Provide an overview of major
research literature databases useful in bioinformatics research.
Provide a brief overview of RSS
feeds and how to use them as a current awareness tool.
Note: For the resources discussed
in sections I - IX, you'll find links to these in the Indexes &
Abstracts list on the Library website.
NEW!!! Bioinformatics &
Computational Biology Resource Guide - http://ref.iastate.libguides.com/bcb
Includes most of the resources listed on this guide. This will be updated
periodically. You may also suggest resources to add to the guide.
I. MEDLINE
database
- Produced by the National Library
of Medicine
- Indexes the health sciences and
life sciences literature
II. PubMed http://www.ncbi.nlm.nih.gov/sites/entrez?otool=usiaslib
- Freely available version of
MEDLINE (your Federal tax dollars at work!)
- PubMed vs. PubMed Central - PubMed Central
is a free full-text archive of biomedical and life sciences journal
literature.
- Access PubMed (ISU affiliate version)
from the library's website. By doing so, you will see the
button in every
PubMed record. "Get
it@ISU" quickly links you to full-text articles if available.
- View photographs of NLM's
various computers from the 1960s to the present at: http://www.nlm.nih.gov/news/history_nlm_computerroom.pdf
III. Using PubMed
- For additional information:
- Search Tips
- Most functionalities accessed
through tabs
- Recommend using Boolean operators,
AND, OR, NOT. Must be in capital letters!
- Sample Search: (honeybee
OR bees OR honey bees OR Apis mellifera) AND gene expression
- Click on author name
for "AbstractPlus" view.
- Publisher-provided
links to full-text and "Get it@ISU"
- Look at "Medline"
display view to look at the complete database record with fields.
- Limits Tab and Field Tags
- Can limit a search by various
parameters, e.g. dates, review articles, language, etc.
- Field tags can be very useful.
For example,
- signal transduction AND
cell vs.
- signal transduction AND
cell [TA]
- Complete list of tags available
in the "Help" document. Search "tags" ->Search Field Descriptions and
Tags
- Affiliation tag [AD];
Journal title [TA]; Unique Identifier [PMID]
- Preview/Index Tab
- Displays an alphabetical list
of words and phrases present in MEDLINE, along with their frequency
- Useful for identifying synonyms
and related terms, e.g. RNAi
- History and Clipboard tabs
- History: provides review of
previous searches
- Allows "set-based" searching
- Clipboard: Allows you to store
a set of results for a short period of time. Can email or save results
to a text file. Click checkbox for records of interest, then use "Send
To" command -> Clipboard. Then you can email, create text, file, etc,
from the clipboard.
- MeSH (Medical Subject Headings)
- Controlled vocabulary terms
that are assigned by indexers. To view MeSH headings for PubMed records,
switch to "Citation" view.
- Other Features
- Journals Database: locate
complete journal titles from abbreviations and vice versa
- Single Citation Matcher: locate
journals with incomplete citations
- My NCBI: can set up searches
to run automatically and have results emailed to you
- PubMed Bookshelf: collection
biomedical and basic science textbooks.
IV. Biosis Previews
(part of the Web of
Knowledge)
V. CAB Abstracts
- Strong in agriculture, plant science,
animal science, and veterinary medicine. It
is the most comprehensive resource for all of these subject areas.
- Covers many international
publications.
- The ISU subscription allows for
8 simultaneous users.
- Coverage: 1910 - present
VI. SciFinder
Scholar
- Searches Chemical Abstracts and
MEDLINE
- Important resource for some
areas of bioinformatics research, e.g. proteomics, protein folding, mass
spectrometry analysis, sequencing technologies.
- Useful for patent
searching.
- Requires downloading software to
your desktop the first time you use it. Note: A web-based version is coming
soon!
- The ISU subscription allows for
8 simultaneous users.
VII. Web of Science
(part of the Web of
Knowledge)
- Web of Science
- Provides access to the ISI
Citation Indexes: Science Citation Index, Social Sciences Citation Index,
Arts & Humanities Citation Index
- Science Citation Index: Approximately
5,900 covered journals
- Publications are selected
for inclusion in Web of Science based on the following criteria. For more
information, visit: http://scientific.thomson.com/knowtrend/essays/selectionofmaterial/journalselection/
(Note: Newer journals may/may not be included.)
- ISU subscription goes back
to 1945 for the Science Citation Index.
- Can search by topic or do
cited reference searching
- A cited reference search
tells you who has cited the article since it was published, so you
can search forward in time.
VIII. Computer Engineering
Resources
- Computer and Information Systems
Abstracts - provides broad coverage of journal articles and conference papers
dealing with computer and network technology and their applications, as well
as developments in theoretical computer science. Coverage is from 1981 -
present.
- Computer Science Index - Covers
academic journal articles, professional publications, and other reference
sources in computer science at a scholarly/technical level. The collection
indexes more than 6,500 periodicals and books, with material back to the
1960s.
- Compendex - includes
engineering-related journals, conference proceedings, and technical reports.
Coverage is from 1884 - present. Indexes Lecture Notes in Computer
Science.
- IEEE Xplore - provides full-text
online access to publications of the Institute of Electrical and Electronics
Engineers (IEEE) and the Institution of Electrical Engineers (IEE). Contains
full-text proceedings from IEEE Symposium on Computational Intelligence in
Bioinformatics and Computational Biology; IEEE Symposium on
Bioinformatics and Bioengineering as well as others. Most IEEE
publications should be indexed in Compendex.
- ACM Digital Library -
publications of the Association for Computing Machinery
IX. Other Parks Library
Resources
X. National Center for Biotechnology
Information (NCBI) - http://www.ncbi.nlm.nih.gov/
- Created in 1988 as a part of the
National Library of Medicine at the National Institutes of Health
- What does the NCBI
do?
•NCBI accepts submissions of
primary data (e.g. GenBank). Original research data submitted by
researchers.
•NCBI develops tools to analyze these data. (e.g.
BLAST)
•NCBI uses these tools to create derivative databases based on the
primary data (e.g Refseq). Content controlled by a third party.
•NCBI
provides free searching, linking, and retrieval of these data, primarily
through the Entrez system.
- Types of databases by level of
curation http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/Databases/databases_curation.html
- Useful links available from
the homepage
XI. Genomic
Biology Resources -
many organism specific resources available
- Entrez Gene - http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
- database of genes that provides
a "gene-based" view of information
- records include chromosomal
map, Gene Ontology classifications, RefSeq records, GeneRIFs (gene references
into function, links to PubMed records)
- Examples: zea mays [orgn] AND
sugary1; HD [sym] AND human [ORGN]
XII. OMIM
XIII.
Other Resources
XIV. Getting Started with RSS
Feeds
http://www.public.iastate.edu/~adinkelm/RSS_Feeds_August_2008.pdf
XV. Suggested Reading
1. PLoS Comput Biol. 2005
Dec;1(7):e76.
Time to organize the bioinformatics resourceome.
Cannata N, Merelli E, Altman RB.
PMID:
16738704
Article: http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010076&ct=1
2. Nucleic Acids Research
- 2008 Database
Issue & 2008 Web
Server Issue - The database
issue and web server issue is published yearly. A good place to learn about
new databases.
3. J Biomed Discov Collab. 2007 Feb 12;2:1.
Biological information specialists for biological informatics.
Heidorn PB, Palmer CL, Wright D.
PMID: 17295920
Article: http://www.j-biomed-discovery.com/content/2/1/1
4. bio1NF0RM: 10th Anniversary Special Issue - Interviews with 6 bioinformatics
researchers.
http://www.genomeweb.com/pdfs/BioInform10thAnniv.pdf
Questions? Contact Andrea Dinkelman, Assistant Professor and Science &
Technology Librarian
Email: adinkelm@iastate.edu
Homepage: http://www.public.iastate.edu/~adinkelm/homepage.html