Literature SearchingBiochemical Engineers

Lynne Meehan Room 314, UCL Science LibraryEmail : l.meehan@ucl.ac.uk ☎: 020 7679 2634

Literature searching

Carrying out literature searches takes time. Developing your information skills will help you to produce literature reviews faster and to a higher standard.

It is possible to “speed up” the searching process by using consistent, structured approach as well as by making use of alerting services and “saved searches”

You can improve your standard of your review by including material from a broad range of information sources, including those with which you are less familiar.

Sources of Information (or where to look for your assignment)

Assignment Search engine (e.g. Google)

Wikipedia Library Catalogue

Database

Writing a short assignment

- Look for news items on climate change - Google Scholar

An overview of your topic

Find a book on climate change that you can use

Look for references to journal articles if you had time to do it.

Writing a long assignment

- Look for news items on climate change - Google Scholar- Finding organisations linked to climate- Political policies relating to climate change

- An overview of your topic- Suggested keywords you can use when searching the database's.

- Find a book on climate change that you can use - Possibly find conference papers

You might try using a database of journal articles to look for what research there has been over the last few years into climate change.

Tracking progress

It's a good idea to keep a list of which resources you plan to use, where you're going to look for information and what you're going to look for. Keep some sort of diary, journal or log book to track the progress of your thinking and learning. In the diary you may want to record details of:

Places you have looked or need to look Useful search terms Contacts who can help you with one aspect or another of your work Decisions you

are making as you go along e.g. when particular bits of information have caused you to shift your thinking

Things that didn't work out e.g. search terms that were too broad

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Types of Information

Type of Information Useful for ExamplesJournalsUsually published monthly or quarterly, and contain a selection of articles providing details of recent research.

Up-to-date research developments within the field, or reports on technological innovations, current affairs, business matters, conferences, practical experience 'in the field

-Nature-Scientific american-Science

BooksTake a general approach to the subject, typically covering basic principles, facts and theories

Useful to provide an introduction or overview of a topic or building on research published in journal articles.

-Textbooks as part of your course material -Knovel is our largest collection of engineering books.

Technical data Traditionally found in printed handbooks or manuals, many of these are available online now

Quick and convenient retrieval of facts and figures

-National Institute of Standards and Technology's NIST WebBookhttp://webbook.nist.gov/chemistry/ -Knovel

Standards are accepted current methodologies and technologies relating, for example, to dimensions, quality, testing, terminology and codes of practice.

Standards represent a level of quality that manufacturers and service providers can work toward achieving.

-British Standards Online for full text of British Standards-IEEE Xplore for full text of over 1000 standards in electronics, telecommunications, robotics, automatic control and computer science.

Patents are Intellectual Property protecting working parts and processes. They are a great source of scientific, technological and competitor information

Patents provide up-to-date comprehensive information about technological innovations that is often not available elsewhere.

-esp@cenet for european patent-UK Patent Office is responsible for Intellectual Property in the UK.-US Patent and Trademark Office for US patents

Web Useful for official information, specialist organisations, statistics and data, news, journal articles.

-Librarians’ Internet Index - www.lii.org-Intute – www.intute.ac.uk

Official publications Publications issued by the government and its departments.

Governments are involved with most areas of society, and there are few subjects that are not covered. Official publications will ultimately affect corporate strategy to a greater or lesser degree.

-Directgov website provides access to a wealth of government information and services online. -Department for Business, Enterprise and Regulatory Reform website is a good example of an government website

Reference materialSuch as dictionaries, directories, and encyclopedia

Looking up company facts, data, statistics, standards, product information, specialist organisations and definitions.useful for providing specific pieces of information (i.e. facts) quickly.

-CRC Handbook of Chemstry and Physics- Biotechnology : a comprehensive treatise -Ullmann's Encyclopedia of Industrial Chemistry

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Topic- Overview and Define

Overview of topic

Before you begin, get an overview of the topic you are researching. Especially if you are not familiar with the topic. Good places to get an overview are:-

Encyclopedias e.g. Encyclopedia Britannica, WikipediaSubject dictionaries e.g. Macmillan Dictionary of Biotechnology, edited by J. CoombsSubject websites e.g. www.ucl.ac.uk/library/guides/subjengin.shtmlLecture notes

This will also help choose concepts and keywords to describe your topic when searching.

Define your topic

Go through the following steps :-

Think about the question you want to answer and break it down into its braod areas or concepts. You usually find that your question breaks down into a couple of areas or concepts.

Brainstorm for words and phrases associated with the major areas or concepts. Remember to include synonyms and alternative spellings and colloquial and

scientific/chemical terms-abbreviations – UK, United Kingdom-Variations in spelling – colour, color, specialised, specialized-Variations in terminology used in different cultures and countries – for instance, ‘children with emotional and behavioural problems’ (UK) are referred to as ‘maladjusted children’ in the US. This will help to ensure that you find things that an author might have referred to using different terms.

But don't worry if you can't always find any sensible substitutes for the words you have chosen – there might not be any.

Are there any grographical or date limitations you need to build in to our search? (e.g. are you looking for the worldwide or european perspective? Are you interested in historical or very current materials?.

The process may help you decide what you don’t want to investigate as well as what you do – saving you time when deciding what to read and what not to read.

Task 1

In groups discuss the topic “Adult stem cell therapies” and write down the main concepts and find keywords and synonyms for the concepts.

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Search techniques

Boolean

If you want an online database or search engine to understand you, you need to speak its language. That's why syntax - the way you put your search terms together - matters.

Since syntax can vary between databases and search engines, you should refer to the help.

For an online tutorial of any of the databases listed here, see section 3 of WISE (Finding information) for online tutorials: go to http://www.moodle .ucl.ac.uk/ , log in, click on WISE, and select WISE for Engineering and Built Environment.

Connectors (or 'boolean operators') Connectors determine how multiple search terms are combined in a search. Three common connectors are and, or and not. Sometimes symbols are used instead of words, i.e. + or –

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Extra search tips

Phrase searching: Some databases will treat two or more words entered into the search box as a phrase, while others require you to place a phrase in double quotation marks.

Example: "adult stem cells" will only find documents where the whole phrase is present.

Stem cells Stem cell therapy Therapy

Stem cell OR Therapy

Stem cell AND Therapy

Stem cell NOT Therapy

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Nesting: The order in which search engines execute your commands is not always obvious. You can use round brackets to control the search sequence.

Example: the search term “adult stem cell” and (therapy or treatment) will find documents that contain one of the words in brackets - i.e. therapy or treatment - but only if they also contain the phrase “adult stem cell”.

Proximity operators: locate terms that are close to one another. One such proximity operator is w/#, which you can use to find two words that are # number of pages apart.

Example: “adult stem cell” w/3 therapy will find documents where adult stem cell and therapy occur within three words of one another, in either order.

Truncation: Most databases allow end of word truncation, using one character, such as an asterisk *, to replace the remaining letters.

Example: therap* will find documents containing therapy, therapies, therapeutic, therapeutics.

'Wild cards': Wild cards are characters, such as a question mark, ?, used to replace replace a single letter in the middle of a word. They are used to accommodate spelling variations.

Example: wom?n will find woman and women; organi?ation will retrieve organization and organisation.

Searching specific fields: Field searching allows you to designate where to search for a specific term. Sometimes there is a drop-down menu to select the field, at other times a field 'qualifier' is added to the search term, such as Smith:au or Smith in au

Web

The web is a useful source of information but it is quite unlike library catalogues and databases in that it isn't so neatly organised and varies greatly in quality and usefulness.

Below are some ideas to try and improve your web searching.

Google is not the only search engine, tryYahoo www.yahoo.com Exalead, www.exalead.com/search

You can also take advantage of human selectivity, using the websites belowLibrarians’ Internet Index - www.lii.orgIntute – www.intute.ac.uk

Refining your search terms will help. On most web search engines you can use the ‘refine’ or ‘advanced’ search to limit the number of ‘hits’ for any particular search

Think “full text” and be specific e.g. war of 1812 economic causes vs. history

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Use academic & professional termse.g.domestic architecture vs. houses

Limit your search to …Web page title

intitle:hybrid allintitle:hybrid mileage

Website or domainsite:whitehouse.gov “global warming”site:edu “global warming”

File typefiletype:ppt site:edu “global warming”

Definitionsdefine:pixeldefine:“due diligence”

Remember social bookmarking, youtube, blogs

Some useful subject sites to useScirus – www.scirus.com

Invisible Web- What is the "Invisible Web", a.k.a. the "Deep Web"?The "visible web" is what you can find using general web search engines. It's also what you see in almost all subject directories. The "invisible web" is what you cannot find using these types of tools. - Why isn't everything visible?There are still some hurdles search engine crawlers cannot leap. Here are some examples of material that remains hidden from general search engines:

The Contents of Searchable Databases. Excluded Pages. Dynamically generated pages of little value beyond single use. Pages deliberately excluded by their owners.

- How to Find the Invisible Web Use Google and other search engines to locate searchable databases by searching a subject term and the word "database". If the database uses the word database in its own pages, you are likely to find it in Google. The word "database" is also useful in searching a topic in the Google Directory or the Yahoo! directory, because they sometimes use the term to describe searchable databases in their listings.

The Wikipedia "Deep Web" article provides a fairly up-to-date summary, with links to other resources.

Database's

A database is a way of storing, indexing, organising and retrieving informationThe specialised databases we can use to search for references to journal articles are called 'bibliographic' databases (because they contain information in summary form about books and journal articles). They are electronic indexes to the contents of thousands of journals. They are a very quick means of accessing thousands of references to academic material.

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Some databases have a very narrow focus, while others contain information on many topics. Select a database that is appropriate for your topic - see the subject guides http://www.ucl.ac.uk/Library/guides/subjengin.shtml or browse the list of databases http://www.ucl.ac.uk/Library/database/index.shtml A brief list of databases for your subject, including search tips unique to that database, is below

Web of Science – Science Citation IndexWeb of Science is a ‘Citation database’. This means that it contains bibliographic information from journals and also the article's cited reference list (often called its bibliography). It is a multi-disciplinary database, which is in three separate indexes: The Science Citation Index indexes more than 6650 major journals across 164 scientific disciplines from 1945 onwards. Social Sciences Citation Index and the Arts & Humanities Citation Index are also available.

Scopus

Comprehensive scientific, medical, technical, social science, and arts and humanities database containing references to journal articles, conference proceedings, trade publications, book series and web resources. Indexed from 1823 onwards.

Knovel

Knovel is an interactive e-book and database package which gives searchable access to the full text of a range of text and reference books. It covers all aspects of engineering and applied science.

Biotech abs

Biotechnology abstracts is an index of around 1,200 major scientific publications, including journals, conference proceedings and patents. It extends to all aspects of biotechnology, from genetic manipulation to biochemical engineering and fermentation to downstream processing.

Search tips Advanced Ovid Search is the recommended search method to choose. It allows you to

develop a strong search strategy and to produce very relevant and comprehensive results.

Pubmed

Pubmed contains references to articles in biomedical journals. It covers all areas of biomedicine, including, biochemistry and pharmacology. Over 4500 journals are indexed from 1950 onwards. Pubmed is free to use and updated daily. SFX links only present if you go to site from UCL library database pages.

Search tips Click on the details tab after performing a search to see the MESH headings (subject

headings used to describe the article) to help find synonyms and keywords

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Web of Science Step by step guide of demo

1. Go to the Web of Science page

Go to UCL library homepage www.ucl.ac.uk/library Click on Electronic Resources Click on Databases Click on W Click on Web of Science

You should now be at the main search screen. You can search by keyword, author, title, publication name and so on.

2. Entering a search

For example, our search for papers about “Adult stem cell therapies”

Enter search into Web of Science as follows 1st search box “adult stem cell” 2nd search box therap* or treatment Change search type to topic for both boxes Click on help if you want more info on the search rules that Web of Science uses. Click on search. How many results do you get?

3. Results screen

The default setting is to display 10 results per page in year order with the most recent first

For each result, you can see brief information of title, author and journal details. There are links to click on to see abstract and full text. You can mark (check the boxes) the results you find useful to make your own list of

resources. Once you have done this you can print, email the selected reference or save them to reference manager

4. Limiting search

If you have too many results you may want to reduce them. You can do this by “refining” our search. On the left is taskbox called “refine research”, here you can refine by

Subject areaDocument typeAuthor Source titlesPublication yearLanguage

Lets limit to last five years as we want current research Click on Publication years Click on more options/values Check the boxes of 2006, 2007, 2008, 2009, 2010 Click on refine

The number of results should decrease

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5. SFX

Click on SFX to see if you can obtain full text. (If no full-text available, remember to check the library catalogue in case we have it in print and M25 Union list of serials to see if any neighbouring libraries have it)

If we have full-text click on Go and a new window/tab should open with the full-text of the article available to read.

Click back onto the Web of Science tab or window to see your results list again

6. Search history

Click on Search History (at the top of the screen), here you can see the results you have created so far.

For the most recent set of results you can save search/create alert by clicking on the save search/ create alert button.

You will be prompted to name the search and you can also set up email alerts.

Saved search means you can always access the search you did. By setting up email alerts, you will be notified when any new results for your search are added to the database.

7. Cited reference search

This allows you to follow a strand of research through from one article to the next, by seeing who has cited a particular article that you know about.

Click the Cited Reference Search

Here, I will look for all of Professor Ewing’s articles that have appeared in the Journal of Chemical Thermodynamics in 2002 (you need to enter the abbreviated title, using the abbreviations list).

Enter EWING M* into the author search box Enter J CHEM THERMODYN into the cited reference box Click on Search

The next screen shows the articles that match your search query. You will see not just articles that have cited your article accurately, but also citations that the later articles have got wrong. No Link means that the citation might be wrong, look at the citation above and below to see whether the information is similar.

It looks like 4 articles were published in 2002, however they have very similar details, so it is very likely to be the same article.

Tick all 4 boxes on the left Click finish search.

This will show us all the articles with both the correct and incorrect citations.

That is the end of the demo, but don’t close the window we will use these results again later.

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Evaluation

It is important not to accept information and ideas at face value but to take time to reflect, compare ideas, evaluate the work done and build your own reasoned arguments. Treat the information you find with caution. Remember to scrutinise and ask questions and don’t form conclusions until you see what others have written.

The ability to critically evaluate information is an essential skill for a researcher. Try using PROMPT, a structured approach to critical evaluation of information (Provenance, Objectivity, Method, Presentation, Timeliness)

PROMPT checklist

Item 1

Presentation(is the information clearly communicated?)Look at language, layout, structure, etc.

Relevance(does the information match the needs of the searcher?)Look at the introduction or overview – what is it mainly about?

Objectivity(Is the author´s position of interest made clear?)Look for an introduction or overview – do the writers state their position on the issue?Is the language emotive?Are there hidden, vested interests?

Method (research reports only)

(Is it clear how the data was collected?)Were the methods appropriate? Do you trust it?

Provenance

(Is it clear where the information has come from?)Can you identify the authors or organisations? How was it published?Websites- Look at the URL - personal page or site ? Domain name appropriate for the content ? Restricted: edu, gov, mil, a few country codes (ca) Unrestricted: com, org, net, most country codes (us, uk)Published by an entity that makes sense ? News from its source? E.g. www.nytimes.comAdvice from valid agency? E.g www.nih.gov/www.nimh.nih.gov/

Timeliness

(Is it clear when the information was produced?)

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Does the date of the information meet your requirements? Is it obsolete?

Thanks to the Open University Information Literacy toolkit for this section

For web resources there are some additional tools to check websites and help you evaluate them.

Alexa - www.alexa.com Click on “Site info for …” Who links to the site? Who owns the domain?

Wayback machine - http://www.waybackmachine.org/ What did the site look like in the past?

Task 2: Try evaluating some sitesSearch a controversial topic in Googlenuclear armageddonprions danger“stem cells” abortionScan the first two pages of results

Visit one or two of these sitesUse PROMPT checklist to evaluate their quality and reliability

Finding References in other Libraries http://www.ucl.ac.uk/Library/otherlib.shtml

If you cannot get an article online you can try searching the UCL library catalogue (http://library.ucl.ac.uk) to see if there is a paper copy available. If not, try searching another Library?

The Library web page (http://www.ucl.ac.uk/Library/otherlib.shtml) gives a thorough list of alternative libraries and websites where you can check for holdings of other libraries in and around London.

Interlibrary loansIf you cannot find a location for a book or journal that you require, it is possible to order an inter-library loan. This will cost £3. More information can be found on our website http://www.ucl.ac.uk/Library/ids.shtml.

Citing sources

It is important to include references in your work in order to indicate that you have used relevant information resources, to avoid plagiarism and to allow readers of your work to be able to find the information sources for themselves. You should remember to list all the details of the books/journals that you consult so that you can reference them correctly. Failure to cite your sources constitutes plagiarism and you may be penalised!

Citing acknowledging within your piece of work the source from which you obtained information.

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Reference full details of the source from which you obtained your information. Bibliography a list of the references you have used, usually placed at the end of

your text.

For help with citing sources, See section 5 of WISE (Working with information): go to

http://www.moodle.ucl.ac.uk/, log in, click on WISE, and select your WISE for Engineering and Built Environment.

Read Neville, C. (2008). Complete guide to referencing and avoiding plagiarism. Milton Keynes: Open University Press. Held at MEDICAL SCIENCES A 9 NEV and GEOGRAPHY A 9 NEV

Try Internet detective - http://www.vts.intute.ac.uk/detective/ Library guide to references, citations and avoiding plagiarism available online at

http://www.ucl.ac.uk/library/References_and_Plagiarism.pdfand at enquiry desks

Reference Management

Bibliographic software enables you to store your references electronically. It also allows you to automatically generate bibliographies and reference lists in a variety of styles in seconds. Currently UCL provides access to Reference Manager. A full guide is available at http://www.ucl.ac.uk/library/Reference_Manager_Guide.pdf. Freely available bibliographic software incude: Zotero http://www.zotero.org/ and Mendeley http://www.mendeley.com/

Social bookmarking enables you to store Web addresses on the internet and access them from any computer with a connection to the Internet. You will be asked to ‘tag’ your bookmarks with a word, or words, so that these words can be used as search terms to help you re–find and re–organise resources on the same topic. Some popular ones are:Delicious http://www.delicious.com/ and Diigo http://www.diigo.com. For a list of websites used in this handout see http://delicious.com/LynneMeehan/biochem3

Reference Manager step by step guide

You need to login to cluster WTS

1. Create a new database in Reference Manager

Click on Start Software P-R Reference Manager 10 Click on File Click on New Database Choose a location and remember it , give it a name, click on New

2. Download references from database Click on your Web of Science window or tab Select 5 references from your results Click on Save to Endnote, RefMan, Procite (either at top or bottom of page)If using Internet Explorer

Click on Okay to open uml_view.cgi

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If using Firefox Click on OK to open with Web Export Helper (default)

Choose Reference Manager and click on OkayIt should automatically pick out the Reference Manager database you have created, if not, you should be able to browse to that location Click on Open

This opens the import window in Reference Manager and you can see the references you selected are imported. They are also sent to the database you created.

3. Cite while you write

Reference Manager allows you to work with Word to create bibliographies or insert references from you Reference Manager database in a Word document. You can then format the document in to a citation style of yor choice e.g. Harvard, Vancouver. This facility is called Cite While you Write.

Open a word document.A special tool bar is installed in Word when you install Reference Manager on your computer. If it hasn’t : From the View menu, select Toolbars and then Reference Manager 10 Place your cursor in the place where you wish to insert a citation in your word

document. Click on the Insert Citation button( the first icon on the Cite While you write toolbar)

N.B. This will search all open reference manager databases. It is therefore advisable to ensure that the relevant database is the only open database and that you close any other databases or Search tabs.

Click on Perform Search. Highlight the reference in the list and click on Insert. Your reference is entered as a

citation in your document,together with an automatically formatted bibliography/reference list.

Access to e-resources

UCL users are advised to access resources through the lists of ejournals (http://www.ucl.ac.uk/Library/ejournal) and databases (http://www.ucl.ac.uk/Library/database) available on MetaLib. This will guarantee that you get free access to all the resources to which you are entitled as a UCL member. If you are on-site you will not need to log in to resources. If you are off-site, you will be prompted for your UCL userid and password automatically.

Further informationFor more information on access to e-resources, visit http://www.ucl.ac.uk/Library/e-res.shtml. To report a problem with access, please fill in a problem report form at http://www.ucl.ac.uk/Library/e-res_prob.shtml.

Current Awareness

Current awareness is a term that describes the methods used to keep up to date with the most recent information in your subject area. Access to the most recent research, theories,

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news and debates in your subject area can give you a clear idea of the way in which your subject area is developing.

Tools to helpThere are a variety of electronic tools that will provide automated alerts with details of recent material in your area of interest.ZETOC - http://zetoc.mimas.ac.uk/TicTOcs - http://www.tictocs.ac.uk/ Database search alerts – see individual database pages for details

You will need to register with these services to receive alerts. Once you have set up an alert by registering your specific interests, you will automatically be sent details of recent journal articles on your topic.

Help

WISE: go to http://www.moodle.ucl.ac.uk, log in, click on WISE, and select Engineering and the Built Environment.

Subject Guides: go to http://www.ucl.ac.uk/Library/guides/subjengin.shtml Science Enquiry Desk: located on the ground floor of the Science Library. It is

staffed from 09:30-18:00, Monday, Wednesday and Friday and 09:30-17:30 Tuesday and Thursday. Telephone on ext. 37789 or 020 7679 7789.

Lynne Meehan (science subject librarian) contact me on l.meehan@ucl.ac.uk or 020 7679 2634 or come and see me in Room 314, Science Library.

Links to slides and resources used in this course: http://delicious.com/LynneMeehan/biochem3

Please fill in the evaluation form about your session at

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