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    Biological Databases: DR Z Chikwambi Biotechnology

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    Mutsawashe Munetsi
    The document describes the objectives and key concepts of biological databases. It aims to describe databases, their features, an ideal database, their purposes, how they are integrated through resource portals, and problems associated with databases. Specifically, it defines what a database is, describes different types of databases like sequence databases and how they are structured and searched, and provides examples of major biological databases like Swiss-Prot, GenBank, OMIM, and their functions.

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    Biological Databases: DR Z Chikwambi Biotechnology

    Uploaded by

    Mutsawashe Munetsi
    86 views47 pages
    The document describes the objectives and key concepts of biological databases. It aims to describe databases, their features, an ideal database, their purposes, how they are integrated through resource portals, and problems associated with databases. Specifically, it defines what a database is, describes different types of databases like sequence databases and how they are structured and searched, and provides examples of major biological databases like Swiss-Prot, GenBank, OMIM, and their functions.

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    The document describes the objectives and key concepts of biological databases. It aims to describe databases, their features, an ideal database, their purposes, how they are integrated through resource portals, and problems associated with databases. Specifically, it defines what a database is, describes different types of databases like sequence databases and how they are structured and searched, and provides examples of major biological databases like Swiss-Prot, GenBank, OMIM, and their functions.

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    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    86 views47 pages

    Biological Databases: DR Z Chikwambi Biotechnology

    Uploaded by

    Mutsawashe Munetsi
    The document describes the objectives and key concepts of biological databases. It aims to describe databases, their features, an ideal database, their purposes, how they are integrated through resource portals, and problems associated with databases. Specifically, it defines what a database is, describes different types of databases like sequence databases and how they are structured and searched, and provides examples of major biological databases like Swiss-Prot, GenBank, OMIM, and their functions.

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    of 47

    Biological

    Databases

    Dr Z Chikwambi
    Biotechnology
    Objectives of lecture:
    You are expected to describe/ understand
    the following:

    1. To describe databases.
    2. Describe features of a database.
    3. Describe an ideal database.
    4. Describe the purposes of databases.
    5. Describe how databases are integrated
    supported by resource portals.
    6. Describe problems associated with
    databases.
    DATABASES
    Database or databank?

    Initially
    • Databank (in UK)
    • Database (in the USA)

    Solution

    • The abbreviation db
    What is a Database?

    A structured collection of data held in computer storage; esp. one that


    incorporates software to make it accessible in a variety of ways; transf., any
    large collection of information.

    database management: the organization and manipulation of data in a


    database.

    database management system (DBMS): a software package that provides


    all the functions required for database management.

    database system: a database together with a database management system.


    What is a database?
    • A collection of data
    – structured
    – searchable (index) -> table of contents
    – updated periodically (release) -> new edition
    – cross-referenced (hyperlinks) -> links with other db

    • Includes also associated tools (software) necessary for


    access, updating, information insertion, information
    deletion….

    • Data storage management: flat files, relational databases…

    6
    What are Databases?
    • A database is a structured collection of
    information.
    – A database consists of basic units called records or
    entries.
    – Each record consists of fields, which hold pre-
    defined data related to the record.
    – For example, a protein database would have
    protein sequences as records and protein
    properties as fields (e.g., name of protein, length,
    amino-acid sequence, …)
    Database: a « flat file » example
    Flat-file database («  flat file, 3 entries  »):

    Accession number: 1
    First Name: Amos
    Last Name: Bairoch
    Course: Pottery 2000; Pottery 2001;
    //
    Accession number: 2
    First Name: Dan
    Last name: Graur
    Course: Pottery 2000, Pottery 2001; Ballet 2001, Ballet 2002
    //
    Accession number 3:
    First Name: John
    Last name: Travolta
    Course: Ballet 2001; Ballet 2002;
    //
    • Easy to manage: all the entries are visible at the same time !
    8
    • A Database
    – Can be thought of as a large table, where the rows
    represent records and the columns represent fields.

    Field Name Length Sequence Enzyme


    Record
    QA001 MTGA 243 MYQWI… yes
    QA002 Ribosomal 267 MAAPV… no
    protein L9
    QA003 Flagellin 374 GSSIL… no
    QA004 GDPMH 157 MFLRQ… yes

    Accession Numbers: Unique identifiers of the


    database records. 9
    Database: a « relational » example
    Relational database (« table file »):

    Teacher Accession Education


    number
    Amos 1 Biochemistry
    Dan 2 Genetics
    John 3 Scientology

    Course Year Involved


    teachers
    Advanced 2000; 2001 1; 2
    Pottery
    Ballet for Fat 2001; 2002 2; 3
    People
    10
    Ideal Minimal Content of an Entry
    in a Sequence Database
    • Sequence
    • Accession number (AC)
    • Taxonomic data
    • References
    • Annotation/Curation
    • Keywords
    • Cross-references
    • Documentation
    • Source of data
    Why biological databases?
    • Exponential growth in biological data.

    • Data (genomic sequences, 3D structures, 2D gel


    analysis, MS analysis, Microarrays….) are no longer
    published in a conventional manner, but directly
    submitted to databases.

    • Essential tools for biological research. The only way to


    publish massive amounts of data without using all the
    paper in the world.
    12
    Primary & Secondary Databases
    • Primary
    – Sequence information
    – Structural information

    • Secondary
    – Information derived from primary databases
    – Signature sequences, domains, motiffs, pathways, diseases

    • Integrated
    Categories of databases for Life Sciences
    • Sequences (DNA, protein)
    • Genomics
    • Mutation/polymorphism
    • Protein domain/family
    • Proteomics (2D gel, Mass Spectrometry)
    • 3D structure
    • Metabolic networks
    • Regulatory networks
    • Bibliography
    • Expression (Microarrays,…)
    • Specialized
    14
    Databases: Examples
    • Integrated systems of databases:
    » E.g., NCBI (Protein, Nucleotide, Gene, OMIM, BLAST etc.)

    • Protein Databases:
    » E.g., ExPASy (SwissProt + TrEMBL)

    • Protein structures:
    » E.g., PDB and PDBsum

    • Pathway databases:
    » E.g., KEGG (Kyoto Encyclopedia of Genes and Genomes)

    15
    Databases: Protein sequences
    • SWISS-PROT: created in 1986 (Amos Bairoch) http://www.expasy.org/sprot/

    • TrEMBL: created in 1996; complement to SWISS-PROT; derived from


    EMBL CDS translations (« proteomic » version of EMBL)

    • PIR-PSD: Protein Information Resources http://pir.georgetown.edu/

    • Genpept: « proteomic » version of GenBank

    • Many specialized protein databases for specific families or groups of


    proteins.

    – Examples: AMSDb (antibacterial peptides), GPCRDB (7 TM


    receptors), IMGT (immune system), YPD (Yeast), etc.
    Sequence-based Database
    Searching
    • Basic Assumptions:
    • Sequences of homologous Genes/Protein diverge
    over time even though structure and/or function
    change little
    • Significant sequence similarity inferred as potential
    structural /functional similarity or common evolutionary
    origin
    • Based on well-characterised protein, infer the function
    of an unknown sequence at gene or protein sequence
    level.
    Text based Database/ searching: Eg.
    PubMed
    • Terminology: query, hit, fields, logical/Boolean
    operator.
    • General principles:
    1. All main databases provide a convenient tool for text base
    searching.
    2. We can search for key/query words in specific fields.
    3. We can search more than one database at a time.
    4. We can pose additional limits, such as modification date.

    Eg. PubMed
    – Contains entries for more than 11 million abstracts of scientific
    publications.
    – Enables user to do keyword searches, provides links to a selection of
    full articles, and has text mining capabilities, e.g. provides links to
    related articles, and GenBank entries, among others.
    – Efficient searching PubMed requires some skill. For example, 18
    searching with a keyword “interleukin” returns 108,366 matches.
    The OMIM (Online Mendelian
    Inheritance in Man)

    – Online Mendelian Inheritance in Man (OMIM) is a


    database that catalogues all the known diseases with a
    genetic component, and when possible links them to the
    relevant genes in the human genome and provides
    references for further research and tools for genomic
    analysis of a catalogued gene.
    • Genes and genetic disorders
    • Edited by team at Johns Hopkins
    • Updated daily
    Searching OMIM
    • Search Fields
    – Name of trait, e.g., hypertension
    – Cytogenetic location, e.g., 1p31.6
    – Inheritance, e.g., autosomal dominant
    – Gene, e.g., coagulation factor VIII

    20
    OMIM search tags

    All Fields [ALL]


    Allelic Variant [AV] or [VAR]
    Chromosome [CH] or [CHR]
    Clinical Synopsis [CS] or [CLIN]
    Gene Map [GM] or [MAP]
    Gene Name [GN] or [GENE]
    Reference [RE] or [REF]

    21
    Start working: Tarea

    Open: UniprotKB
    Search for nitrogen fixing genes

    How many genes are they?


    How many have been reviewed?
    Categorize the genes into types/function.

    22
    What is Google Scholar?

    Enables you to search specifically for scholarly


    literature, including peer-reviewed papers, theses,
    books, preprints, abstracts and technical reports from
    all broad areas of research.

    23
    What other DATA can we retrieve from the record?

    24
    There are approximately
    286,730,369,256 sequence
    records in the traditional
    GenBank divisions as of 2011.
    EMBL: The Genome divisions
    http://www.ebi.ac.uk/genomes/

    Schizosaccharomyces pombe strain 972h- complete genome


    GOBASE: resource for organelle genomes

    http://megasun.bch.umontreal.ca/gobase/
    Single Nucleotide Polymorphisms
    (SNPs) Database
    Within a database, the format needs to be
    consistent.
    A SwissProt entry, in Fasta format:

    >sp|P01588|EPO_HUMAN ERYTHROPOIETIN PRECURSOR - Homo sapiens (Human).


    MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHCSLN
    E
    NITVPDTKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVDKA
    VSGLRSLTTLLRALGAQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACR
    TGDR
    Why Databases?

    • The purpose of databases is not merely to collect and


    organize data, but to allow intelligent data retrieval.
    • A query is a method to retrieve information from
    the database.
    • The organization of each record into predetermined
    fields, allows us to use queries on fields.
    Databases on the Internet
    • Biological databases often have web
    interfaces, which allow users to send queries to
    the databases.
    • Some databases can be accessed by different
    web servers, each offering a different interface.

    request query

    web page result

    User Web server Database server


    Database Download

    • Nearly all biological databases are available for


    download
    » As simple text (flat) files.

    • A local version of the database allows one


    greater freedom in processing the data.
    • Processing data in files requires some
    computer-programming skills.
    » PERL is an easy programming language that can be used for
    extraction and analysis of data from files.
    The “Perfect” Database
    1. Comprehensive, but easy to search.

    2. Annotated, but not “too annotated”.

    3. A simple, easy to understand structure.

    4. Cross-referenced.

    5. Minimum redundancy.

    6. Easy retrieval of data. 37


    Problems with General Sequence
    Databases
    • Databases that strive for encyclopedic completeness are now
    so huge as to be close to unmanageable.

    1. Redundancy (nothing ever goes out, correct or wrong).


    2. Inadequate sequence quality.
    – old sequences
    – partially annotated sequences
    – inconsistent & outdated annotations (submitter annotation)
    – error sequences, low-quality sequences
    – contaminations
    – anonymous sequence

    – Annotation and management of databases is therefore, very


    important

    38
    THE NCBI
    http://www.ncbi.nlm.nih.gov/
    http://www.ncbi.nlm.nih.gov/About/glance/organizational.html
    • National Center for Biotechnology Information.
    • The heart of bioinformatics.
    • It’s like an integrated library and resource portal for
    bioinformatics databases data analysis.
    • Houses the following:
    – Genome sequencing data
    • In GenBank.
    – An index of biomedical research articles
    • In PubMed Central and PubMed.
    – Other information relevant to biotechnology.
    – All these databases are available online through the Entrez
    search engine.
    Database Resource Portals

    • ExPASy is a bioinformatics resource portal.


    • Operated by the Swiss Institute of Bioinformatics (SIB).
    – Particularly the SIB Web Team.
    • It is an extensible and integrative portal accessing many
    scientific resources, databases and software tools.
    Database Resource Portals
    Submitting Information to Databases
    • You can submit your sequences to respective
    databases through their sequence submission
    interfaces:
    – DNA sequence data
    – Protein sequence data
    – Proteomics data
    – Microarray data
    – Protein 3D structures
    – Etc.
    Submitting Information to Databases
    Submitting Information to Databases
    END

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