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 - VIII, you'll find links to these in the Indexes &
Abstracts list on the Library website.
Bioinformatics & Computational
Biology Resource Guide - http://instr.iastate.libguides.com/bcb
Includes most of the resources listed on this guide. 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!)
- 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 (Note: The
interface for PubMed is being redesigned; the tabs may go away. Can use
Advanced Search for some of these functions.)
- Recommend using Boolean operators,
AND, OR, NOT. Must be in capital letters!
- Sample Search: (swine
OR pigs) AND (meat OR pork) AND quality AND genetics
- Click on author name
for "AbstractPlus" view.
- Publisher-provided
links to full-text and "Get it@ISU"
- 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 " field tags" ->Search Field Descriptions
and Tags
- Affiliation tag [AD];
Journal title [TA]; Unique Identifier [PMID]
- 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
- PubMed Bookshelf: collection
biomedical and basic science textbooks.
- My NCBI: can set up searches
to run automatically and have results emailed to you
- Journals Database: locate
complete journal titles from abbreviations and vice versa
- Single Citation Matcher: locate
journals with incomplete citations
IV. Biosis Previews (part
of the Web of Knowledge)
-
Comprehensive
life sciences database
-
Includes some
conference proceedings, meeting reports, and patents.
-
Covers much of
the same literature as MEDLINE. However, this is definitely worth searching
if you're working in plant biology, and evolution/systematics.
- Coverage: 1926 - present
V. CAB Abstracts (part
of the Web of Knowledge)
- 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.
- Coverage: 1910 - present
VI. Web of Science (part
of the Web of Knowledge)
- Provides access to the ISI Citation
Indexes: Science Citation Index, Social Sciences Citation Index, Arts &
Humanities Citation Index
- Science Citation Index: Over 7,100
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
1900 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.
VII. SciFinder Scholar (More information:
http://www.lib.iastate.edu/collections/db/scifnd2007.html)
- 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.
- The ISU subscription allows for
8 simultaneous users.
VIII. Computer Engineering Resources
(More information: Electrical
& Computer Engineering Resources guide &
Computer Science
Resources Guide
- 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. 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.
- Useful links available from
the homepage
X. 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]
XI. OMIM
XII.
Other Resources
XIV. Getting Started with RSS
Feeds: http://www.public.iastate.edu/~adinkelm/RSS_Feeds_August_2009.pdf
Questions? Contact Andrea Dinkelman, Email: adinkelm@iastate.edu
Homepage: http://www.public.iastate.edu/~adinkelm/homepage.html