Finding Information

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Finding Information

• Nov 14 2007

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Finding Information

• The purpose of this session is to show you some
  simple approaches that will enable you to access
  non-standard information (for teaching,
  illustrations, essays) more easily
• Search machines
• Using citation indices
• Boolean searches
• Knowledge of an unknown area

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Search Machines

• Can be found on home pageSearch the www
• Google
• Text Images Google Scholar
• Yahoo AltaVista
• Scirus. Try yeast cdc28
• WebCrawlers show most popular sites in a range
  of search machines

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Citation searches

• Enables you to find recent articles that cite an
  older article
• Useful for finding the most recent material
  related to an older reference that you might have
• Best older reference is probably a review
• Wheals a / trends biotechnol / 1999

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Boolean methods (rules)

• Use of AND, NOT, OR, BOTH
• is exact phrase
• ( ) used to separate or override Boolean
  operators
• Use wildcards ( ? ) to search for singular and
  plural forms of words and for word variants.
• Enter enzym to find enzyme, enzymes, enzymatic,
  enzymology.
• Enter wom?n to search for records that contain
  woman, women, or womyn.
• Enter vapor to find vapor and vapour.

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Boolean methods (examples)

• Stationary phase in yeast Saccharomyces 833
• Stationary phase in yeast Saccharomyces 773
• Stationary phase AND Saccharomyces 909
• Stationary phase AND Saccharomyces since 2000
  56
• Stationary phase AND Saccharomyces Review 48
• Stationary phase AND Saccharomyces Title 0
• Stationary phase AND Saccharomyces NOT
  cerevisiae 0
• Stationary phase" AND yeast OR Saccharomyces
  80,092
• Stationary phase" AND (yeast OR Saccharomyces)
  1207
• (Stationary phase) AND (yeast OR Saccharomyces)
  1352

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Test

• How much bioethanol was produced in Brazil in
  2005
• 15.9 BL (10 secs)
• How many staff did UniBath have at the end of
  academic year 2006?
• As of 31/08/06 we had 2570 staff
• http//www.bath.ac.uk/about/facts/
• What is the penalty for interfering with fire
  extinguishers in residences?
• 25 - 50
• http//www.bath.ac.uk/rules/accom.html

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Task 1

• I want to do a PhD or post-doc on genetics of
  filamentous fungi, preferably in France. How do I
  find suitable places?
• Searched for Fungi Genetics France research
• 2nd results was EU-Agrinet GENOMYCA - Genes and
  genetic engineering for arbuscular mycorrhiza
  technology and applications in sustainable
  agriculture
• 6th result was INRA - The biodiversity of
  filamentous fungi
• 10th was Nancy Ecology and genetics of
  ectomycorrhizal fungi
• Alternative is to use WoK for recent good papers
  from France on fungi

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Task 2

• You are interested in plant crop genotyping.
• Has anyone done DNA fingerprinting of avocado?
• Lavi, U., J. Hillel, A. Vainstein, E. Lahav D.
  Sharon, 1991. Application of DNA fingerprints for
  identification and genetic analysis of avocado.
  J. Amer. Soc. Hort. Sci. 116 10781081
• Correct name is Persea americana 
• Fiedler J et al (1998) Genetic relationships of
  avocado (Persea americana Mill.) using RAPD
  markers Euphytica 101 249-255
• Other possibilities are using that to search for
  other citations
• Schnell RJ et al. (2003) Evaluation of avocado
  germplasm using microsatellite markers J Am Soc
  Hort Sci 128 (6) 881-889.
• From Biosis came
• Kobayashi, M et al. (20000 Quantitative analysis
  of avocado outcrossing and yield in California
  using RAPD markers Scientia Horticulturae
  (Amsterdam) 86 (2) 135-149 2 October, 2000

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Task 3

• Is there a conference on avocado genetics that I
  should attend?
• http//www.worldavocadocongress.com/index.html
• Get on plane NOW!
• Note that congress is an alternative for
  conference other words would be meeting,
  symposium, colloquium

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Task 4

• Is there a good general Mycology site?
• http//www.resourcehelp.com/bio_mycology.htm
• http//mycology.cornell.edu/findex.html Big
  hairy index to the WWW Virtual Libary Mycology
• http//mycology.cornell.edu/
• The WWW Virtual Library Mycology

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Task 5

• Candidiasis is a serious human disease.
  Identification is important and can take time.
  You want to know about rapid identification.
• How many hits do you get?
• Candida rapid identification
• WoK BioSci?
• WoK Biosis
• Patents
• Does anyone use Google Scholar?

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Strategies

• Ask someone!
• Try the direct approach first (eg Google, WoK)
• Try alternative words (eg genetics, genome, gene,
  gene or gen)
• Think laterally or indirectly (eg look for
  something similar to what you want)
• If you dont find something quickly try a
  different approach

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Some great sites

• Information Hyperlinked over Proteins
• http//www.ihop-net.org/UniPub/iHOP/
• Wellcome Trust human genome and ethics
• http//genome.wellcome.ac.uk/node30120.html
• Online Mendelian Inheritance in ManTM
• http//www.ncbi.nlm.nih.gov/sites/entrez?dbOMIM
• Broad Institute (MIT and Harvard)
• http//www.broad.mit.edu/tools/data.html
• Saccharomyces Genome Database
• http//www.yeastgenome.org/
• NCBI (PubMed BLAST TaxBrowser Structure)
• http//www.ncbi.nlm.nih.gov/
• Netwatch websites chosen by iScience
• http//www.sciencemag.org/netwatch/

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Storing and sharing

• Social Bookmarking
• Bookmarks / favorites
• Del.icio.us
• http//wiki.bath.ac.uk/display/bucswebdev/Socialb
  ookmarkingfornews

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Caution!

• Is the site reliable? owner?
• Never quote Wikipedia as a reference
• Always cite the source if you found it so can a
  plagiarism detector!
• Include the date of searching contents change

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Over to you

• Do you know of any great sites?
• Do you know of any useful tricks?
• Do you know about successful strategies

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