Databases

1
Databases especially for literature June 17,
2008

• Learning objectives
• Become aware of the general arrangement of
  biological data in the public databases.
• Be able to retrieve information on a particular
  subject in the literature.
• Databases
• National Center for Biotechnology Information
  (NCBI)
• Databases outside of NCBI
• Writing assignment

2
Today

• Announcements
• Due dates
• Wed, 9 AM, email inclass and homework from
  Molecular Life Science Review
• Friday PM know whether you prefer the patent or
  primary article writing assignment

3
Today

• Schedule
• Finish last part of Molecular Life Science
  review
• Heme binding domain in sickle and wt
• Homologies in evolutionary and structural/function
  al sense
• vs. in ClustalW
• Lecture on Lit Databases
• Workshop for Lit Databases

4
Who . . .

• Has used PubMed?
• Has done a search using PubMed
• Has NCBI report to them weekly on new articles
  regarding a specific topic?
• Has published an article in a journal listed on
  PubMed?

5
Some public domain bioinformatics servers
Public Domain Bioinformatics Facilities
Genome Net (KEGG DDBJ) Japan
European Bioinformatics Institute (EBI) United
Kingdom
National Center For Biotechnology Information
(NCBI) United States
Databases
Analysis Tools
Databases
Analysis Tools
Databases
Analysis Tools
Kyoto Encyclopedia of Genes and Genomes DNA Data
Bank of Japan
6
NCBI ENTREZ

• A platform that provides access to and links to
  databases with biological information

ENTREZ
PubMed
Others!
Genomes
PopSet
Protein databases
GenBank
MedLine

• NCBI Handbook

Yellow Databases
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NCBI ENTREZ
MedLine
Literature Database
OMIM
Database of human genes and genetic disorders
GenBank
Database of all publicly available DNA sequences
Database of amino acid sequences from SwissProt,
PIR, PRF, PDB, and translations from annotated
coding regions in GenBank and RefSeq.
Protein databases
Database of genomes from organisms and viruses
Genomes
Database of DNA sequences that have been
collected to analyze the evolutionary relatedness
of a population.
PopSet
Taxonomy
Database of names of organisms with sequences in
GenBank or PIR
8
Literature Databases

• At NCBI
• http//www.ncbi.nlm.nih.gov/Literature/
• CSULA Library
• Melvyl (Books at UC Libraries)
• Other molecular life science databases
• Science Direct
• Pub Med Central
• Free Medical Journals
• LinkOut Journals
• Wiley InterScience

9
Medline Database

• Producer National Library of Med
• Database size gt14 million references
• Publications Indexed More than 4500 journals
• Years Covered 1966-present
• Update Frequency Daily
• Index Medicus, Index to Dental Literature, and
  International Nursing Index
• Papers in press are available

10
Medline databases (the part the user doesnt
see)

• Handbook on PubMed/Medline
• Medline Developer Tools
• Record-describes a publication
• Journal article
• Book
• Book chapter
• Meeting abstract
• Records are subdivided into fields
• Author
• Title
• Publication Name
• Language
• Each field has a two-letter (or more) label
  associated with it. This label tags the field.

11
MEDLINE Sample Record

• Garbo GM, et al. In vivo and in vitro
  photodyna...PMID9796439
• UI - 99012531 (Unique Identifier)
• PMID- 9796439 (PubMedIdentifier)
• DA - 19981130
• DCOM- 19981130 (Date completed)
• LR - 20010323
• IS - 0031-8655 (International Standard
  Serial Number)
• VI - 68
• IP - 4
• DP - 1998 Oct (Date of Publication)
• TI - In vivo and in vitro photodynamic
  studies with benzochlorin iminium salts . . .
  (Title)
• PG - 561-8
• AB - Benzochlorin iminium salts (BIs) are
  hydrophobic photosensitizers based on
• an octaethylbenzochlorin nucleus that
  absorb in the near-IR region of the . . .
• AD - Division of Surgical Oncology,
  University of Louisville, KY 40202, USA.
• gmgarb0I_at_pdt.bcc.louisville.edu
  (Authors address)
• LA - eng (Language)
• ID - CA 65561/CA/NCI

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MEDLINE Sample Record

• SB - IM (Subset)
• MH - Adenocarcinoma/drug therapy (Medical
  Subject Heading)
• MH - Animal
• MH - Cell Survival/drug effects/radiation
  effects
• MH - Deuteroporphyrins/therapeutic
  use/toxicity
• MH - Drug Carriers
• MH - Emulsions
• MH - Female
• MH - Fibrosarcoma
• MH - Imines/therapeutic use/toxicity
• MH - Leukemia L1210
• MH - Light
• MH - Mammary Neoplasms, Experimental/drug
  therapy
• MH - Mice
• MH - Mice, Inbred C3H
• MH - Neoplasms, Radiation-Induced
• MH - Photochemotherapy
• MH - Photosensitizing Agents/therapeutic
  use/toxicity
• MH - Support, U.S. Gov't, P.H.S.

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Medical Subject Headings (MeSH)

• MeSH is NLM's controlled vocabulary used for
  indexing articles for MEDLINE. MeSH terminology
  provides a consistent way to retrieve information
  that may use different terminology for the same
  concepts.
• Who has published?

14
OMIM-Online Mendelian Inheritance in Man

• A catalog of human genes linked to diseases
• Started by Victor A. McKusick at Johns Hopkins
  University
• A good place to start when you want to research a
  certain disease or biological molecule associated
  with a disease.
• This database is cross-referenced to PubMed and
  other NCBI-based databases

15
In-Class Assignment

• Before beginning this assignment, decide on a
  molecular topic in which you are interested and
  keep it in mind as you work through the
  tutorials.
• Complete the PubMed tutorial, starting at
• http//www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.h
  tml
• Be sure to use the menu at left, and complete at
  least
• Using PubMed
• My NCBI
• For each menu item, use next arrow to progress
  through the tutorial.
• You will automatically be moved from tab to tab.
• We will confirm that the next two items have been
  completed in class on Thursday.
• Set up a My NCBI account to keep a running tab on
  your favorite subject
• Make at least one of your NCBI weekly searches
  relevant to your internship.
• http//www.ncbi.nlm.nih.gov/books/bv.fcgi?ridhelp
  pubmed.section.pubmedhelp.My_NCBI
• Bring up you r My NCBI page, print scrreen to a
  word document, print it out, and hand in..
• Subscribe to NCBI newsletter
• http//www.ncbi.nih.gov/About/newsletter.html
• Copy me on your email request.