The BLUEPRINT Data Analysis Portal

Cell Systems - Tập 3 - Trang 491-495.e5 - 2016
José María Fernández1,2, Victor de la Torre1,2, David Richardson3, Romina Royo2,4, Montserrat Puiggròs4, Valentí Moncunill4, Stamatina Fragkogianni4, Laura Clarke3, Paul Flicek3, Daniel Rico1, David Torrents4,5, Enrique Carrillo de Santa Pau1, Alfonso Valencia1,2
1Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
2Spanish Bioinformatics Institute INB-ISCIII ES-ELIXIR, Madrid 28029, Spain
3European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
4Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB, Research Program in Computational Biology, BSC - CRG - IRB, Barcelona 08028, Spain
5Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain

Tài liệu tham khảo

Adams, 2012, BLUEPRINT to decode the epigenetic signature written in blood, Nat. Biotechnol., 30, 224, 10.1038/nbt.2153 Albrecht, 2016, DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets, Nucleic Acids Res., 44, W581, 10.1093/nar/gkw211 Bard, 2005, An ontology for cell types, Genome Biol., 6, R21, 10.1186/gb-2005-6-2-r21 BP-analysis (2016). BLUEPRINT analysis descriptions release 20160816. ftp://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/. BP-Data_analysis (2016). BLUEPRINT data analysis portal GitHub repository. https://github.com/inab/epico-data-analysis-portal. BP-FPKM (2016). A description file about how FPKMs were calculated in release 20160816. ftp://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816. BP-Schema-tools (2015). Bioinformatic Pantry Schema tools GitHub repository. https://github.com/inab/BP-Schema-tools. CEEHRC (2016). McGill Epigenomics Mapping Centre. http://epigenomesportal.ca/edcc/. CEMT. (2016). Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network. http://www.epigenomes.ca/. Chen, 1976, The entity-relationship model—toward a unified view of data, ACM Trans. Database Syst., 1, 9, 10.1145/320434.320440 Codd, 1979, Extending the database relational model to capture more meaning, ACM Trans. Database Syst., 4, 397, 10.1145/320107.320109 CREST (2016). International human epigenome consortium, IHEC, team Japan. http://crest-ihec.jp/english/index.html. Croft, 2014, The Reactome pathway knowledgebase, Nucleic Acids Res., 42, D472, 10.1093/nar/gkt1102 DCC_portal (2016). The BLUEPRINT DCC portal. http://dcc.blueprint-epigenome.eu. DEEP (2016). Welcome to DEEP. http://www.deutsches-epigenom-programm.de/. ENCODE (2016). The ENCODE Project: ENCyclopedia of DNA elements. https://www.genome.gov/encode/. EPICO-data-loading-scripts (2016). EPICO database loading scripts GitHub repository. https://github.com/inab/EPICO-data-loading-scripts. EPICO-data-model (2016). EPICO data model GitHub repository, designed using BP-Schema-tools. https://github.com/inab/EPICO-data-model. EPICO-REST-API (2016). EPICO REST API GitHub repository. https://github.com/inab/EPICO-REST-API. Flicek, 2014, Ensembl 2014, Nucleic Acids Res., 42, D749, 10.1093/nar/gkt1196 Harrow, 2012, GENCODE: the reference human genome annotation for The ENCODE Project, Genome Res., 22, 1760, 10.1101/gr.135350.111 ICGC (2016). International cancer genome consortium. http://icgc.org. ICGC-DCC-Docs (2016). ICGC DCC documents. http://docs.icgc.org/. IHEC (2016). International human epigenome consortium. http://ihec-epigenomes.org/. Kent, 2002, The human genome browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102 Kurotaki, 2014, IRF8 inhibits C/EBPα activity to restrain mononuclear phagocyte progenitors from differentiating into neutrophils, Nat. Commun., 5, 4978, 10.1038/ncomms5978 Malone, 2010, Modeling sample variables with an Experimental Factor Ontology, Bioinformatics, 26, 1112, 10.1093/bioinformatics/btq099 Meehan, 2013, Ontology based molecular signatures for immune cell types via gene expression analysis, BMC Bioinformatics, 14, 263, 10.1186/1471-2105-14-263 Roadmap Epigenomics Project (2016). The NIH Roadmap Epigenomics Mapping Consortium. http://www.roadmapepigenomics.org/. Rodriguez, 2013, APPRIS: annotation of principal and alternative splice isoforms, Nucleic Acids Res., 41, D110, 10.1093/nar/gks1058 Sarntivijai, 2014, CLO: The cell line ontology, J. Biomed. Semantics, 5, 37, 10.1186/2041-1480-5-37 Smith, 2007, The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nat. Biotechnol., 25, 1251, 10.1038/nbt1346 Ye, 2009, International Union of Basic and Clinical Pharmacology. LXXIII. Nomenclature for the formyl peptide receptor (FPR) family, Pharmacol. Rev., 61, 119, 10.1124/pr.109.001578