Digital information cycle. Database. Database. BINF 630: Bioinformatics Methods
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1 Digital information cycle BINF 630: Bioinformatics Methods Iosif Vaisman Creation and capture Storage and management Rights management Search and access Distribution Electronic publishing Quality (peer review, retrospective evaluation) Reliability (stability of serves, control over alterations, proper archiving and mirroring) Hypertext Functionality in Scientific Literature Active references Forwarding references Dynamic publishing Database Ethical, Legal, and Economical Issues of Electronic Publishing Intellectual property rights Ownership of information Information as a commodity Database Database Organization database file record field character a collection of related structured information about entities a collection of records a set of fields a single characteristic of an entity a symbol used in data field
2 Database Management System (DBMS) Data Model A named logical unit (record type, data item) Relationships among logical units Relationships among logical units Four major components of DBMS: Data * Hardware * Software * Users one to one one to many many to one Relational Database Model Object-oriented Database Model G A Komatsoulis et al., 2008 Database administration Data integration Redundancy eliminated Inconsistency avoided Data shared Standards enforced Security applied Integrity maintained Requirements balanced Large-scale, complex data sets are shown as a network in which the nodes represent variables of biological interest, such as DNA variation, RNA variation, protein levels, protein states, metabolite levels and diseaseassociated traits, and the edges between these nodes represent causal relationships between the variables. Schadt et al., 2010
3 Data Warehouse InterPro Database Operational data Data fusion Data cleansing Metadata Databases in Bioinformatics Molecular Databases Nucleic acid sequences: GenBank (189 million, Dec 2015) WGS (317 million, Dec 2015) Protein sequences: UniProtKB: Swiss-Prot (550 thousand, Jan 2016) TrEMBL (59 million, Jan 2016) Protein structures: PDB (115 thousand, Jan 2016) NAR Molecular Databases NAR Molecular Databases NAR Database Summary Paper Category List Todd Smith, 2015 Nucleotide Sequence Databases International Nucleotide Sequence Database Collaboration Coding and non-coding DNA Gene structure, introns and exons, splice sites Transcriptional regulator sites and transcription factors RNA sequence databases Protein sequence databases Structure Databases Genomics Databases (non-vertebrate) Metabolic and Signaling Pathways Human and other Vertebrate Genomes Human Genes and Diseases Microarray Data and other Gene Expression Databases Proteomics Resources Other Molecular Biology Databases Organelle databases Plant databases Immunological databases Cell biology NAR 2016 database issue: 15 categories, 41 subcategories, 1685 databases
4 Dec-82 Oct-84 Aug-86 Jun-88 Apr-90 Feb-92 Nov-93 Sep-95 Jul-97 May-99 Mar-01 Jan-03 Nov-04 Sep-06 Jul-08 May-10 Mar-12 Molecular Databases NCBI integrated search and retrieval system Entrez NCBI Databases Growth of GenBank nr - All non-redundant GenBank CDS translations+pdb+swissprot+pir month - All new or revised GenBank CDS released in the last 30 days swissprot - the last major release of the SWISS-PROT protein sequence database (no updates) yeast - Yeast (Saccharomyces cerevisiae) protein sequences. E. coli - E. coli genomic CDS translations pdb - Sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank kabat - Kabat's database of sequences of immunological interest 160,000,000, ,000,000, ,000,000, ,000,000,000 80,000,000,000 60,000,000,000 40,000,000,000 20,000,000,000 0 Base pairs Entries December ,338 bp 606 seq December ,390,863,904 bp 161,140,325 seq 180,000, ,000, ,000, ,000, ,000,000 80,000,000 60,000,000 40,000,000 20,000,000 0 GenBank Selected Per-Organism Statistics NCBI Databases Homo sapiens Mus musculus Rattus norvegicus Bos taurus Zea mays Sus scrofa Danio rerio Hordeum vulgare subsp. vulgare Strongylocentrotus purpuratus Macaca mulatta Oryza sativa Japonica Group Xenopus (Silurana) tropicalis Nicotiana tabacum Arabidopsis thaliana Triticum aestivum Drosophila melanogaster Pan troglodytes Vitis vinifera Canis lupus familiaris Solanum lycopersicum
5 NCBI Databases (cont.) Derivative databases doi: /nar/gkt1146 Lu, 2011, Example of a Genbank entry LOCUS VIBHALUXA 3141 bp DNA BCT 15-FEB-1996 DEFINITION V.harveyi luciferase alpha and beta subunit (luxa and luxb) genes, complete cds. ACCESSION M10961 M13494 NID g KEYWORDS luciferase. SOURCE Vibrio harveyi DNA. ORGANISM Vibrio harveyi Eubacteria; Proteobacteria; gamma subdivision; Vibrionaceae; Vibrio. REFERENCE 1 (bases 1 to 1838) AUTHORS Cohn,D.H., Mileham,A.J., Simon,M.I., Nealson,K.H., Rausch,S.K., Bonam,D. and Baldwin,T.O. TITLE Nucleotide sequence of the luxa gene of Vibrio harveyi and the complete amino acid sequence of the alpha subunit of bacterial luciferase JOURNAL J. Biol. Chem. 260 (10), (1985) MEDLINE REFERENCE 2 (bases 1745 to 3141) AUTHORS Johnston,T.C., Thompson,R.B. and Baldwin,T.O. TITLE Nucleotide sequence of the luxb gene of Vibrio harveyi and the complete amino acid sequence of the beta subunit of bacterial luciferase JOURNAL J. Biol. Chem. 261 (11), (1986) MEDLINE Example of a Genbank entry FEATURES Location/Qualifiers gene /gene="luxa" CDS /gene="luxa" /codon_start=1 /product="luciferase alpha subunit" /db_xref="pid:g155175" /transl_table=11 /translation="mkfgnflltyqppelsqtevmkrlvnlgkasegcgfdtvwlleh HFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFR FGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNP SAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYD VTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYDFNKGQ WRDFVLKGHKDTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEE EIIASMKLFQSDVMPYLKEKQ" BASE COUNT 883 a 665 c 741 g 852 t ORIGIN 1 bp upstream of EcoRI site. 1 gaattcacca tgacgacggg caaaaatagt ttgtgcactg tttatcactg gctgcagacc 61 aagggcacac aaaacattgg cttgattgcg gcaagtctct cagctcgtgt cgcctatgaa 121 gttatctctg atctggagct gtcttttctg attactgcgg ttggtgtggt gaacttgcgt 181 gacacactag aaaaagcgct tggttttgat tacctcagtt tgcctatcga tgagctacca... Example of a Pubmed entry PMID OWN - NLM STAT- MEDLINE DA DCOM IS (Electronic) IS (Linking) DP Aug 15 TI - New method for protein secondary structure assignment based on a simple topological descriptor. PG AB - A simple, five-element descriptor, derived from the Delaunay tessellation of a protein structure in a single point per residue representation, can be assigned to each residue in the protein. The descriptor characterizes main-chain topology and connectivity in the neighborhood of the residue and does not explicitly depend on putative hydrogen bonds or any geometric parameter, including bond length, angles, and areas. Rules based on this descriptor can be used for accurate, robust, and computationally efficient secondary structure assignment that correlates well with the existing methods. AD - Laboratory for Structural Bioinformatics, School of Computational Sciences, George Mason University, Manassas, Virginia 20110, USA. FAU - Taylor, Todd AU - Taylor T FAU - Rivera, Margarita AU - Rivera M FAU - Wilson, Glenda AU - Wilson G FAU - Vaisman, Iosif I AU - Vaisman II LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States Example of a Pubmed entry TA - Proteins JT - Proteins JID RN - 0 (Proteins) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Biophysical Phenomena MH - Biophysics MH - Computational Biology/*methods MH - Computer Simulation MH - Hydrogen Bonding MH - Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteins/chemistry MH - Proteomics/*methods MH - Sensitivity and Specificity MH - Software MH - Structural Homology, Protein EDAT- 2005/05/12 09:00 MHDA- 2006/05/23 09:00 CRDT- 2005/05/12 09:00
6 ID Converters ID Converters Features of mapping services Interface Gene/Clone ID converter Output format Html, text, spreadsheet ID mapping by UniProt MatchMiner Web-based GUI form Web-based GUI form Web-based GUI form, command line Html, text Organisms Human, mouse, rat Human, mouse, rat and many other species Input/output gene Input/output protein HUGO gene names, Entrez gene Ids, Ensembl gene Ids, UniGene cluster Ids, RefSeq RNAs (Additional output: CCDS) a RefSeq peptides, SwissProt names (Additional output: IPI, PDB)* Entrez Gene, HGNC, Ensembl, UniGene, TIGR (JCVI) UniProtKB, RefSeq, GenPept, IPI, PDB Html, text, spreadsheet Human, mouse Gene Symbol HUGO/Alias, Name, UniGene Cluster Id, Entrez Gene Id, RefSeq RNA RefSeq protein DAVID gene ID conversion tool Web-based GUI form Html, text, spreadsheet Human, about another 90,000 species Entrez gene Id, Ensembl gene/transcript Id, RefSeq mrna accession, UniGene Id PIR accession, PIR Id, PIR NREF Id, RefSeq Protein accession, Uniprot Id/accession, UniRef Id Chavan et al., 2011 Mapping services Gene/Clone ID converter ID mapping by UniProt MatchMiner DAVID gene ID conversion tool g:convert CRONOS biodbnet:db2db Link Chavan et al., 2011 Genome sequencing costs Sequencing and storage cost $100,000,000 $10, $10,000,000 $1, $1,000,000 $100,000 $ $10,000 $10.00 $1,000 $100 $10 $1 Cost per Genome Cost per Mb $1.00 $0.10 $0.01 L D Stein, 2010
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