Introduction to Entrez The Life Science Search Engine

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Introduction toEntrez The Life Science Search
Engine

• Helen Hed
• Umeå universitetsbibliotek
• http//www.ub.umu.se/tjanste/hehe/

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Contents

• An overview of Entrez
• From a librarians point of view
• The databases in Entrez
• Contents and relationships
• Short presentation of each database
• The individual databases (and PubMed)
• From data to literature or the other way
  around?
• Exercises and other useful resources

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PubMed

• Help-text on searching PubMed
• Relevant literature is indexed in PubMed if it
  has to do with data in any of the Entrez
  databases.

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Everything is linked to PubMed?

• All entries in all of the Entrez databases are
  connected to relevant entries in PubMed
• If there is one or more articles in PubMed about
  data that is to be found in one of the Entrez
  databases - these are linked to relevant data
  entries in the databases

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Relationship between Entrez databases
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Entrez portal

• Portal to all NCBI genome related resources
  including PubMed
• A search here will show how info on a subject is
  available in all or some of the separate databases

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Bookshelf

• 50 e-books are available from the PubMed
  starting page (mars 2006)
• 5 are different handbooks and guides to using
  Entrez
• Some are textbooks that are used here at Umeå
  University
• Alberts Mol Biol of the Cell (4th ed)
• Griffith Introd to Genetic Analysis (7th ed)

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Genes and Disease

• Information about genetic diseases
• an e-book
• Available from NCBIs Bookshelf
• Find the book in the booklist
• Search for the disease you need information about
• Organised by type of disease and by chromosome

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example
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OMIM

• Online Mendelian Inheritance in Man
• A database with information about human genes,
  genetic diceases and phenotypes
• Links to nucleotide, protein, structure and
  genome.
• Now also OMIA animals
• Info about OMIA

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OMIM - exemple

• A search for diabetes will give 500 hits in
  OMIM
• Click on rekord number -gt full record is
  displayed with a table of contents and links out
  in the blue field
• Also link to clinical synopsis
• And to gene map

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• Table of contents - in this case for the record
  about diabetes in the previous slide
• Headings are dependent on available information

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OMIM example SOD

• This is the entry for SOD1 (147450)
• means gene with known sequence
• Information about symbols and numbering system
  and morehttp//www.ncbi.nlm.nih.gov/entrez/query.
  fcgi?dbOMIM
• Notice that table of contents does not have
  identical headings for all entries.

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OMIM Help and FAQs

• http//www.ncbi.nlm.nih.gov/Omim/omimhelp.html
• http//www.ncbi.nlm.nih.gov/Omim/omimfaq.html
• There is a help-file or FAQ-file for all the
  databases
• Can be found in the table of contents on the left
  side of the screen

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Map viewer organism map

• Search for organism and find the right chromosome
• Graphical view http//www.ncbi.nlm.nih.gov/mapview
  /MVgraph.html?
• FAQ at http//www.ncbi.nlm.nih.gov/mapview/static/
  MapViewerHelp.html

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Genbank - Nucleotide

• Database of nucleotide sequences from 130 000
  organisms
• Gathered from DDBJ (DNA Data Bank of Japan), EMBL
  (European Molecular Biology Laboratory), and NCBI
  (National Center for Biotechnology Information).
• Updated daily
• Example of a sequence document

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Nucleotide

• Contains data about nucleotide sequences (both
  DNA and RNA) from different databases. The
  biggest is Genbank.
• In every sequence document there are references
  to the article where the sequence was first
  presented.
• Genetic code scheme. Translation from DNA
  molecule to amino acid.
• Amino acid abbreviations.

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Nucleotide - search example

• Enter name of protein (and maybe more search
  terms) for which you want to know the nucleotide
  sequence
• myelin AND homo sapiens
• Gives 1400 hits in the database
• RefSeq 170
• RefSeq the best non-redundant and
  comprehensive collection of naturally occurring
  DNA, RNA, and protein molecules for major
  organisms

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RefSeq accession numbers

• Curated sequences
• RefSeq accession numbers can be distinguished
  from GenBank accessions by their prefix distinct
  format of 2 charactersunderbar. For example,
  the RefSeq protein accession number for citrate
  synthase is NP_015325.
• Each sequence has a unique statusPredicted,
  provisional, reviewd, validated, et c.
  http//www.ncbi.nlm.nih.gov/RefSeq/key.html

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Part of list describing accession formats
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Nucleotide example cont.

• Enter accession number - NM_021694
• Will produce a single hit in the database
• Click on accession number
• Displays the complete record
• At the end of this record you will find the amino
  acid sequence translated part of gene and the
  DNA sequence

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Reports

• Different formats in which the information is
  available

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Links

• How many links depends on how much data exists
  and in what dbs
• Wellstudied sequences have many links other can
  have very few

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Search result display of

• Hits are sorted into groups
• All ReSeq are collected in one of the lists
• http//www.ncbi.nlm.nih.gov/RefSeq/

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Protein

• Contains protein sequence data collected from
  different databases.
• In every sequence document there is a reference
  to the article where the discovery of the
  sequence was decribed.

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Protein - example

• Myoglobin
• This search will retrieve all entries about
  myoglobin
• Myoglobin AND humanorg will return hits
  predominantly from human genome

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Example - myoglobin

• Reports different formats available
• Links Blink, conserved domains et c

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Structure

• Contains visalization possibilities for
  3D-representation of structures
• For viewing the structures you need a plug-in
  that can be downloaded for free (Cn3D)

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Example - Azurin

• 53 hits
• click on the link above the short description or
  on MMDB new page where 3D structure of the
  molecule can be viewed.
• Tutorial and software
• http//www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.sh
  tml

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Changing database

• From Nucleotide database to Protein database
• In the complete record - find CDS protein ID -
  NP_067726.3 -gt
• By clicking on the link we will move from the
  nucleotide database to the protein database

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Genome

• Contains data on the nucleotide sequences that
  constitutes a whole genome.
• There are both whole chromosomes and pieces of
  chromosomes from about 800 different organisms
• Gives a graphical overview of genomes and
  chromosomes (called sequence maps).

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Genome - cont

• Limit search to one species by
• Write species name in search box
• Enter the Limit organism
• Or for example
• Homoorganism

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Genome - cont

• Alternative entrypoints
• Choose organism group and type of genome in
  left-hand column 7 table of contents for the web
  page
• Example
• Eucaryota Genome
• Choose Homo sapiens
• Or choose Drosophila melanogaster

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Gene

• Search for genes that are defined in either the
  Nucleotide database or in Map Viewer.
• Search by
• Free text (human muscular dystrophy)
• Gene name (BRCA1sym)
• Chromosome number (YCHR AND humanORGN)
• EC number (1.9.3.1EC)
• etc

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Blast

• BLAST stands for Basic Local Alignment Search
  Tool http//www.ncbi.nlm.nih.gov/BLAST/
• A tool for comparing sequences
• Introduction to BLAST
• Blast program selection guide
• There is more than one version

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Practice excersises

• How many chromosomes does Anopheles gambiae have?
• Search for curated sequences (RefSeq) on actin
  mRNA for a mouse.
• Find a 3D picture of a stress protein.
• Search for documents on human albumin and find
  the information about who submitted the
  information.
• I dont know anything about porfyria but would
  like to know what it is. Is it heritable? And if
  so, on what chromosome is the gene for porphyria
  situated?

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Homework ?

• Renata C. Geer (2003) Entrez Making use of its
  power. Briefings in Bioinformatics, vol.4, no.2,
  pp.179-184.
• http//www.ncbi.nlm.nih.gov/entrez/query/static/he
  lp/entrez_tutorial_BIB.pdf

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Other ways of accessing data

• DDBJ (DNA Data Bank of Japan),
• EMBL (European Molecular Biology Laboratory)
  Ensembl very neat genome browser
• NCBI (National Center for Biotechnology
  Information) Entrez.
• These three are the largest
• They exchange data daily
• Most data end up in these

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Web resources

• Looking for an easy way to search for literature
• Google Scholar a new Google-tool with less junk
• Scirus specialized search engine
• OAIster searches digital archives (mostely free
  material)
• Use Google to find a definition Definegenetics