Introduction of NCBI overview

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Introduction of  NCBI (overview)

• ???
• ???

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National Center for Biotechnology information

• ?????????
• ?????????
• ???????

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U.S. National Library of Medicine ?????????
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?????????
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?????????

• Health information
• Library services
• Research programs
• New and noteworthy
• General information

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National Institutes of Health (NIH)???????
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???????
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???????

• Health information
• Grants and funding opportunities(???????)
• News
• Scientific resources(????)
• Institutes, Centers and offices(????)

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?????Bioinformatics
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What is Bioinformatics

• ?????????????????????--??????????????????????????,
  ?????????????????????????????????????,????????
  ?????????????????,??????????,?????????????????????
  ??????????????????????,?????????????????,?????????
  ??????????????

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Bio-information of DNA

• Sequence submission(????)
• Sequence alignments(????)
• Motifs and Patterns(???????)
• Genes, Exons and Introns(?????)
• Promoters, Transcription-factor binding
  sites(???????)

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Bio-information of RNA

• Secondary structure(????)
• RNA-specifying genes, Motifs(????)

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Bio-information of Proteins

• Sequence alignment(????)
• Motifs, Patterns, and Profiles (????)

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Overview of Bio-information

• Information network(??)
• Protein information resources(????????)
• Genome information resources (????????)
• DNA sequence analysis(??????)

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Overview of Bio-information

• Pairwise alignment techniques(????)
• Multiple sequence alignment(????????)
• Building a sequence search protocol(?????????)
• Analysis packages(????)

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Computational Molecular Biology

• ???????
• Finding genes(????)
• Predicting structures or functions(?????????)
• Clustering (????)
• Alignments(????)

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• NCBI ??
• http//www.ncbi.nlm.nih.gov/

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NCBI ??
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NCBI ??

• National Center for Biotechnology information

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NCBI???

• NCBI(National Center for Biotechnology
  Information,????????)?1998?11?4???,????? Claude
  Pepper??????????????????????,????????NCBI,????????
  ???(NIH)????????(NLM)?NLM??????????????,?????NIH??
  ??,????????????????????,???????????????????????

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Internet

• NCBI??????,????????????,???????????????????,??????
  ???????,?????????

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NCBI ???

• NCBI???1988?,??????????????,?????????????,????????
  ????????????,????????????????????????????????????
  ?????,??????????????

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NCBI ????????

• ????,??????????????????????????
• ??????? (NIH) ???????????????????
• ??????????????????????????
• ??????? (NIH) ???????,?????????????????????????

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NCBI ????????

• 5. ???????????????????????????????
• 6. ???????????????????????????????
• 7. ?????????????????????????????

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?????

• NCBI??????????,???????????????????????????????????
  ???,?????????????????????????????????????,???????,
  ???????????????????????????????,??????????,???????
  ????????????????????????

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?????

• ??????????????????????????????????(domains)??????
  ?????????????????????HIV ?????????????????????????
  ????????????(multiple sequence alignment)?????????
  ????(non-redundant)???????????????????????????????
  ??vector models???, NCBI ?????????????????????????
  ?????

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????

• NCBI?????????????,????????????????????????????????
  ???????????????????,???????????????????????,?NCBI
  RefSeq ????mRNAs???????????RefSeq
  ?mRNAs??????????????????????,NCBI?????????????????
  ??????,??????????????????????,??????????????????

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?????

• ??????????????????????,?????????????,????????,????
  ?????????????????,NCBI?????????????????????????,??
  ??????????????????,????????????????????????

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NCBI ??
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???????????
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Part 1
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Contents of part I

• PubMed
• Entrez
• BLAST
• OMIM
• Books
• TaxBrowser
• Structure

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NCBI ??
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PubMed
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PubMed

• ??NCBI?Entrez retrieval system?????
• ?NCBI?????????????
• ????????????????

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PubMed

• PubMed?????????????
• ?? LinkOut ??????????
• PubMed ????????????????

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PubMed

• ??????????????,???
• 1960???????????????
• ?12000000?????????????
• ????????????????

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http//www.ncbi.nlm.nih.gov/entrez/query/static/he
lp/pmhelp.htmlIndex

• PubMed Help
• ??web site???????

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PubMed Help
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http//www.ncbi.nlm.nih.gov/entrez/query/static/ov
erview.html

• PubMed Overview
• ??web site???PubMed??

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PubMed Overview
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NCBI ??
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Entrez
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Entrez

• ???????
• Entrez ? NCBI ????????,????????????????????????,
  ???????????????
• Entrez ?????????????????Entrez????????????????????
  ?????????
• NCBI ???????????GenBank???????

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Entrez??????

• Entrez is the text based search and retrieval
  system used at NCBI for all major databases
  including PubMed, Nucleotide, and Protein
  Sequences, Protein Structures, Complete Genomes,
  Taxonomy, OMIM and many others. 

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?????

• PubMed The biomedical literature (PubMed)
• Nucleotide sequence database (GenBank)
• Protein sequence database
• Structure three-dimensional macromolecular
  structures
• Genome complete genome assemblies
• PopSet population study data sets

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?????

• OMIM Online Mendelian Inheritance in Man
• Taxonomy organisms in GenBank
• Books BookShelf online books
• ProbeSet gene expression and microarray datasets
• 3D Domains domains from Entrez Structure
• UniSTS markers and mapping data

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?????

• SNP single nucleotide polymorphisms
• CDD conserved domains
• Journals journals in Entrez
• UniGene gene-oriented clusters of transcript
  sequences
• PMC full-text digital archive of life sciences
  journal literature
• NCBI Web Site NCBI Web site search

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????????
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Entrez Help Document

• http//www.ncbi.nlm.nih.gov/entrez/query/static/he
  lp/helpdoc.html
• ??web site???????

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Entrez Help Document
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NCBI ??
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BLAST

• Basic Local Alignment Search Tool

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BLAST

• Basic Local Alignment Search Tool
• Similarity search programs
• Available for all DNA or Protein sequence
• Heuristic algorithm(?????)
• Opposed to global (???????)

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BLAST

• BALST????NCBI????--????????????,????????????????BA
  LST???DNA?????????????,??15 ?????

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BLAST

• ?NCBI??????????Open Reading Frame Finder (ORF
  Finder)??????????(Electronic PCR)??????? Sequin
  ? BankIt NCBI??????????????? WWW ? ??FTP??,
  NCBI??????????????????????????????????

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BLAST
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BLAST

• Nucleotide BLAST searches allow one to input
  nucleotide sequences and compare these against
  other nucleotides.
• Protein BLAST allows one to input protein
  sequences and compare these against other protein
  sequences.

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BLAST
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Translating BLAST

• Translating BLAST searches translate either query
  sequences or databases from nucleotides to
  proteins so that protein - nucleotide sequences
  can be performed.

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(No Transcript)
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Pairwise BLAST

• BLAST 2 sequences
• Pairwise BLAST performs a comparison between two
  sequences using the BLAST algorithm. Not that the
  program considers a "Sequence 1" to be the Query
  sequence and "Sequence 2" to be the Subject
  sequence.

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QBLAST

• New queuing system (????)
• Format results
• Reducing connect to NCBI simultaneously
• RIDs will be available for 24 Hours (Records
  Identifications).

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NCBIs BLAST services

• WWW BLAST(NCBI home page)
• Standalone BLAST(local BLAST)
• Network BLAST(Blastc13, batch search)
• BLAST URL API(application program interface)

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NCBI ??
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OMIM

• Online Mendelian Inheritance in Man

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OMIM

• OMIM is now incorporated into NCBI's Entrez
  system and can be queried using the same approach
  as the other Entrez databases such as PubMed and
  GenBank.

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OMIM

• Online Mendelian Inheritance in Man (OMIM) is a
  catalog of human genes and genetic disorders,
  with links to literature references, sequence
  records, maps, and related databases.
• Mendelian Inheritance in Man. The online version
  is updated daily. The OMIM FAQs provide
  additional information about the book and the
  online database.

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OMIM

• OMIM ??????,???????????????,?????????????????
• OMIM ??????????,????????????????,\
• OMIM??????????(?????)?

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OMIM

• ????????????????,??????????????????,??????????????
  ??,??????????????????????,?????OMIM?PubMed(NCBI???
  ????)???

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OMIM
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OMIM

• This database is a catalog of human genes and
  genetic disorders authored and edited by Dr.
  Victor A. McKusick and his colleagues at Johns
  Hopkins and elsewhere, and developed for the
  World Wide Web by the National Center for
  Biotechnology Information.
• The database contains textual information and
  references. It also contains copious links to
  MEDLINE and sequence records in the Entrez
  system, and links to additional related resources
  at NCBI and elsewhere.

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OMIM

• NOTE OMIM is intended for use primarily by
  physicians and other professionals concerned with
  genetic disorders, by genetics researchers, and
  by advanced students in science and medicine.
• The OMIM database is open to the public, users
  seeking information about a personal medical or
  genetic condition are urged to consult with a
  qualified physician for diagnosis and for answers
  to personal questions.

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OMIM help

• http//www.ncbi.nlm.nih.gov/entrez/Omim/omimhelp.h
  tml
• ??web site???????

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OMIM help
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NCBI ??
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Books
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Books

• Collaboration with authors and publishers, the
  National Center for Biotechnology Information
  (NCBI) is adapting biomedical books for the web.

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The books may be accessed in two ways

• Searched directly using any search term or phrase
  (in the same way as the bibliographic database
  PubMed)
• Each PubMed abstract has a "Books" button that
  displays a facsimile of the abstract, in which
  some phrases are hypertext links. Clicking on a
  hyperlinked results in a list of books in which
  the phrase is found

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Books

• Majority of the links are between the books and
  PubMed.
• In the future, more links will be made between
  the books and other types of information, such as
  gene and protein sequences and macromolecular
  structures.

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NCBI ??
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Taxonomy browser

• New scientific data can improve our understanding
  of the relationship among organisms.
• The classification found in the NCBI/GenBank
  taxonomy database will occasionally change to
  incorporate new systematic schemes. Some of the
  recent changes to our classification system are
  discussed

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Taxonomy browser
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????????
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NCBI ??
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Structure

• Maintains MMDB, a database of macromolecular 3D
  structures, as well as tools for their
  visualization and comparative analysis.
• MMDB, the Molecular Modeling Database, contains
  experimentally determined biopolymer structures
  obtained from the Protein Data Bank

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Structure
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MMDB

• NCBI's Entrez includes a database of
  experimentally determined three-dimensional
  biomolecular structures.
• Most 3D-structure data are obtained from X-ray
  crystallography and NMR-spectroscopy they
  provide a wealth of information on the biological
  function, on mechanisms linked to the function,
  and on the evolutionary history of and
  relationships between macromolecules.

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MMDB

• Our goals in adding structure data to Entrez are
  to make this information easily accessible to
  biologists, and to facilitate comparative
  analysis involving 3-D structure.

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• Text searches in MMDB (use the search toolbar at
  the top of this page) will yield Structure Query
  pages, providing access to entries which matched
  the keywords. Structure Summary pages for
  one/several/all of these may be retrieved.

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Cn3D
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Cn3D
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Cn3D ???????????3D??
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????????

• PubMed
• Entrez
• BLAST
• OMIM
• Books
• TaxBrowser
• Structure