Finding information for Ccourse in Genetics

1
Finding information for C-course in Genetics

• Helen Hed
• http//www.ub.umu.se/tjanste/hehe/

2
Aims and Goals for this lecture

• Give you a perspective on scientific publication
• Demonstrate a number of useful informations
  sources
• Entrez (PubMed , OMIM, NCBI)
• Other useful databases (BA, WoS, )
• Point you in the right direction on how to cite
  and write reference lists

3
Contents

• Scientific publication, history
• Search strategies and searching
• Evalution of information
• Databases, demonstration of
• Writing references and citing other peoples work

4
History of scientific publication

• Books - printed
• Journals - printed
• Abstract journals
• Electronic journals
• Electronic books

5
Recent developments

• From print only to print and electronic
• E-journals
• Print and electronic
• E-version only
• 1995-1998 the big expansion in number of titles
• E-books
• P- and e-versions
• E-version only

6
Today at Umeå UB

• 7- 8 000 e-journals
• Most are scientific journals
• Access via Umeå UB web site
• Tanstaafl ?
• Open access
• HighWire http//highwire.stanford.edu/
• DOAJ http//www.doaj.org/
• BioMed Central http//www.biomedcentral.com/

7
The Publication Process - 1

• Project proposal and project initiation
• research
• Poster / paper at conference
• Manuscript
• Where to publish?
• Prepare manuscript for publication
• Peer review
• Article primary publication

8
The Publication Process - 2

• Textbooks secondary publications
• Encyclopedias secondary publ
• New results falcify old truths
• Old data replaced by new when new edition of
  textbook is prepared
• and the cycle continues

9
Databases basic types

• Bibliographical databases (db)
• Covers a subject as specified
• For example
• PubMed
• Web of Science
• Biological Abstracts
• Can have links to fulltext that is located
  somewhere else

10
Databases

• Fulltext db
• Contains both the bibliographical data and the
  texts (articles)
• Hybrid db
• are hybrids
• All db-searches are complete
• Each search compares your key words to all
  biblographical entries in the database

11
Databases

• Library catalogues
• Are bibliographical databases
• Each library catalogue has in it information
  about all the books, reports, journals, et c, in
  one particular library
• Each search is complete
• All records are compared to your search question

12
Alternatives

• Subject guides
• BIOSIS web site http//www.biosis.org/
• BiologyBrowser http//www.biologybrowser.org/
• Ämnesguide Biologi
• http//www.ub.umu.se/amnesguider/biologi/biologi.h
  tm
• Scirus
• http//www.scirus.com/
• Google Scholar http//scholar.google.com
• Och Google

13
Web searches are

• Never complete
• quick and dirty bad algoritms and incomlete
  indexes results in suboptimal informations
  retrieval
• Search time used to answer your question depends
  on number of concurrent users
• Many users -gt short search
• Few users -gt longer search

14
Search strategies

• Quick and dirty
• Useful if you are looking for inspiration,
  synonyms,
• The proper way
• Worth the extra time
• Takes more time to prepare
• Is quicker to execute
• Gives more useful results

15
The search process (the proper way)

• Choosing and developing a topic
• Designing the search
• Carrying out the search and evaluating the
  results
• Handling the products of your search

16
Preparing for the Search

• Find useful key word
• Dont forget synonyms!
• Dictionaries, encyclopaedias and your text books
  are useful tools
• Select databases
• Always pick more than one
• How many and which depends on subject and level
  of detail

17
The Search

• Make test-search(es)
• To test key words and as test of choosen
  databases
• Analyse test search(es)
• Make full literature search
• Save search results for future use
• Reference list
• For comparison

18
No hits !?!?

• If a search results in no hits.Maybe You have
• Misspelled one or more search terms
• Used invalid search terms
• Do not give up!
• Check spelling
• Check tesaurus in database
• Try another database
• Ask someone for help (a librarian or your tutor)

19
Boolean search

• AND, OR, NOT, NEAR, SAME, ..
• WoS use SAME
• To retrieve hits with two key word in same
  context
• BA use NEAR
• To retrieve hits with two key words in same
  context

20
From search result to actual text

• Link from bibliographical information to fulltext
• So easy click -gt click -gt click
• No link to fulltext in the database?
• Check if UB has the journal (p or e) anyway on
  the Journals page on the web
• Or choose another article

21
Evaluate

• Have you found the answers you were looking for?
• If not revise your search and do it again
• Do all sources agree?
• If not WHY?
• Do you feel that you can trust the information
  you have found?

22
Getting a copy of the article

• Pdf-format is always preferred when article is
  avaliable as fulltext
• Making a paper copy from p-journal
• Locate the journal (either at the KBC Library or
  the main library)
• copy
• If info about source is not printed on at least
  every second page write that information on the
  copy

23
Your favourite bibliographical databases

• Biological Abstracts
• Entrez - PubMed and the whole NCBI site
• Web Of Science, Science Citation Index
• ALBUM (and Libris) for books
• For links to the above see http//www.ub.umu.se/

24
PubMed (1955 present)

• Very simple user interface
• Default search field is a kind of easy search
• Write key words in search field
• Press enter or click on GO
• Limits will allow more specifications but
  excludes new entries from being searched

25
PubMed cont.

• Part of a larger set of interlinked databases at
  National Library of Medicine (NLM)
• OMIM database
• Very useful for finding information on human
  genes

26
PubMed cont.

• Symbols in front of reference indicates
• Blank symbol
• Reference only
• Symbol with 3 lines
• Reference and abstract
• Symbol with 5 lines and green line
• Reference, abstract and free full text

27
PubMed cont.

• History
• Saves your search history
• Details
• Shows you details about the search you made as it
  was performed by PubMed
• Clipboard
• A place where you can place parts of your
  searches while you are searching

28
PubMed cont.

• Saving by E-mailing searches
• Choose e-mail in the selection box to the right
  of the send to-button
• Best to make a selection and mark those articles
  you are interested in and save these to the
  clipboard and then e-mail them.

29
PubMed cont.

• MeSH
• Medical Subject Headings
• Use to increase precision of search
• Newest entries in PubMed are not indexed with
  MeSH it takes time to index
• MeSH-SweMeSH
• Useful if you are uncertain of english terminology

30
Nucleotide

• Database of nucleotide sequences from 130 000
  organisms
• Gathered from DDBJ (DNA Data Bank of Japan), EMBL
  (European Molecular Biology Laboratory), and NCBI
  (National Center for Biotechnology Information).
• Updated daily
• Example of a sequence document

31

• Contains data about nucleotide sequences (both
  DNA and RNA) from different databases. The
  biggest is Genbank.
• In every sequence document there are references
  to the article where the sequence was first
  presented.
• Genetic code scheme. Translation from DNA
  molecule to amino acid.
• Amino acid abbreviations.

32

• Enter name of protein (and maybe more search
  terms) for which you want to know the nucleotide
  sequence
• insulin AND homo sapiens
• Gives 9000 hits in the database
• RefSeq 1181
• RefSeq the best non-redundant and
  comprehensive collection of naturally occurring
  DNA, RNA, and protein molecules for major
  organisms

33

• Hits are sorted into groups
• All ReSeq are collected in one of the lists
• http//www.ncbi.nlm.nih.gov/RefSeq/

34
RefSeq accession numbers

• Curated sequences
• RefSeq accession numbers can be distinguished
  from GenBank accessions by their prefix distinct
  format of 2 charactersunderbar. For example,
  the RefSeq protein accession number for citrate
  synthase is NP_015325.
• Each sequence has a unique statusPredicted,
  provisional, reviewd, validated, et c.
  http//www.ncbi.nlm.nih.gov/RefSeq/key.html

35
Part of list describing accession formats
36
Nucleotide example cont.

• Enter accession number - NM_021694
• Will produce a single hit in the database
• Click on accession number
• Displays the complete record
• At the end of this record you will find the amino
  acid sequence translated part of gene and the
  DNA sequence

37
Reports

• Different formats in which the information is
  available

38
Links

• How many links depends on how much data exists
  and in what dbs
• Wellstudied proteins have many links other can
  have very few

39
Protein

• Contains protein sequence data collected from
  different databases.
• In every sequence document there is a reference
  to the article where the discovery of the
  sequence was decribed.

40
Structure

• Contains visalization possibilities for
  3D-representation of structures
• For viewing the structures you need a plug-in
  that can be downloaded for free (Cn3D)

41
Example - Azurin

• 53 hits
• click on the link above the short description or
  on MMDB new page where 3D structure of the
  molecule can be viewed.
• Tutorial and software
• http//www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.sh
  tml

42
Genome

• Contains data on the nucleotide sequences that
  constitutes a whole genome.
• There are both whole chromosomes and pieces of
  chromosomes from about 800 different organisms
• Gives a graphical overview of genomes and
  chromosomes (called sequence maps).

43
Genome - cont

• Limit search to one species by
• Write species name in search box
• Enter the Limit organism
• In general search will find one (1) entry per
  chromosome (inkluding mitochondrial genome

44
Genome - cont

• Alternative entrypoints
• Choose organism group and type of genome in
  left-hand column
• Example
• Eucaryota Genome
• Choose Homo sapiens
• Or choose Drosophila melanogaster

45
Map viewer organism map

• Search for organism and find the right chromosome
• Graphical view
• http//www.ncbi.nlm.nih.gov/mapview/MVgraph.html?
  

46
OMIM

• Online Mendelian Inheritance in Man
• A database with information about human genes,
  genetic diceases and phenotypes
• Links to nucleotide, protein, structure and
  genome.
• Now also OMIA animals
• Info about OMIA

47
OMIM

• Catalogue of human genes and genetic disorders
• Links to literature, sequence records, maps, and
  related databases

48
OMIM

• OMIM has three different search pages.
• Search OMIM
• Search Gene map
• Search morbid map
• And a default start page

49
OMIM - exemple

• A search for diabetes will give 500 hits in
  OMIM
• Click on rekord number -gt full record is
  displayed with a table of contents and links out
  in the blue field
• Also link to clinical synopsis
• And to gene map

50
OMIM example SOD

• This is the entry for SOD1 (147450)
• means gene with known sequence
• Information about symbols and numbering system
  and morehttp//www.ncbi.nlm.nih.gov/entrez/query.
  fcgi?dbOMIM
• Notice that table of contents does not have
  identical headings for all entries.

51
Entrez the life sciences search engine

• All databases from NCBI can be searched from this
  page
• Searching here lets you get an idea about how
  much information is available and where it is

52
Biological Abstracts

• Use latin species namesnot common names
• BIOSIS web site
• http//www.biosis.org
• Tutorials available
• Biology Browser
• http//www.biologybrowser.org/
• Good starting point for finding relevant material
  on the web

53
BA exemple

• Start from Umeå UB home page
• Click on link to database page
• Locate BA in
• Alphabetical list or
• By subject list
• Choose years
• Start searching

54
Web of Science (1986-present)

• 3 parts
• Science Citations Index Expanded
• Social Sciences Index
• Arts Humanities Index
• 3 search forms (actually 4)
• General search
• Cited Reference Search
• Advances Search
• Quick search

55
WoS cont.

• TOPIC
• Searches within article titles, keywords and
  abstracts
• Dont enter too many words
• Use boolean operators between words
• AND to include
• OR for synonym search
• NOT to exclude
• SAME join words for phrase

56
WoS cont.

• Limits
• Language
• Articles may have abstracts in english even if
  the article is in another language
• Type of publication
• Very useful if you only want review articles
• Source title
• Useful if you want to restrict search to a single
  journal

57
WoS cont.

• Search history
• Keeps a record of searches
• Until you log out
• Allows further modification of searches
• Example drug and malaria

58
E-books

• E-books are books that you can read online
• Quick-link on UBs homepage
• Ebrary
• link to on http//www.ub.umu.se/infosok/ebooks.ht
  m
• Books in PubMed
• Contains some books that are relevant

59
E-books cont.

• NAP national Academy Press
• http//www.nap.edu/info/browse.htm
• Searchable
• Free fulltext
• One page att a time print-out option
• Some free full-text resources
• http//library.com.edu/internet/intsub/bio_gen.htm
  

60
List of references

• Allows readers to find and read the same article,
  book chapter, et cetera, as you read
• if they feel they need to check the data you are
  quoting your list of references should make it
  easy!But you are only expected to give a
  reference not a shortcut to the fulltext.

61
References data to includefor an article in a
journal

• Author(s)
• Year of publication
• Title
• Source (journal name)
• Volume, issue
• Pages
• Link to web or other e-source (URL or DOI)
• Date of access (when you downloaded)

62
Examples

• See Biblioteksguiden for examples
• http//www.ub.umu.se/infosok/distans_guide/modul8/
  8-2.htm
• Only in swedish
• Also in Att skriva referenser till dokument
  hämtade från Internet
• http//www.ub.umu.se/global/internetref.htm
• Only in swedish

63
Example - Thesis online

• Deutschmann, Mats (2003). Apologising in British
  English. Thesis. Umeå university.
  http//urn.kb.se/resolve?urnurnnbnseumudiva-4
  3 2004-02-05
• Author Year Titel Type of publication and
  place of publication URL Accessed by you
• You have to add info about what part (page(s))
  you are citing
• In this case one proper way to write the citation
  is given to you by the publishers.

64
Now its your turn