Browsing through
Biology & Medicine
Paul R Earl
Sistemas e Informática
Universidad Autónoma de Nuevo León
San Nicolás, NL, 66451, Mexico
pearl@dsi.uanl.mx
What do HTTP and WWW mean ?
WEB BROWSERS were developed around 1991 by Tim Berners-Lee.
WorldWideWeb (WWW) was the first. To browse is to look up or
search for. Web browsers communicate with Web servers primarily
using HTTP (hypertext transfer protocol) to fetch webpages. HTTP
allows Web browsers to give information to Web servers as well as
fetch Web pages from servers. HTTP/1.1 is commonly used. Pages are
located by means of a URL (uniform resource locator). The file format
for a Web page is usually HTML (hypertext markup language) and is
identified in the HTTP protocol using a MIME content type. MIMEs are
multipurpose internet extensions as used in email (electronic mail).
Popular Browsers
WorldWideWeb, February 26, 1991
Mosaic, April 22, 1993
Netscape Navigator, 1994
Netscape Communicator, October 13, 1994
Internet Explorer, August 1995
Opera, 1996
Safari, January 7, 2003 (Apple = Mac)
Mozilla Firefox, November 9, 2004
The Browser Inventor
An Oxford graduate, Tim Berners-Lee holds the 3Com
Founders chair and is a Senior Research Scientist at the
Laboratory for Computer Science and Artificial
Intelligence (CSAIL) at the Massachusetts Institute of
Technology (MIT).
He is codirector of the new Web Science Research Initiative (WSRI) and is
a professor in the Computer Science Department at the University of
Southampton, UK. He directs the World Wide Web Consortium, founded
in 1994
In 1989 he invented the World Wide Web, an internet-based hypermedia
initiative for global information sharing while at CERN, the European
Particle Physics Laboratory. In 2004 he was knighted by Queen Elizabeth.
He wrote Weaving the Web with Mark Fischetti, (Harper, San
Francisco,1997).
Browse Subjects
Agricultural & Biological Sciences
Arts & Humanities
Biochemistry, Genetics & Molecular Biology
Business, Management & Accounting
Chemical Engineering
Chemistry
Computer Science
Decision Sciences
Earth & Planetary Sciences
Economics, Econometrics & Finance
Energy
Engineering
Publication Types of PubMed
The publication type limit will restrict your search
based on the type of material the article
represents, such as:
Clinical Trial
Editorial
Letter
Meta-Analysis
Practice Guideline
Randomized Controlled Trial
Review
The complete list of publication types is available
under the Limits Type of Article, More Publication
Types of PubMed. What is ToxNet ?
Biomedical Orientation
Pubmed
Leads to
Pubmed Central, MeSH and Entrez of the US health
system along with browsers like Stanford’s great HighWire
dominate biomedical searching. This is distant from the
demands of world commerce on the Internet, e. g.,
taxonomy is academic. HighWire will bring home free full
texts.
Sciuris, BIOSIS Previews, Biological Abstracts, CAB
Abstracts, Index of Organism Names, Open Helix, ZooBank
and the Zoological Record, while necessary for biomedical
and other subjects have little or no impact in business.
PubMed, available via the NCBI Entrez retrieval system, was
developed by the National Center for Biotechnology
Information (NCBI) at the US National Library of Medicine
(NLM), located at the US National Institutes of Health
(NIH). Entrez is the text-based search and retrieval system
used at NCBI for services including PubMed, Nucleotide and
Protein Sequences, Protein Structures, Complete Genomes,
Taxonomy, OMIM and others. LinkOut provides access to
full-text articles at journal Web.
See the fine article by Edwin Sequeira (2000) which is found
at:
http://www.cendi.gov/presentations/ref_link_sequera.ppt#
303,18,PubMed Central
MEDLINE is the NLM's premier bibliographic
database that contains references to journal articles
in the life sciences with a concentration on
biomedicine. A distinctive feature of MEDLINE is
that the records are indexed with NLM's Medical
Subject Headings (MeSH).
MeSH terms, publication types, GenBank accession
numbers and other indexing data are available and
displayed with the tag [PubMed - indexed for
MEDLINE]. See also the MEDLINE/PubMed
Resources Guide.
Chemical, Toxicological and Environmental Health Data
ChemIDplus Chemical Identification/Dictionary
HSDB
CCRIS
CPDB
GENETOX
IRIS
ITER
LactMed
TRI
TOXMAP
Haz-Map
Hazardous Substances Data Bank
Chemical Carcinogenesis Information
Carcinogenic Potency Database
Genetic Toxicology Data
Integrated Risk Information
International Toxicity Estimates for Risk
Drugs and Lactation Database
Toxics Release Inventory
Environmental Health e-Maps
Occupational Exposure/Toxicology
Household
Products
Health & Safety Information on Household Products
Your Dictionary
Seven Languages
English
French
German
Italian
Japanese
Spanish
Russian
Yahoo! Fish Babel does translations, and many
other translation programs are available.
Using the Boolean Operators AND,
OR and NOT
Many many people browse without the so
logical algebra of George Boole (1814-1864),
and that’s OK. Next: What does binary
mean?
It means a state of 2 like on-off,
man:woman, False:True. Most browsers are
binary.
Addition x+y, multiplication xy and negation -x, have their
counterparts in the algebra created by George Boole (18151864) by 1854 as the Boolean operations OR, AND and NOT
respectively, also called disjunction x∨y, conjunction x∧y, and
negation ¬x.
Conjunction x∧y behaves on 0 and 1 as multiplication does for
ordinary algebra. If either x or y is 0 then so is x∧y, but if both
are 1 then so is x∧y.
Disjunction x∨y works almost like addition with 0∨0 = 0 and
(1∨0 = 0∨1 = 1). However, there is a difference: 1∨1 is 1 not 2.
This difference is written x∨y to be (x+y-xy, not simply x+y).
Complement is defined arithmetically as ¬x = 1−x.
The values of x∧y, x∨y, and ¬x are expressed
in this truth table...
x
0
1
0
1
y
0
0
1
1
x∧yx∨y
0 0
0 1
0 1
1 1
X ¬x
0 1
1 0
The 3 Venn diagrams below represent respectively conjunction x∧y,
disjunction x∨y, and complement ¬x.
Venn diagrams use circles to visually represent Boolean search results.
We have A, B, both and B-A.
You should know that your search results depend on
Boolean analysis.
Addition x+y, multiplication xy and negation -x, have their
counterparts in the algebra created by George Boole (1815-1864) by
1854 as the Boolean operations OR, AND and NOT which are
disjunction x∨y, conjunction x∧y, and negation ¬x.
Conjunction x∧y behaves on 0 and 1 exactly as multiplication does
for ordinary algebra: if either x or y is 0 then so is x∧y, but if both
are 1 then so is x∧y.
Disjunction x∨y works almost like addition with 0∨0 = 0 and 1∨0 =
0∨1 = 1. However there is a difference: 1∨1 is not 2 but 1. This
difference is written x∨y to be x+y-xy, not simply x+y.
Complement can be defined arithmetically as ¬x = 1−x.
Doublequotes are used to combine space-separated
words into a single search term.
Use upper case for the operators !
Check on this.
A space is used to specify logical AND, as it is the
default operator for joining search terms.
"Search term 1" "Search term 2"
The OR
keyword is used for logical OR:
"Search term 1" OR "Search term 2"
The
minus sign is used for logical NOT (AND NOT):
"Search term 1" -"Search term 2"
Let us review what the Boolean
terms mean.
For any
system, there must be initial
assumptions or postulates that
the system follows.
Final Remarks
The main communication problem is
jargon. Shoptalk with names for newly
invented products may only be
understood by a certain group of people.
One objective of this lecture is to cut
through jargon. This lecture could be
much enhanced if you feed back terms
and other suggestions in the field of
information retrieval.