kegel KB, Sapp E, Alexander J, Reeves P, Bleckmann D, Sobin L, et al.: Huntingtin cleavage product A forms in neurons and is reduced by gamma-secretase inhibitors. 5:58. http://www.molecularneurodegeneration.com/content/5/1/58/abstract webcite. [PMID: 21156064]
• [30]Harmelen F, Kampis G, Börner K, Besselaar P, Schultes E, Goble C, et al.: Theoretical and technological building blocks for an innovation accelerator. Eur Phys J Spec Topics 2012, 214:183-214. http://epjst.epj.org/index.php?option=com_article&access=standard&Itemid=129&url=/articles/epjst/abs/2012/14/epjst214009/epjst214009.html webcite