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The National Center for Biotechnology Information (NCBI) a primary resource for molecular biology information

Database Resources . The National Center for Biotechnology Information (NCBI) a primary resource for molecular biology information. www.ncbi.nih.gov. NCBI Mission.

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The National Center for Biotechnology Information (NCBI) a primary resource for molecular biology information

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  1. Database Resources The National Center for Biotechnology Information (NCBI) a primary resource for molecular biology information www.ncbi.nih.gov

  2. NCBI Mission • …. to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. • What does this involve ? • creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics; • facilitating the use of such databases and software by the research andmedical community; • coordinating efforts to gather biotechnology information both nationallyand internationally; • performing research into advanced methods ofcomputer-based information processing for analyzing the structure and function of biologically important molecules.

  3. What is a Database ? • A model or representation of some aspect of the real world • An organized collection of data. May contain many different types of data • Coherent, consistent and designed for a specific purpose • A computational system for managing and querying the data.

  4. What is a Database ? • A collection of information organized in such a way that a computer program can quickly select desired pieces of data. • An electronic filing system • Traditional databases are organized by fields, records, and files. • A field is a single piece of information; • a record is one complete set of fields • a file is a collection of records. For example, a telephone book is analogous to a file. It contains a list of records, each of which consists of three fields: name, address, and telephone number.

  5. What is a Database ? • To access information from a database, you need a database management system (DBMS). This is a collection of programs that enables you to enter, organize, and select data in a database. • Most molecular biology databases primarily use relational database management systems (RDBMS).

  6. Relational Database • A relational database is like a large spreadsheet. Each field is a column, each row is an entry. Relational databases use a set of tables to organize data. • Each entry must be unambiguously identified • Names are not reliable e.g. incorrectly assigned gene function • Unique IDs (UID)s are used, e.g. in GenBank these are called accession numbers

  7. Relational Database • Achieving consistency • Repeated information is stored in a single place. • Only one copy needs to be updated TaxonomyTaxonomy ID*GenusSpecies *May be referred to by a secondary ID SequenceUIDDefinitionLocusAccessionTaxonomy ID*Sequence Ref IndexMedline IDAuthorsTitleJournal Ref Index*UIDMedline ID * May be referred to indirectly via an index

  8. Relational Database • Language used is SQL or structured query language • Easy to understand (essentially English?) • Relatively consistent across RBDMS • Supplies a set of commands to define tables, insert data and make queries • Queries • SELECT some fields FROM some table WHERE some condition is met • E.g. select accession, sequence FROM sequence WHERE Accession = BU039022BU039022 CATACAAATACTGCTACHTAAATC …. • More complex queries require two or more tables be joined to produce a result

  9. Relational Database • Most RDBMS do not allow users to directly query the database by SQL. • An ill formed query can overload or crash the system • SQL still too complex for biologists? • Provide a search interface for the user instead • E.g. user enters a phrase and the database identifies what part of the database should be searched. • The queries that make it through the web interface have to be translated to SQL

  10. Relational database : Example GenBank Query

  11. What Constitutes a Good Database ? • Broad coverage of the chosen topic • Up to date information gathering • Curated • Support staff • Commitment to the future • Good query interface Issues for Molecular Biological Databases ? • Annotation • Archives • Updates • Redundancy

  12. Issues for Molecular Biological Databases ? • Annotation • Adding biological information to genome sequence. Textual descriptive information • Correctness • Many genes are incorrectly annotated. May assign a function to a novel gene from a similar sequence that may itself be incorrectly annotated so the error is propagated throughout the database. • Routine error • Quality • Expert or non expert curation? Who provided the curation? • Is there any biological verification? • What vocabulary is used • Has their been any peer review ?

  13. Issues for Molecular Biological Databases ? • Archival Quality • Is the database archival or curated • Can the same data be recovered later • Don’t overwrite primary key (each accession numbers) • The best databases note any changes to the data. • Updates • How often is the database updated? • Major databases take direct submissions • Only the direct submitter can make changes, even if you can prove its wrong. • When is a sequence finished ? • How is annotation updated as more knowledge is available • Redundancy • This is a major issue, how do we deal with it without losing potentially valuable information. • Also relates to archival quality

  14. NCBI and GenBank • Genbank is the genetic sequence database of all publicly available DNA and derived protein sequences, with annotations describing the biological information in them. • GenBank is hosted within NCBI • Researchers submit their sequences to GenBank • NCBI provides analysis and retrieval resources for the data in GenBank (and many other NCBI hosted databases).

  15. NCBI Databases (http://www.ncbi.nlm.nih.gov/guide/all/#Databases_) • SNP (dbSNP) • dbVAR – large scale genomic variation • dbGAP– integration of genotype & phenotype • PopSetDatabase • Taxonomy Database • GEO Profiles • GEO Datasets • Cancer Chromosomes • Epigenomics • PubMedCentral • Journals • MeSH • Bookshelf • OMIM Database • Nucleotide Database • EST (dbEST) • GSS (dbGSS) • Protein Database • Structure Database • Genome • 3D Domains • Conserved Domains • UniSTS • Gene • UniGene • HomoloGene • Reference Sequence (refseq)

  16. Retrieving Data from NCBIusing Entrez • Entrez is a text based retrieval system that integrates all the information resources available at the NCBI such as; • Scientific literature • DNA and protein sequence databases • 3D protein structure and protein domain data • Population study datasets • Expression data • Assemblies of complete genomes • Taxonomic information

  17. http://www.ncbi.nlm.nih.gov/guide/all/#howto_

  18. Create/login to the myNCBI portal

  19. Understanding GenBank records Go to http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#ModificationsDateB Click on the links on the left to get a description of what the term means, Copy the description into a word document and after completed, save the document on your drupalweb site

  20. Entrez Sequences Help http://www.ncbi.nlm.nih.gov/books/NBK44864/

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