Bioinformatics Databases: Getting Knowledge from InformationPowerPoint PresentationWhat is Bioinformatics?With a field this extensive and skill sets so varied, where do we begin?Slide 5Moving from Information to Knowledge to Understanding: Genetic testingHow can Bioinformatics facilitate the extraction of information?Bioinformatics will not replace experiments, but can greatly streamline and enable the discovery process.One of the fundamental tools of bioinformatics: DatabaseIndustry Challenge #1: Genome annotationWhat does the genome data look like?What does the genome annotation look like today?Slide 13The value of a genome is only as good as its annotationNucleic Acids Research article lists 1078 public databases (up from 719 in 2005):Slide 16Industry Challenge #2: Too much unintegrated dataPublic Data ResourcesNCBI Database ResourcesMajor Sequence RepositoriesSlide 21Entrez Gene: a unified query environment for genes defined by sequenceGenBankGenBank GrowthSlide 25Potential Errors in GenBankSlide 27Slide 28Slide 29Slide 30Slide 31Slide 32Many Databases available:The principal requirements on the public data servicesComparative Genomics: COGGene ExpressionGenetic MapsGenomic DatabasesIntermolecular InteractionsMetabolic Pathways and Celluar RegulationMutation DatabasesPathologyProtein DatabasesProtein Databases: Swiss-ProtProteome Resources: Proteome BKLRNA SequencesStructureVaried Biomedical ContentExtinct: Gene Identification & StructureNational Center for Biotechnology Information (NCBI): A network of linked resourcesNCBI resourcesSlide 52Slide 53Slide 54Slide 55Slide 56Slide 57Slide 58Slide 59Slide 60Slide 61Slide 62Slide 63Slide 64Slide 65Slide 66Slide 67Slide 68Slide 69Slide 70Slide 71Slide 72Slide 73Slide 74Slide 75Slide 76Bioinformatics Databases:Getting Knowledge from InformationKristen AntonDirector of BioInformaticsDartmouth Medical SchoolBioInformatics @ Dartmouth Medical SchoolWhat is Bioinformatics?Bioinformatics provides the backbone computational tools, databases and domain expertise that facilitates modern biomedical, biological and genomic research.BioInformatics @ Dartmouth Medical SchoolBioInformatics @ Dartmouth Medical SchoolWhat is Bioinformatics?•‘Wet-lab’ science•Sequence analysis•Modeling & structural work•Algorithm development•Clinical and Translational research•Hardware & software infrastructureThe expertise is multidisciplinary,and the skills fall on a continuum from‘pure’ science to ‘pure’ computing:With a field this extensive and skill sets so varied, where do we begin?BioInformatics @ Dartmouth Medical SchoolBioInformatics @ Dartmouth Medical SchoolFrom Information Design, Nathan ShedroffMoving from Information to Knowledge to Understanding: Genetic testing•BRCA1 and BRCA2 gene mutations: what is the real risk to women carriers? 25% - 80%•Huntington’s Disease: mechanism defined, but what does that mean for the individual in terms of age of onset, severity of disease, or how disease will progress?BioInformatics @ Dartmouth Medical SchoolHow can Bioinformatics facilitate the extraction of information?•Development of tools that support laboratory experiments•Design, implementation and integration of biological databases•Development of various analytical tools, algorithms and models•Development of systems to collect, validate, manage and integrate clinical and research data to facilitate translational researchBioInformatics @ Dartmouth Medical SchoolBioinformatics will not replace experiments, but can greatly streamline and enable the discovery process.BioInformatics @ Dartmouth Medical SchoolOne of the fundamental toolsof bioinformatics: Database•A database is a body of information stored in two dimensions (rows and columns)•The power of the database lies in the relationships that you construct between the pieces of information (tables)•SQL (Structured Query Language) - interactive and embedded•Good design and application ensure data integrity•InteroperabilityBioInformatics @ Dartmouth Medical SchoolIndustry Challenge #1:Genome annotationThe Human Genome is sequenced. It is estimated that 2% of the human genome codes for genes. The function of the remaining 98% (non-coding regions) is largely unknown but likely include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made.BioInformatics @ Dartmouth Medical SchoolWhat does the genome data look like? 1 gcggagggtg cgtgcgggcc gcggcagccg aacaaaggag caggggcgcc gccgcaggga 61 cccgccaccc acctcccggg gccgcgcagc ggcctctcgt ctactgccac catgaccgcc 121 aacggcacag ccgaggcggt gcagatccag ttcggcctca tcaactgcgg caacaagtac 181 ctgacggccg aggcgttcgg gttcaaggtg aacgcgtccg ccagcagcct gaagaagaag 241 cagatctgga cgctggagca gccccctgac gaggcgggca gcgcggccgt gtgcctgcgc 301 agccacctgg gccgctacct ggcggcggac aaggacggca acgtgacctg cgagcgcgag 361 gtgcccggtc ccgactgccg tttcctcatc gtggcgcacg acgacggtcg ctggtcgctg 421 cagtccgagg cgcaccggcg ctacttcggc ggcaccgagg accgcctgtc ctgcttcgcg 481 cagacggtgt cccccgccga gaagtggagc gtgcacatcg ccatgcaccc tcaggtcaac 541 atctacagtg tcacccgtaa gcgctacgcg cacctgagcg cgcggccggc cgacgagatc 601 gccgtggacc gcgacgtgcc ctggggcgtc gactcgctca tcaccctcgc cttccaggac 661 cagcgctaca gcgtgcagac cgccgaccac cgcttcctgc gccacgacgg gcgcctggtg 721 gcgcgccccg agccggccac tggctacacg ctggagttcc gctccggcaa ggtggccttc 781 cgcgactgcg agggccgtta cctggcgccg tcggggccca gcggcacgct caaggcgggc 841 aaggccacca aggtgggcaa ggacgagctc tttgctctgg agcagagctg cgcccaggtc 901 gtgctgcagg cggccaacga gaggaacgtg tccacgcgcc agggtatgga cctgtctgcc 961 aatcaggacg aggagaccga ccaggagacc ttccagctgg agatcgaccg cgacaccaaa ...Multiply times eighteen millionBioInformatics @ Dartmouth Medical SchoolWhat does the genome annotation look like today?BioInformatics @ Dartmouth Medical SchoolBioInformatics @ Dartmouth Medical SchoolThe value of a genome is onlyas good as its annotation•Two steps: annotation & curation•Each genome is annotated individually•Manual curation is standard practice•New tools, ie. NCBI Mapviewer, ESTAnnotator, NCBI Annotation Pipeline•Many databases available …BioInformatics @ Dartmouth Medical SchoolNucleic Acids Research article lists1078 public databases (up from 719 in 2005):BioInformatics @ Dartmouth Medical SchoolNucleic Acids Research, 2008, Vol. 36, Database