Transcript - Cal State LA - Instructional Web Server

Databases – especially for literature
June 19, 2007
Learning objectives:
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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
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National Center for Biotechnology Information (NCBI)
Databases outside of NCBI
Writing assignment
Today
Announcements
Picture taking during noon hour
 Due dates
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Tonight by midnight – Internship prefs to Ronnie
and me
 Thursday at beginning of class – hardcopy Life
Science Review workshop
 Julyx, x,x, x – writing assignment
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Writing assignment and internship preferences
are online at 2007 dropdown menu
Today
Schedule
Lecture on Lit Databases
 Workshop for Lit Databases
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Public domain bioinformatics
servers
Public Domain
Bioinformatics
Facilities
National Center
For Biotechnology
Information (NCBI)
United States
Databases
Analysis
Tools
European Bioinformatics
Institute (EBI)
United Kingdom
Databases
Analysis
Tools
Genome
Net
(KEGG & DDBJ)
Japan
Databases
Analysis
Tools
NCBI ENTREZ
A platform that provides access to and links to
databases with biological information
ENTREZ
PubMed
MedLine
GenBank
Protein Genomes
databases
NCBI Handbook
PopSet
Taxonomy
OMIM
Others!
NCBI ENTREZ
MedLine
OMIM
Literature Database
Database of human genes and genetic disorders
GenBank
Database of all publicly available DNA sequences
Protein
databases
Database of amino acid sequences from SwissProt, PIR, PRF,
PDB, and translations from annotated coding regions in
GenBank and RefSeq.
Genomes
Database of genomes from organisms and viruses
PopSet
Taxonomy
Database of DNA sequences that have been collected to
analyze the evolutionary relatedness of a population.
Database of names of organisms with sequences in GenBank or PIR
Literature Databases
At NCBI
 http://www.ncbi.nlm.nih.gov/Literature/
CSULA Library
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BIOSIS
Melvyl (Books at UC Libraries)
Other molecular life science databases
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Science Direct
Pub Med Central*
Free Medical Journals
LinkOut Journals
Wiley InterScience
Medline databases (the part the
“user” doesn’t see)
Handbook on PubMed/Medline
Medline Developer Tools
Record-describes a publication
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Journal article
Book
Book chapter
Meeting abstract
Records are subdivided into fields
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Author
Title
Publication Name
Language
Each field has a two-letter (or more) label associated with it. This label
tags the field.
Medline Database
Producer:
National Library of Med
Database size:
>14 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
MEDLINE Sample Record
Garbo GM, et al. In vivo and in vitro photodyna...[PMID:9796439]
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.
[email protected] (Authors’ address)
LA - eng (Language)
ID - CA 65561/CA/NCI
PT - Journal Article (Publication type)
CY - UNITED STATES (Country of Publication)
TA - Photochem Photobiol
JC - P69
JID - 0376425
RN - 0 (Deuteroporphyrins) (CAS Registry No. or EC No.)
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.
MH - Tumor Cells, Cultured
EDAT- 1998/10/31 03:03
MHDA- 1998/10/31 03:03
PST – ppublish (print publication)
SO - Photochem Photobiol 1998 Oct;68(4):561-8. (Source)
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.
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
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
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http://www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.html
Be sure to use the menu at left, and complete at least:
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Using PubMed
My NCBI
For each menu item, use “next” arrow to progress through the tutorial.
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You will automatically be moved from tab to tab.
We will confirm that the next two items have been completed in class on
Thursday.
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Set up a My NCBI account to keep a running tab on your favorite subject
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Make at least one of your NCBI weekly searches relevant to your internship.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.My_NC
BI
Subscribe to NCBI newsletter
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http://www.ncbi.nih.gov/About/newsletter.html