Literature survey in biotechnology

GUIDED BY: DR.D.MANJULAKUMARI

PROFESSOR,DEPT.OF BIOTECHNOLOGYBANGALORE UNIVERSITY

BENGALURU

PRESENTED BY:

JYOTHI.R RESEARCH SCHOLAR

DEPT.OF BIOTECHNOLOGY BANGALORE UNIVERSITY

BENGALURU

LITERATURE SURVEY

WHAT IS LITERATURE ?

Literature is a term used to describe anything from creative writing to more technical or scientific works, but the term is most commonly used to refer the works of the creative imagination, including works poetry,drama,fiction,and nonfiction.

TYPES OF LITERATURE

PRIMAR

Y

PRIMARY LITERATURE

• Primary literature is the first hand information provided by the researcher which includes analysis of data collected in the field or the laboratory in the form of a research article.

• It is very current and specialized.

Examples:• Research articles • Dissertations and thesis• Technical reports• Conference proceedings

SECONDARY LITERATURE

• The secondary literature summarizes the primary literature. It is both broader and less current than the primary literature.

• Since most information sources in the secondary literature contain exhaustive bibliographies, they can be useful for finding more information on a particular topic.

Examples:• Monographs (books dealing with a specific area of

research in the sciences)• Literature reviews (or review articles)

TERTIARY LITERATURE

• The tertiary literature deals with broad, discipline-level topics in the sciences (like biochemistry or evolution) and can be a useful starting point when looking for background information on a research topic.

• The tertiary literature primarily reports very well-established facts in the scientific literature.

Examples :• Encyclopedias• Textbooks• Handbooks

GREY LITERATURE

• Grey literature is generally defined as academic literature that is not formally published.

• It is an expanding field in library and information science that deals with the supply and demand side of publications not controlled by commercial publishing.

WHAT IS A LITERATURE SURVEY/REVIEW?

A literature survey or review is a text of a

scholarly paper, which includes the current knowledge including substantive findings, as well as theoretical and methodological contributions to a particular topic.

TYPES OF REVIEW

SYSTEMATIC REVIEW

META ANALYTICAL REVIEW

DESCRIPTIVE REVIEW

1. DESCRIPTIVE REVIEW

It involves three main categories: Observation case studies

surveys

2.SYSTEMATIC REVIEW

• It is also called as structured literature review(SLR)

• It is focused on a research question that tries to identify, appraise, select and synthesize all high quality research evidence relevant to that question.

• It is not limited to medicine and is quite common in all other sciences where data are collected, published in the literature, and an assessment of methodological quality for a precisely defined subject would be helpful.

3.META-ANALYTIC REVIEW

• A form of systematic review (reductive)• Takes findings from several studies on the same

subject and analyzes them using standardized statistical procedures

• Integrates findings from a large body of quantitative findings to enhance under-standing (study=unit of analysis)

• Draws conclusions and detect patterns and relationships.

PURPOSE OF LITERATURE SURVEY?

1. Provide a context for the research 2. Justify the research 3. Ensure it is not just a "replication study” 4. Show where the research fits into the existing

body of knowledge 5. Enable the researcher to learn from previous

theory on the subject

6. Illustrate how the subject has been studied previously

7. Shows gaps in previous research 8. Show that the work is adding to the

understanding and knowledge of the field 9. Help refine, refocus or even change the topic 10. Highlight flaws in previous research

WHAT IS A JOURNAL?

• A Journal is a periodical publication intended for the progress in science,literature,economics etc. usually with a report of new research.

• The history of scientific journals dates from 1665, when the French Journal des scavans and the English Philosophical Transactions of the Royal Society first began systematically publishing research results.

TYPES OF JOURNALS

ACADEMIC/SCHOLARLY JOURNALS

TRADE JOURNALS

POPULAR MAGAZINES

CURRENT AFFAIRS/OPINION MAGAZINES

NEWSPAPERS

IMPACT FACTOR (IF)

• The Impact factor (IF) of an academic journal is a measure reflecting the average number of citations to recent articles published in that journal.

• It is frequently used as a proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones.

• It was devised by Eugene Garfield, the founder of the Institute for Scientific Information.

• It is calculated yearly starting from 1975 for those journals that are indexed in the Journal Citation Reports.

• Impact Factor calculation is an attempt to create a quantitative tool for evaluating journals.

• It represents the frequency with which the "average article" in a journal has been cited in a given period of time.

For example:• If there are 100 papers published in a journal in 2009-2010

and there are 100 citations of articles from this journal in 2011 the Impact Factor'2011 is 1

(number of published articles/number of citations).

• Most journals have impact factors that are below 2. Journals with impact factors above 4 tend to be regarded as having a high impact factor, and those above 10 are stellar.

WHAT IS ABSTRACT?

• An abstract is a self-contained, short, and powerful statement that describes a larger work.

• Components vary according to discipline. An abstract of a scientific work may contain the scope, purpose, results, and contents of the work.

• It is not a review, nor does it evaluate the work being abstracted. While it contains key words found in the larger work.

• It is an original document rather than an excerpted passage.

• It allow readers who may be interested in a longer work to quickly decide whether it is worth their time to read it.

Example taken from the Journal of Biology, Volume 3, Issue 2

The hydrodynamics of dolphin drafting by Daniel Weihs, Faculty of Aerospace Engineering, Technion, Israel Institute of Technology, Haifa 32000, Israel. Abstract: Background Drafting in cetaceans is defined as the transfer of forces between individuals without actual physical

contact between them. This behaviour has long been surmised to explain how young dolphin calves keep up with their rapidly moving mothers. It has recently been observed that a significant number of calves become permanently separated from their mothers during chases by tuna vessels. A study of the hydrodynamics of drafting, initiated in mechanisms causing the separation of mothers and calves during fishing-related activities, is reported here.

Results Quantitative results are shown for the forces and moments around a pair of unequally sized dolphin-like slender bodies. These include two major effects. First, the so-called Bernoulli suction, which stems from the fact that the local pressure drops in areas of high speed, results in an attractive force between mother and calf. Second is the displacement effect, in which the motion of the mother causes the water in front to move forwards and radially outwards, and water behind the body to move forwards to replace the animal's mass. Thus, the calf can gain a 'free ride' in the forward-moving areas. Utilizing these effects, the neonate can gain up to 90% of the thrust needed to move alongside the mother at speeds of up to 2.4 m/s. A comparison with observations of eastern spinner dolphins (Stenella longirostris) is presented, showing savings of up to 60% in the thrust that calves require if they are to keep up with their mothers.

Conclusions A theoretical analysis, backed by observations of free-swimming dolphin schools, indicates that hydrodynamic interactions with mothers play an important role in enabling dolphin calves to keep up with rapidly moving adult school members.© 2004 Weihs; licensee BioMed Central Ltd.

TYPES OF ABSTRACT

DISCRIPTIVE

INFORMATIVE

CRITICAL

1. DESCRIPTIVE ABSTRACTS

• It indicates the type of information found in the work. • It makes no judgments about the work, nor does it

provide results or conclusions of the research. It does incorporate key words found in the text and may include the purpose, methods, and scope of the research.

• It describes the work being abstracted. Some people consider it an outline of the work, rather than a summary. Descriptive abstracts are usually very short 100 words or less.

2.INFORMATIVE ABSTRACTS

• The majority of abstracts are informative. • In this the writer presents and explains all the main

arguments and the important results and evidence in the complete article/paper/book.

• It includes the information that can be found in a descriptive abstract (purpose, methods, scope) but also includes the results and conclusions of the research and the recommendations of the author.

• It is rarely more than 10% of the length of the entire work.

3.CRITICAL ABSTRACT

• It is a critical evaluation of the document. • An abstractor evaluates the document and

often compares it with other works on the same subject.

• Critical abstract is a "condensed critical review."

INDEXING

 • Besides selection, the other main purpose of the abstract

is for indexing. Most article databases in the online catalog of the library enable you to search abstracts.

• Indexes provide subject, author, and/or title indexing to a particular set of periodicals and gives a full citation for each article. The citation includes the title of the periodical, date, volume, pages, as well as the author and title of the article.

USE OF COMPUTERS IN LITERATURE SURVEY

The Internet provides:• Access to a wealth of information on countless topics

contributed by people throughout the world.• A user has access to a wide variety of services such as vast

information sources, electronic mail, file transfer, interest group membership, interactive collaboration, multimedia displays, and more.

• It is a self-publishing medium• Anyone with little technical skills and access to a host

computer can publish on the Internet.

WHAT IS e-JOURNAL?

• An electronic journal is a periodical publication which is published in electronic format, usually on the Internet.

• Some of the advantages of these are: 1.We can search the contents pages and/or the full text of journals to find

articles on a certain subject.2.We can read journal articles on your desktop, you don't have to be in the

Library.3.We can e-mail articles to yourself or download them for printing.4.Hypertext links allow us to move to different sections within individual

journals or articles and can link to related resources on the Internet.5.Journals can include more images and audio-visual material.6.Journals can be interactive : we can e-mail to the author or editor with

comments.

EXAMPLES OF e-JOURNALS

• Title Applied Biochemistry and Biotechnology (Springer Link) Publisher Springer New YorkSubject: Applied Biochemistry and Biotechnology ISSN: 0273-2289 ; 1559-0291(E)

• Title Applied Microbiology and Biotechnology (Springer Link) Publisher SpringerSubject: Microbiology, BiotechnologyISSN: 0175-7598 ; 1432-0614(E)

e-BOOKS

• An electronic book is also called as e-book ,digital book, or even e-edition.

• It is a book-length publication in digital form, consisting of text, images, or both, readable on computers or other electronic devices.

•  Although sometimes it is defined as "an electronic version of a printed book", many e-books exist without any printed equivalent.

• Commercially produced and sold e-books are usually intended to be read on dedicated e-readers, however, almost any sophisticated electronic device that features a controllable viewing screen, including computers, tablets and smart phones can also be used to read e-books.

SEARCH ENGINES

• These are programs that search documents for specified keywords and returns a list of the documents where the keywords were found.

• It is really a general class of programs, however, the term is often used to specifically describe systems like Google, Bing and Yahoo!

• It enable users to search for documents on the World Wide Web.

• Some of the examples are as follows:

• Google- The search engine giant holds the first place in search with a stunning difference of 45% from second in place Bing. According to the latest report (October 2012) 69.5% of searches were powered by Google and 25% by Bing. Google is also dominating the mobile/tablet search engine market share with 89%.

• Bing – Bing is Microsoft’s attempt to challenge Google in the area of search but despite their efforts they still did not manage to convince users that their search engine can produce better results than Google.

• Yahoo – Since October 2011 Yahoo search is powered by Bing. Yahoo is still the most popular email provider and according to reports holds the third place in search.

• Ask.com – Formerly known as Ask Jeeves, Ask.com receives approximately 3% of the search share. ASK is based on a question/answer format where most questions are answered by other users or are in the form of polls. It also has the general search functionality but the results returned lack quality compared to Google or even Bing and Yahoo.

• AOL.com – According to net market share the old time famous AOL is still in the top 10 search engines with a market share that is close to 0.6%. The AOL network includes many popular web sites like engadget.com, techchrunch.com and the huffingtonpost.com.

• Blekko.com – Blekko.com was developed by ex-Googlers and they present themselves as the “spam free search engine”.  It is better suited for webmasters.

• Wolfram alpha – wolfram alpha  is different that all the other search engines. They market it as a Computational Knowledge Engine which can give you facts and data for a number of topics. It can do all sorts of calculations, for example if we enter  “mortgage 2000” as input it will calculate loan amount, interest paid etc. based on a number of assumptions.

• DuckDuckGo  – Has a number of advantages over the other search engines. It has a clean interface, it does not track users, it is not fully loaded with ads and has a number of very nice features (only one page of results, one can search directly other web sites etc).

• Way Back Machine – archive.org is the internet archive search engine. We can use it to find out how a web site looked since 1996. It is very useful tool if we want to trace the history of a domain and examine how it has changed over the years.

• ChaCha.com – According to alexa chacha.com is the 8th most popular search engine with a ranking position of 297 in the US. It is similar to ask.com where users can ask or answer a particular question. They also have a number of quizzes that can help you decide on a number of topics.

SCIENTIFIC SEARCH ENGINE

• OJOSE (Online Journal Search Engine) is a free powerful scientific search engine enabling us to make search-queries in different databases by using only 1 search field.

• It helps us to find, download or buy scientific publications (journals, articles, research reports, books, etc.) in up to 60 different databases.

DATABASES

• It is an organized collection of data. IMPORTANT BIOTECHNOLOGY DATABASES

• Primary nucleotide sequence databases International Nucleotide Sequence

Database(INSD) consists of the following databases.

• DNA Data Bank of Japan(National Institute of Genetics)

• EMBL (European Bioinformatics Institute)• GenBank (National Center for Biotechnology

Information)• These three databases are primary databases,

as they house original sequence data.

Meta databases These databases of databases collect data from different

sources and make them available in a new and more convenient form, or with an emphasis on a particular disease or organism.

BioGraph (University of Antwerp, Vlaams Instituut voor Biotechnologie) A knowledge discovery service based on the integration of more than 20 heterogeneous databases

Bioinformatic Harvester(Karlsruhe Institute of Technology) - Integrating 26 major protein/gene resources.

• Neuroscience Information Framework (University of California, San Diego) - Integrates

hundreds of neuroscience relevant resources, many are listed below.

• ConsensusPathDB - A molecular functional interaction database, integrating information from 12 other databases.

• Entrez (National Center for Biotechnology Information)

Genome databases These databases collect genome sequences, annotate and analyze them, and provide public access. Some curation of experimental literature to improve computed

annotations. These databases may hold many species genomes, or a single model organism genome.

Bioinformatics HarvesterGene Disease DatabaseSNPediaCAMERA Resource for microbial genomics and metagenomicsCorn, the Maize Genetics and Genomics Database

• Repbase:Repbase is the most commonly used database for repetitive elements (transposons).

• Saccharomyces Genome Database, genome of the yeast model organism.

• Viral Bioinformatics Resource Center Curated database containing annotated genome data for eleven virus families.

• The SEED platform for microbial genome analysis includes all complete microbial genomes, and most partial genomes. The platform is used to annotate microbial genomes using subsystems.

• Xenbase, genome of the model organism Xenopus tropicalis and Xenopus laevis

• Worm base, genome of the model organism Caenorhabditis elegans

• Zebrafish Information Network, genome of this fish model organism.

• TAIR, The Arabidopsis Information Resource.

Protein sequence databases• UniProt Universal Resource (EBI, Swiss Institute

of Bioinformatics, PIR)• Protein Information Resource (Georgetown

University Medical Center (GUMC))• Swiss-Prot Protein Knowledgebase (Swiss

Institute of Bioinformatics)• PEDANT Protein Extraction, Description and

Analysis Tool.

Proteomics databases Proteomics Identifications Database (PRIDE) A public

repository for proteomics data, containing protein and peptide identifications and their associated supporting evidence as well as details of post-translational modifications. (European Bioinformatics Institute)

Proteome Scout - A public repository of processed proteomics datasets concerning post-translational modifications, includes quantification across conditions (if applicable). Also includes a graphics exports of protein annotations.

• MitoMiner - A mitochondrial proteomics database integrating large-scale experimental datasets from mass spectrometry and GFP studies for 12 species. (MRC Mitochondrial Biology Unit)

• Gel Map - A public database of proteins identified on 2D gels (University of Hanover Proteomics Department)

Protein structure databases• Protein Data Bank (PDB) comprising:• Protein Databank in Europe (PDBe)• Protein Databank in Japan (PDBj)• Research Collaboratory for Structural

Bioinformatics (RCSB)

RNA databases• LncRNAWiki, a wiki-based database for

community curation of human long non-coding RNAs

• Rfam, a database of RNA families• miRBase, the microRNAdatabase• snoRNAdb, a database of snoRNAs• lncRNAdb, a database of lncRNAs

Carbohydrate structure databasesEuroCarbDB, A repository for both carbohydrate

sequences/structures and experimental data.Protein-protein and other molecular interactionsBIND Bio molecular Interaction Network DatabaseBioGRID A General Repository for Interaction

Datasets (Samuel Lunenfeld Research Institute)

Signal transduction pathway databasesCancer Cell MapNet path- A curated resource of signal

transduction pathways in humansNCI-Nature Pathway Interaction DatabaseReactome - Navigable map of human biological

pathways, ranging from metabolic processes to hormonal signaling.

Microarray databasesArray Express (European Bioinformatics

Institute)Gene Expression Omnibus (National Center for

Biotechnology Information)GPX(Scottish Centre for Genomic Technology

and Informatics)

• PCR and quantitative PCR primer databases• PathoOligoDB: A free QPCR oligo database for

pathogens• RTPrimerDB - a public primers and probes

database for real-time PCR reactions

Phenotype databasesPhenCodelinking human mutations with phenotypePhenomicDB multi-organism database linking

genotype to phenotypePHI-base Pathogen-host interaction database. It links

gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer reviewed literature.

Specialized databasesAntibody Central Antibody information database

and search resource.AntibodyRegistry.org assigns unique identifiers used

to track antibody reagents in published literature.Bgee Bgee is a database to retrieve and compare

gene expression patterns between species.BIOMOVIE movies related to biology and

biotechnology

Taxonomic databases• Catalogue of Life source databases• Encyclopedia of Life• Integrated Taxonomic Information System• EzTaxon-e, database for the identification of

prokaryotes based on 16S ribosomal RNA gene sequences

Metabolomic DatabasesMetaboLightsHuman Metabolome Database (HMDB)Yeast Metabolome Database (YMDB)E. coli Metabolome Database (ECMDB)

PUBMED

• Pub Med is a service of the US National Library of Medicine®

• It Provides free access to MEDLINE®, the NLM® database of indexed citations and abstracts to medical, nursing, dental, veterinary, health care, and preclinical sciences journal articles

• It Includes additional selected life sciences journals not in MEDLINE

• Adds new citations daily.

• It Was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM)

• Pub Med features include: 1.A "See Related Citations" feature to get

articles that are similar to a given article 2.LinkOut®links to full-text articles on

participating publishers' Web sites

• Provides quality control in scientific publishing. Only journals that meet Pub Med's scientific standards are indexed.

• In addition to MEDLINE, Pub Med provides access to older references from the print version of Index Medicus back to 1951 and earlier.

• References to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science, BMJ, and Annals of Surgery;

• very recent entries to records for an article before it is indexed with Medical Subject Headings (MeSH) and added to MEDLINE.

PMC

Pub Med Central® (PMC) is a free archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM).

• In keeping with NLM’s legislative mandate to collect and preserve the biomedical literature, PMC serves as a digital counterpart to NLM’s extensive print journal collection.

• PMC was Launched in February 2000 and is managed by NLM’s National Center for Biotechnology Information (NCBI).

• As an archive, PMC is designed to provide permanent access to all of its content, even as technology evolves and current digital literature formats potentially become obsolete.

• NLM believes that the best way to ensure the accessibility and viability of digital material over time is through consistent and active use of the archive. For this reason, free access to all of its journal literature is a core principle of PMC.

• PMC is a repository for journal literature deposited by participating publishers, as well as for author manuscripts that have been submitted in compliance with the Public Access Policy mandated by NIH and similar policies of other research funding agencies.

• PMC is not a publisher and does not publish journal articles itself.

• NLM is collaborating internationally with other agencies that share the goals of PMC.

• Maintaining copies of PMC’s literature in other reliable international archives that operate on the same principles provides greater protection against damage or loss of the material.

• At the same time, the diversity of sites allows for the possibility of more and even greater innovation, ensuring the permanence of PMC over the long-term.

BOOKSHELF

• Bookshelf is a full-text electronic literature resource of books and documents in life sciences and health care provided by the National Center for Biotechnology Information (NCBI) within the National Library of Medicine (NLM) and complements the other biomedical literature resources at NCBI, including Pub Med and Pub Med Central (PMC).

• Bookshelf titles are of varied publication types and topics, and includes public domain works as well as works the copyright holders of which have granted NCBI permission for distribution.

• Bookshelf includes textbooks, monographs, health reports, documentation, website content and databases, covering genetics to advanced molecular biology, health care, health policy, health care evidence reports, clinical guidelines and health care policy analysis.

VIRTUAL LIBRARY

• Virtual library/digital library/digital repository• Focused collection of literature material stored

as electronic media formats that can include1.Text Material 2.Audio material3.Video material • It allows, for organizing, storing, and retrieving the

files and media contained in the library collection.

• "The World Wide Web Virtual Library was the first index of content on the World Wide Web.

• It was started by Tim Berners-Lee, the creator of HTML and the Web itself, in 1991 at CERN in Geneva."  (Wikipedia, 2005c)

COMPONENTS OF A VIRTUAL LIBRARY

INFRASTRUCTURE

DIGITAL COLLECTION

SYSTEMS FUNCTION

VIRTUAL LIBRARY

ADVANTAGES DISADVANTAGES

1. Immediate access to resources. 1. Restricted by copyright law.

2. Information updated immediately. 2. Requires connectivity

3. No physical boundaries. 3.Skilled professionals are required.

4. Support different learning styles. 4. Increased number of resources challenges student selection.

5. Accessible for the disabled. 5.Power consumption

6. Information retrieval:provides user-friendly interfaces

6.Interface design

7. Storage of information 7.Training and development

8. Networking capabilities 8.Equity of access

WEB HOSTING

• Web hosting is a hosting arrangement in which a web host (often an internet service provider) maintains clients websites on its computers and provides related services.

• The services may include leasing of hard disk space, maintenance of hardware and software, provision of backup and security, content integrity, 

credit card processing, email boxes, and high-speed internet connection.

TYPES OF WEB

HOSTING

FREEHOSTING

SHARED/VIRTUALHOSTING

DEDICATEDHOSTING

COLLOCATEDHOSTING

DIFFERENCES BETWEEN TYPESOF HOSTING

FREE HOSTING SHARED HOSTING DEDICATED HOSTING

COLLOCATEDHOSTING

It's free. Low cost. Cost is shared with others.

Expensive ,Good for large business.

Expensive, High bandwidth

Free email is often an option.

Good for small business and average traffic

Good for high traffic High security

Good for family, hobby or personal sites.

Multiple software options.

Multiple domain names.

High up time

Own domain name. Powerful email and data base solutions.

Unlimited software options

CONCLUSIONLiterature survey can be a best tool for updation of knowledge!

REFERENCEShttp://akaleidoscopicworld.blogspot.in/2008/03/advantages-disadvantages-of-virtual.htmlhttp://bangaloreuniversity.ac.in/e-resources/http://en.wikipedia.org/wiki/Journalhttp://en.wikipedia.org/wiki/Abstract_%28summary%29http://vlib.org/admin/AboutVLhttp://en.wikipedia.org/wiki/Web_hosting_service