Notes on Biological Databases - Fall 2008 | CMSC 423, Study notes of Computer Science

Download Notes on Biological Databases - Fall 2008 | CMSC 423 and more Study notes Computer Science in PDF only on Docsity! CMSC423: Bioinformatic Algorithms, Databases and Tools Lecture 5 Biological databases CMSC423 Fall 2008 2 Biological databases CMSC423 Fall 2008 5 How the data get accessed • Gene by gene/object by object – targeted at manual inspection of data – usually lots of clicking involved – simple search capability – similarity searches in addition to text queries • Bulk – targeted at computational analyses – often programmatic access through web server – most frequently – just bulk download (ftp) CMSC423 Fall 2008 6 NCBI - National Center for Biotech. Info. • Virtually all biological data generated in the US gets stored here! • One-stop-shop for biological data • Primarily focused on gene-by-gene analyses • Provides simple scripts for programmatic access • Provides ftp access for bulk downloads http://www.ncbi.nlm.nih.gov CMSC423 Fall 2008 7 EMBL European Molecular Biology Lab. • European version of NCBI • BioMart query builder http://www.ebi.ac.uk/embl/ CMSC423 Fall 2008 10 Genome browsers • UCSC Genome Browser – http://genome.ucsc.edu • ENSEMBL Genome Browser – http://www.ensemble.org • Gbrowse http://www.gmod.org CMSC423 Fall 2008 11 Direct database access - SQL • CHADO schema – www.gmod.org CMSC423 Fall 2008 12 SQL select pt.phylotree_id, pn.parent_phylonode_id, po.organism_id from phylotree pt, phylonode pn, pylonode_organism po where pt.name = "Archaea" and pt.phylotree_id = pn.phylotree_id and pn.phylonode_id = 1000 and po.phylonode_id = pn.parent_phylonode_id # Selects parent node and organism IDs for archaeon with ID 1000