Literature survey
using web sites
Contents
2.1 The World Wide Web
2.2 Internet connection
2.3 How to view a website.
2.4 Copying and downloading information
3.1 Using PubMed (MEDLINE)
3.1.1 PubMed Searching
3.1.2 MeSH Browser
3.2 Using Science Citation Index
3.3 Current Contents
3.4 Electronic journals on net a source of full text articles
3.4.1 Examples of some electronic journals
3.5 Search Engines
3.5.1 Some good search engines for scientific topics
3.6 Current awareness services
Internet can be very useful in literature survey for a research project, it becomes more important in Pakistan as in Pakistan libraries are few and not a single is of such standard that it can be used for literature survey. In libraries journals are few and are not regular, so Internet is a better alternative.
Even if libraries are good use of Internet is still better as computer searches for you in seconds what you can search manually, using printed journals in days. Internet provides many other facilities like databases and software to be used in research project.
The word wide web and Internet were developed in 1960s by U.S. Department of Defense to ensure continuity of communication during a war. The original work was done by the Advance Research Project Agency, and the network was known as ARPAnet. Later on, academic institutions saw this is a wonder full war for researchers to communicate and so they started to connect their computers to this international network or “internet”.
To use Internet you need an Internet connection. You can get it from an ISP Internet service provider. A telephone line and a modem; which connects your computer to telephone line. Deciding to use the service of which ISP can be difficult as some ISPs have slow speed or disconnection problem, which increases your telephone bill as one local call is charged whenever you connect to your ISP. A common tip in this regard is to use the connection of new companies, as load on their server would be less, which results in a better service.
You can chose a package provided by your ISP, which suits your needs. The flat rate Internet hours are about Rs. 25 / and night packages are about Rs 10. Unlimited accounts range from 1000 to 3000.
2.3 - How to view a
website.
To use Internet you also need some software like Internet Explorer or Netscape. The programs can be installed from a program CD. To go to a Web page, type the Internet address - for example, www.microsoft.com—in the Address bar, and then click the Go button. To return to the last page you viewed, click the Back button. To view a page you viewed before clicking the Back button, click the Forward button. If a page you are trying to view is taking too long to open, click the Stop button. If you get a message that a Web page cannot be displayed, or you want to make sure you have the latest version of the page, click the Refresh button. When you start typing a frequently used Web address in the Address bar, a list of similar addresses appears that you can choose from. And if a Web-page address is wrong, Internet Explorer can search for similar addresses to try to find a match.
You can also type common names or words, and Internet Explorer can automatically take you to the site that most likely matches what you are searching for, and list other likely sites as well. Browse through a list of Web pages you recently visited by clicking the History button on the toolbar. In addition you can rearrange or search the History list.
Sometimes, the time needed to load Web documents can be so long that Web browsing turns into a test for patience. However, you can use more than one browser window at a time to fill your waiting time. Also, you may switch to "No-Graphics mode" because the loading of graphics usually takes most of the time, and you normally don't really need them at all.
When you find any thing interesting you can save it in several ways. Like click file and then save as this would save the web page or you can select the things and then right click it and click copy then you can paste it in any suitable program.
Whenever you click any thing downloadable a window appears asking to download the file at what position, it is recommended to save it on disk and scan it with any antivirus program if the file is not from reliable source. The down load speed is very important and it depends on many factors like your Internet connection, your modem and the traffic on the site from where you are downloading.
When full text of any article is available a number of formats may be encountered; the two main ones being HTML (hypertext markup language, used for formatting standard documents on the www), or in PDF (portable document format). HTML is problematic as the initial full text HTML document is mainly text with thumbnails, or small images, for graphics, tables, etc. to view these one normally has to click on the thumbnail link, which then loads the full image to a separate web page. When printing the document there are also many problems.
The other way is PDF format which displays the article, as it would appear is the printed journal. To view a PDF document you need the Adobe Acrobat Reader, available free from http://www.adobe.com Adobe Acrobat provides viewing and printing facilities but no editing (you can select text and graphics from a PDF file and paste it else ware)
3.1 - Using PubMed (MEDLINE)
Pubmed is the best search facility for scientific literature on Internet, and the best thing about PubMed is that it is free. PubMed was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). It has the data of 11 million publications, going back to 1966. the PubMed is updated weekly for new publications. It contains also the abstracts of articles if available, the articles are from 3900 journals.
PubMed is the best option for searching of scientific literature as it is free, it is largest database for scientific literature, it provides MeSH browser facility to specify the terminology to be used for searching, as in life sciences several terminologies are available for the same thing, and it provides links to databases of DNA and protein sequences.
3.1.1 - PubMed Searching
PubMed searching is easy, just enter search terms in the query box, and press the Enter Go or click Go. The features bar directly beneath the query box provides access to additional search options. The PubMed query box and Features bar are available from every screen, so you don't need to return to the homepage to enter a new search. You may enter one or more terms (e.g., growth hormone gene duplication) in the query box and PubMed automatically combines (ANDs) i.e. it would search for all the articles containing the terms growth and hormones and gene and duplication. If your search includes Boolean operators AND, OR, NOT, they must be in upper case, e.g., growth AND hormone Once you click Go, PubMed will display your search results. http://www.ncbi.nlm.nih.gov/PubMed/
The list of search results is shown you can click to any to see its abstract, each search result has a link to related articles, related books and some may have a link to the site from where you can get the full text of that article.
To search by an author's name enter the name in the format of last name plus initials (no punctuation), e.g., smith ja, jones k. PubMed automatically truncates the author's name to account for varying initials and designations such as Jr. or 2nd. A name entered using this format will search in the author field. If only the author's last name is entered, PubMed searches the name in All Fields. You can also search by journal title.
MeSH (Medical Subject Headings) is NLM's controlled vocabulary. It is used to index citations primarily to reflect subject content. PubMed's MeSH Browser is available on PubMed's sidebar menu. This Browser helps you find MeSH terms that you may want to select and use in your searches. The Browser provides information about each term and displays them in a hierarchical structure. Further information about PubMed can be found at
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
The science citation index (SCI) is a multidisciplinary database of bibliographic information produced by the institute for scientific information (ISI). It provides an important search enhancement to the literature that can be obtained from the MEDLINE database, particularly for basic science journals not included in MEDLINE. Subject coverage in SCI includes all scientific disciplines. Approximately 5600 of the world’s leading journals are covered by SCI. about 70% of the articles contain author generated abstracts. Further information can be obtained from http://www.isinet.com/
SCI on the web of sciences does not have the sophisticated search capabilities of PubMed MEDLINE. This is mainly because of SCI`s lack of controlled vocabulary, like MeSH, for the indexing of articles. Nor does SCI on the web of science have the convenient link to molecular and genetic databases like PubMed. Use of SCI on web of science is not free as PubMed. Access will be available only to users in institutions that have subscribed to the service. The home page of SCI web of science is http://webofscience.com/ from where you can get information about the use of this service and how to search.
Current Contents (CC) is a current awareness service provided by the ISI. It provides the table of contents from more than 7000 journals and 2000 books and conference proceedings. Whereas the print version provides only the table of contents, electronic version provides full bibliographic information for each article as well as author generated abstract when available.
Current Contents is available on net as Current Contents Connect (CCC). The service is not free and you have to subscribe, details of how to subscribe and to search using CCC can be found on http://www.isicc.com/
Access to full text of journals is an emerging phenomenon, lot of possibilities con be encountered like. Some journals provide free full text of all the articles published for example journals available on pubmed site. Some journals provide free full text of articles published at least one year ago for example JBC www.jbc.org Most of the journals provide online full text if you subscribe for there printed version for example hundreds of journals published by Springer
Some journals provide free full text of some selected articles for example journal of molecular endocrinology www.journals.endocrinology.org Nearly all the journals provide free contents, free search for any publication and free abstracts.
As the concept of on line journals developed in last few years, all the above stated facilities are for publications printed since early 1990s or late 1980s.
Pricing for full text access is a major issue, and it varies greatly from journal to journal, or publisher to publisher. Purchasing access is normally afford able and feasible to larger organizations like academic institutions. Home pages of journals can still be a good source of abstracts and full texts even if you do not subscribe.
Nature, Nature Genetics, Nature Medicine, Nature Biotechnology etc are available on internet http://www.nature.com/ . These are available free to individuals who subscribe for paper printed journal.
Science http://www.sciencemag.org is available full text on internet to individual subscribers for an additional $12. This permits the user to access the full text on a single computer workstation. For institutions the price is $25 per computer.
The Proceeding of the national academy of science (PNAS) http://www.pnas.org requires a subscription fee on top of the paper subscription. PNAS is one of the many basic medical science journals made available through the Highwire Press http://www.highwire.stanford.edu
EMBO Journal is also accessible from the Highwire site and is currently free for paper subscribers.
Journal of Biological Chemistry (JBC) http://www.jbc.org was one of the first journals, which provided full text on Internet. The good thing is that it provides full text of articles from 1980 to Articles published at least one year ago.
An individual paper subscription to cell http://www.cell.com/ provides free access to electronic version; institutions have to pay a fee in addition to paper subscription
BMJ provides free full text access www.bmj.com
Web is more like an 'information labyrinth' than a structured electronic library. But you can find almost any word hidden somewhere in this labyrinth by using search engines that store the content of the Web and make it searchable. Use of search engines for scientific information is a simple way to get the desired information. A useful tip for searching through search engines is to use commas at the ends of your topic e.g. if you are looking for growth hormone gene and you write this in the search box of your search engine, the engine would show all the sites about hormone and about growth and about gene. But using commas i.e. “growth hormone gene” would result into only those sites, which have a topic growth hormone gene.
Many Web users rapidly click on the first link that looks interesting, and don't take their time to carefully evaluate a page before selecting the next link. Also, it has been found that the links on the top of the page get selected much more often, because people are reluctant to scroll down. If you avoid this behavior, you will find the Web much more useful.
A creature of Digital Equipment Corporation. In "Advanced Query" you can search documents containing several words joined by AND, OR, NOT, NEAR Boolean operators The result of the search is a list of hyperlinks with short abstract for each document, so it's quite easy to estimate which of found documents may be useful to you. http://altavista.digital.com/
This search engine uses so-called fuzzy AND strategy which combines both AND and OR options when searching for group of words. It does not support "pure" Boolean operators
Lycos, Inc
It claims to be the biggest on the Net. Lycos enables to search for a single word or words joined by Boolean operators AND and OR, and also NOT option but cannot search for a phrase. It returns a list of hyperlinks to found documents with a short abstract for each of them
Infoseek can look for a word, group of words or a phrase. When performing the search, it takes into account different word Forms (such as singular and plural forms). Infoseek returns a list of hyperlinks with a short abstract for each found document http://guide.infoseek.com/
This search engine is not good for finding scientific information. Instead, it is the best place if you're looking for general information in the Internet. http://www.yahoo.com/
The above search engines are one of the several you can find on net.
3.6 -
Current awareness services
Several alerting services are available on Internet, which provide tables of contents of the printed journals, through email. The largest of such service is ISI TOC but it is not free.
The ISI Tables of Contents Corporate Alerting Service (ISI TOC) is a service provided by the institute of scientific information. The user subscribes, selects from approximately 8000 journals in ISI data base, and receives the table of contents with author abstracts (when available), all through electronic mail. Further information can be found at http://www.isinet.com/prodserve/ias/ac.html
Other free alternative can be that several journals provide free alerting service. You have to go to the site of your desired journal, and see if they provide the facility or not. Some times you can find several journals alerting services at the same site, if those journals are published by the same organization.
The awareness services enable researchers to stay aware of what so ever is published, of their interest. Some journals for example British medical journal provides a service; that you specify the topic of your interest and they will notify you through email when ever they will purplish some thing which match your interests
Email can be an easy way to contact other scientists, to obtain any information about their project and to request for offprint of their published article. I had a very good experience and all those scientists replied in 2 or 3 days to whom I contacted. The email addresses can be found with full text of articles or in the abstracts the institute of the author is given. go to the site of that institute and find about that person.
In addition to research articles, one may needs some protein and DNA sequence information. This is most conveniently achieved by using Internet.
There are several softwares, which can be very useful to analyze results of a research; such softwares can be downloaded freely from Internet.
5.1 - Publicly Available Tools and Databases on
the web.
Since the early days of DNA and protein sequencing, such information has been deposited in computer databases. With the expansion of www these databases came on web. The freedom of information act played a major role in the spread of such information on web. Some of the tools and databases are.
BLAST i.e. basic local alignment search tool. Is developed by NCBI and it can compare a DNA or amino acid query sequence with database sequences. www.ncbi.nlm.nih.gov/BLAST
Xprimer is a web based primer design package for more information go to http://alice.med.umn.edu/webprimers
The chromosomal location of complete human genome can be found at http://www.ncbi.nlm.nih.gov/genemap this web site contains data on all chromosomes
The online Mendalian inheritance in man contains information on 10,000 diseases that are linked with particular genes http://www3.ncbi.nlm.nih.gov/omim
Genome of different species have been sequenced, the data can be found at http://www.ncbi.nlm.nih.gov/Entrez/Genome.org.html
For proteins some large databases are 1) the protein information resource http://pir.georgetown.edu 2) SWISS-PORTÒ http://www.expasy.ch/prosite 3) OWL
http://www.biochem.ucl.ac.uk/bsm/dbbrowser/OWL/OWL.html
Free data analysis software is common in the sciences, for example FastA, BLAST, Clustal, MFOLD, PHYLIP, Paup, CAP, are a few. But often these programs lack ease of use and integration with other functions. Commercial software developers have incorporated such algorithms, along with their own, and added a much greater usability and integration, to allow you to analyze your data without spending of time learning how to run the programs. For scientists with limited budgets, students and teachers, free software is often the only choice. You can also find unique programs that do things no commercial package does.
Free software for biosciences has been most widely available through the Internet, since distribution that way is free (from cost and time)
Two commonly used archives of molecular biology software are IUBio Archive, at Indiana University, and the European Bioinformatics Institute (EBI) software archive. Internet resource locators (URLs) for these are.
EBI at http://www.ebi.ac.uk/ or ftp://ftp.ebi.ac.uk/
IUBio at http or ftp://iubio.bio.indiana.edu/
Once on your computer, the steps of installing and configuring free software range from easy to trying. Instructions are usually included, but are not always detailed enough. Further information about free software can be found at http://iubio.bio.indiana.edu/soft/molbio/Listings.html this site contains details of about 150 softwares
Some of the important softwares are as follow.
Clustal sequence alignment ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW
Entrez to search genome data ftp://ncbi.nlm.nih.gov/
NIH Image for image analysis http://www.scioncorp.com/
PHYLIP for phylogeny analyses ftp://evolution.genetics.washington.edu/
RasMol for molecular modeling ftp://ftp.dcs.ed.ac.uk/pub/rasmol/
SeqPup for sequence editing http://iubio.bio.indiana.edu/soft/molbio/seqpup/
Last update 23 January 2002
Institute of biochemistry and biotechnology
University of the Punjab Lahore Pakistan