The BLUEPRINT Data Analysis Portal
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