Biblioteca Centrale P. Arduino

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Biblioteca Centrale P. Arduino CIS
AgripolisEdited by the Group for Training in
Library Resources

• Course
• Access to bibliographic resources
• for post graduate Schools of Agripolis
• (15 hours)

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3 PART

• Bibliographic searches through Scifinder
  (presented by Federico Fogo)
• Bibliographic searches through free data banks as
  PUB MED, AGRICOLA, AGRIS etc.

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Bibliographic searchBasic Principles

• To perform a bibliographic search correctly, you
  have to keep in mind
• The difference between a catalog and a
  bibliography
• Use of logic Boolean operators and jolly
  characters
• The logical sequence of the steps you have to
  follow

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CATALOG/BIBLIOGRAPHY

• A CATALOG
• A catalog comprehends the works that are
  possessed by one or more libraries and tells you
  where you can find them

• A BIBLIOGRAPHY
• A bibliography comprehends the existing documents
  with chosen characteristics (what has been
  published on a subject or what has been published
  of a chosen author) but does not say anything
  about where you can find those documents

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THE TOOLS Logical operators (or Boolean
operators) (They are named after the British
mathematician George Boole who developed that
logical system in mid 18 hundred)

• They are named after the British mathematician
  George Boole who developed that logical system in
  mid 18 hundred
• The logical operators allow to specify
• The relation between the words that you have to
  search
• What words must be in the pages you retrieve
• What words must not be in the pages you retrieve
• What words can be used as an alternative

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THE TOOLS - Logical operators (or Boolean
operators) AND, OR, NOT
AND You will retrieve documents that contain both
words. As a result, you limit your search
WORD 1 AND WORD 2
OR You will retrieve documents that contain word
1 or either word 2 or both. As a result, you
expand your search
WORD 1 OR WORD 2
NOT You will retrieve documents that contains
word 1 but not word 2. As a result, you refine
your search
WORD 1 NOT WORD 2
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IMPLICIT BOOLEAN OPERATORS

• Often using web engines you can notice that the
  symbols and are used instead of AND, NOT
• Before those symbols there must be a space, but
  they must not be separated by a space from the
  word that follows
• forest(blank)Cansiglio Cansiglio AND forest
• Cansiglio(blank)diseases(blank)-firs Diseases
  of Cansiglio forest, but of firs

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THE TOOLS ? and

• ? (Question mark)
• It stands in place of whatever character and can
  be reused as much as you want
• Ex. Nar?elli will find Naraelli, Narbelli,
  Narcelli

(star) It truncates the word both at the top and
at the end Ex. Bio will find biology,
biotechnology, biochemistry
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(No Transcript)
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BIBLIOGRAPHIC SEARCH

• To do a bibliographic search we can
• To look up journals with their indexes
• To search databanks

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Databank

• A databank is an an electronic archive where
  information are organized in a particular
  structure, in order to make it easier and more
  useful to retrieve them through the search
  interface
• The basic unit of an electronic archive is the
  record, divided in fields (title, author, date
  etc.)

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BIBLIOGRAPHIC DATA BANKS

• Bibliographic data banks contain bibliographic
  citations of books, journals and miscellaneous
  works, almost always together with an abstract
• They are usually multidisciplinary or specialized
  on a determined subject
• They usually employ a very powerful searching
  strategy
• They allow to save the results of the query
• They represent a very important tool to start a
  scientific work and/or a thesis

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BIBLIOGRAPHIC DATA BANKS

• Padova University offers a large number of data
  banks on different subjects (Trova risorse on
  AIRE PORTAL)
• Bibliographic data banks are searched to find
  documents on a specific subject. The documents
  can be localized through on line catalogs (OPAC,
  AIRE/SFX, etc.)

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ACCESS TO UNIVERSITY OF PADOVA DATA BANKSHOW
TO CONFIGURE AUTH-PROXY

• Access to University of Padova data banks is
  allowed only from computers connected to the
  University web
• To connect to the University web from your home
  or from another University students have to
  carefully follow the instructions that can be
  found at
• http//www.cab.unipd.it/node/127

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Bibliographic searches through Scifinder

• Scifinder
• (dott. Federico Fogo)

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Bibliographic searches through free data banks

• PubMed,
• Treesearch,
• AGRICOLA,
• AGRIS/CARIS
• (Dott.ssa Micaela De Col)

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PubMed Bibliographic Search

• PubMed is a resource that is developed and kept
  up by the National Center for Biotechnology
  Information (NCBI), at the U.S. National Library
  of Medicine (NLM), located at the National
  Institutes of Health (NIH).
• It is available for free on the Internet at
  http//pubmed.gov.
• Links to full-text articles, information about
  library holdings, and other NLM databases are
  available

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PubMed Bibliographic Search

• PubMed Content
• PubMed comprehends over 20 million citations of
  biomedical literature from MEDLINE, life science
  journals, and online books.
• MEDLINE NLMs database comprehends millions of
  references from articles published in biomedical
  and related journals which have been fully
  indexed
• In-process citations that have not yet been
  analyzed and indexed by MEDLINE
• Publisher supplied citations that may not receive
  full indexing by MEDLINE because they are not
  biomedical in nature

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MEDLINE

• Is the NLM premier bibliographic database that
  contains references to journal articles in life
  sciences with a focus on biomedicine
• Includes the fields of medicine, nursing,
  dentistry, veterinary medicine, the health care
  system, and preclinical sciences

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MEDLINE

• Time coverage generally 1946 to the present,
  with some older documents.
• Source currently, citations from approximately
  5.516 worldwide journals in 39 languages
• for citations added from 2005-2009 about 45 are
  for cited articles published in the U.S., about
  91 are published in English and about 83 have
  English abstracts written by the authors of the
  articles.

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How do I search PubMed?

• Search
• by subject
• by author
• by journal
• Other search

• You can get
• lists of bibliographic citations from articles
• Link to the full-text (if present) or to related
  articles

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MEDLINE structure

• Articles are indexed using a powerful thesaurus,
  called Medical Subject Headings (MeSH). The MeSH
  Database provides the option to identify
  appropriate MeSH terms for searches.
• Records are subdivided in FIELDS
• (Author, title, ect)

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MeSH (Medical subject headings)

• MeSH is the National Library of Medicine's
  controlled vocabulary thesaurus. It consists of
  sets of terms naming descriptors in a
  hierarchical structure that permits searching at
  various levels of specificity.
• The Medical Subject Headings Section staff
  continually revise and update the MeSH vocabulary
• The MeSH database can be searched by MeSH term,
  MeSH Entry Term, Subheading, Publication Type,
  Supplementary Concept, or MeSH Scope Note.

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Esempio

• Animal Diseases C22 
• Abortion, VeterinaryC22.021  
• Actinobacillosis C22.039
• Aleutian Mink Disease C22.062
• Anal Gland Neoplasms C22.073
• Anaplasmosis C22.085
• Bird Diseases C22.131  
• Borna Disease C22.152
• Cat Diseases C22.180  
• Cattle Diseases C22.196  
• Disease Models, Animal C22.232

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Mesh Browser
http//www.nlm.nih.gov/mesh/MBrowser.html
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Before you start a few tools

• Combine search terms with connector words
  (Boolean operators) AND, OR or NOT using
  upper case letters.
• To search for all terms that begin with a word,
  enter the word followed by an asterisk (), the
  wildcard character.For instance, risk will show
  risk, risks, risk-taking The term infection
  will not show infection control because there is
  a blank after the term infection
• Searching for a phrase
• () PubMed processes searches in a left-to-right
  sequence. Use parentheses to nest concepts that
  should be processed as a unit and then
  incorporated into the overall search.
• search by a specific field es. Albertini
  mAU, Liver diseasesMH

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Boolean operators AND, OR, NOT

• Enter Boolean operators in uppercase characters
  to combine or exclude search terms
• Boolean operators must be used when combining
  tagged search terms as follows search term tag
  BOOLEAN OPERATOR search term tag.
• PubMed processes searches in a left-to-right
  sequence. Use parentheses to nest concepts that
  should be processed as a unit and then
  incorporated into the overall search.
• In a tag with more than one Boolean operator AND
  will be processed before OR
• A search with "influenza AND vaccine OR
  vaccination will show articles that contains
  both terms "influenza and "vaccine and will
  show all the articles on "vaccination To obtain
  different results write "influenza AND
  (vaccine OR vaccination)"

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MEDLINE search fields

• You may also search a specific field, and bypass
  the automatic term mapping, by adding the
  appropriate tag to a search term
• The search tag must be enclosed in square
  brackets.
• term tag
• Es. merkel au liver cirrhosis ti cancer
  jour
• Case and spacing do not matter (e.g., crabs mh
  Crabsmh).
• automatic term mapping
• Untagged terms that are entered in the search box
  are matched (in this order) against a MeSH
  (Medical Subject Headings) translation table, a
  Journals translation table, the Full Author
  translation table, Author index, the Full
  Investigator (Collaborator) translation table and
  an Investigator (Collaborator) index.

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Seach field descriptions and Tag
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Searching for a phraseUSING DOUBLE QUOTES ..

• In searching for a phrase enclose the phrase in
  double quotes
• For example myocardial infarction Will show
  all the articles where this phrase appears as I
  wrote it, without any other terms
• Without .. Pubmed applies an AND operator
  between concepts
• When you enter your search terms as a phrase
  PubMed will not perform automatic term mapping
  that includes the MeSH term and any specific
  terms indented under that term in the MeSH
  hierarchy.
• If you use a hyphen or quotes and the phrase is
  not found, the hyphen or quotes are ignored and
  the phrase is processed using automatic term
  mapping.

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Link

• PubMed is available free on the Internet at
• http//www.ncbi.nlm.nih.gov/pubmed

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Esempi

• Search for records in Javma Journal that contain
  the term cancer in text
• Records that contain liver in general, but not
  studies on humans
• 3. Records on neoplasia in cats and dogs
  indifferently

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Simple search Text word

• Includes all words and numbers in the title,
  abstract, other abstract, etc.
• When?
• To use when? Is useful if
• There are no Mesh descriptors to pick up a
  subject
• If the available descriptor is not specific
  enough
• Searchin for in process articles, i.e. articles
  that have not been indexed yet with MESH
  descriptor terms.

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Simple search Text word

• Remember to type in the SEARCH box the synonims
  of the term you are looking for
• To search for all terms that begin with a word,
  enter the word followed by an asterisk (), the
  wildcard character.
• Pro you can use colloquial words and phrases
• Connot all the words used in natural language
  are key words

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Simple search Text word

• .
• Enter the terms or more terms (or key concepts)
  in the search box whitout tags
• Automatic suggestions will display as you type
  your search terms.
• Click Search.

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Simple search Text word

• You can use "AND", "OR" and "NOT".
• Automatic mapping untagged terms that are
  entered in the search box are matched (in this
  order) against a
• MeSH (Medical Subject Headings) translation
  table,
• a Journals translation table,
• the Full Author translation table, Author index,
  the Full Investigator (Collaborator) translation
  table and an Investigator (Collaborator) index.
• When a match is found for a term or phrase in a
  translation table the mapping process is complete
  and does not continue on to the next translation
  table.
• PubMed PubMed ignores stopwords in searches.

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Simple search Text word

• PubMed displays a list of results in Summary
  format in batches of 20 citations.

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Searching by journal title

• Enter in the search box one of the following
• full journal title (e.g., molecular biology of
  the cell) - using the search field JOUR or TA
• title abbreviation (e.g., mol biol cell) - using
  the search field JOUR or TA
• ISSN number, a standardized international code
  (e.g., 1059-1524) using the search field IS
• If you do not use a search field tag the program
  could mistake the term for a key word (ex
  Science)
• Click Search
• REMEMBER
• To find full journal names, use the NLM Catalog,
  or mouse over the citation journal abbreviation.

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Searching by author

• The format to search for this field is last name
  followed by a space and up to the first two
  initials followed by a space and a suffix
  abbreviation, if applicable, all without periods
  or a comma after the last name (e.g., fauci as or
  o'brien jc jr). Initials and suffixes may be
  omitted when searching.
• use the search field AU Es. Smith JB AU
• PubMed automatically truncates on an author's
  name to account for varying initials, e.g.,
  o'brien j au will retrieve o'brien ja, o'brien
  jb, o'brien jc jr, as well as o'brien j. To turn
  off this automatic truncation, enclose the
  author's name in double quotes and tag with au
  in brackets, e.g., "o'brien j" au to retrieve
  just o'brien j.
• If only the author's last name is entered, tag
  the name with the author search field au, to
  find the name in the author field only .

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Searching by author
First authir or co-author
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Searching by author

• If only the author's last name is entered, tag
  the name with the author search field au, to
  find the name in the author field only .
• Without tagging the search field au PubMed will
  search that name in all fields(abstract, text,
  title etc.) not only in the field author

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Searching by author - ADVANCED SEARCH

• Use the Advanced search Search Builder to search
  for terms in a specific search field
• To search by author, select Author from the All
  Fields menu, enter an authors name, and then
  click the Add to Search Box button to add the
  name to the search box.
• The author search box includes an autocomplete
  feature.

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Combining more authors with Boolean operator AND
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Combining more authors with Boolean operator OR
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Search by journal Advanced search
To search by journal, select Journal from the All
Fields menu, enter a journal name, and then click
the Add to Search Box button to add the name to
the search box. The journal search box includes
an autocomplete feature..
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Search by journal Advanced search
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Limits

• You can limit your search by dates, type of
  article, languages, species, sex, subsets, ages,
  text options, and specific search fields.

• Specific search fields tags
• Choose a specific search field tag to limit all
  terms in the search box to that field.

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Limits

• Publication Types
• restricts your search based on the type of
  material the article represents, such as
• Clinical Trial
• Editorial
• Letter
• etc-.
• Languages
• The languages limit restricts your search to
  articles written in a particular language.
• Languages displays a list of the most frequently
  used languages.
• .

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Limits

• Ages
• The age limits restrict your search to a
  specific age group for a human study
• Humans or animals
• The species limit restricts your search to a
  human or animal study
• Gender
• Sex restricts your search to a specific sex for
  a human study (Male/Female)

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Limits

• Subsets
• Journal Groups More Subsets
• The Journal/Citation subsets restrict retrieval
  to specialized journals or articles on
  specialized topics in other journals.
• Topics
• The topics subsets restrict
• retrieval to specific subjects including
• AIDS
• Bioethics
• Cancer
• Complementary Medicine
• Dietary Supplements
• Etc.

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Understanding Your Search Results Display
settings

• Search results initially display in a summary
  format in the order they were entered in PubMed
  as last in, first out. You can change the display
  format.
• A default of 20 citations is displayed per page.
  If there are more than 20 citations, they will be
  displayed on subsequent pages.
• To display the abstract for a journal article,
  click the title link for each citation. Some
  citations do not have abstracts and include the
  note No abstract available..

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Understanding Your Search Results Display
settings
Search results initially display in a summary
format in the order they were entered in PubMed
as last in, first out. You can change the
display format. To change the display format only
for selected citations, click the check box to
the left of each citation before selecting a
display format.
Menu a tendina
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Understanding Your Search Results Display
formats

• PubMed Citation Display Formats
•  
• Summary default (Authors, Title, Journal source,
  etc.)

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Understanding Your Search Results Display
formats

• Abstract include abstract, but the Abstract
  (text) format does not include MeSH data.

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Understanding Your Search Results Display
formats

• MEDLINE Two-character tagged field format (for
  the complete record.  Use this format to export
  citations into reference management programs.

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Search details

• PubMed may modify or add additional search terms
  to your search to optimize retrieval.

• Click Advanced search Details or see the Search
  details portlet to view your search as it was
  translated using automatic term mapping and
  search rules.
• The Query Translation box shows the search
  strategy used to run the search.
• Translations details how each term was translated
  using PubMed's search rules and syntax.
• User Query shows the search terms as you entered
  them in the search box and any syntax errors with
  the query.

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Display settings
From Display Settings, select the number of
items per page to display. You can change the
number of citations displayed on a single page
from 5 to 200 items.
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Sort by

• Sort options include
• Recently Added (Citations in PubMed are displayed
  in reverse date added order last in, first out.
  The Recently Added date is the date that a record
  was initially added to PubMed)
• Publication Date(most recent citations first )
• First Author (sort A to Z )
• Last Author (sort A to Z )
• Journal(sort A to Z )
• Title (sort A to Z)

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Send to

• Use Send to for
• Saving citations in a File
• Saving citations temporarily in your Clipboard
• Saving citations permanently in My NCBI
  Collections
• E-mailing citations
• Ordering journal articles
• Printing search results

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1. AGRIS/CARIS (FAO)

• AGRIS (International Information System for the
  Agricultural Sciences and Technology) is a global
  public domain Database with 2655372 structured
  bibliographical records on agricultural science
  and technology
• The AGRIS initiative was set up by the FAO in the
  70s and created a worldwide cooperation for
  sharing access to agricultural science and
  technology information. Based on available
  technologies, AGRIS was initially collecting
  bibliographic references for a central database.
  However, since the advent of the Internet in the
  late 90s AGRIS has become the brand name for a
  network of centres,
• The Database is maintained by FAO and its content
  is provided by more than 150 participating
  institutions from 65 countries

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1. AGRIS/CARIS (FAO)

• The AGRIS open archives and bibliographical
  databases cover the many aspects of agriculture,
  including forestry, animal husbandry, aquatic
  sciences and fisheries, and human nutrition,
  extension literature from over 100 participating
  countries. Material includes unique grey
  literature such as unpublished scientific and
  technical reports, theses, conference papers,
  government publications, and more.
• 82.11 of records are citations from scientific
  journals. The bibliographic references contain
  either links to the full text of the publication
  or additional information retrieved from related
  Internet resources.

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1. AGRIS/CARIS (FAO)

• http//www.fao.org/Agris/

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2. AGRICOLA

• AGRICOLA (AGRICultural OnLine Access) serves as
  the catalog and index to the collections of the
  National Agricultural Library, as well as a
  primary public source for world-wide access to
  agricultural information.
• The database covers materials in all formats and
  periods, including printed works from as far back
  as the 15th century.

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2. AGRICOLA

• The records describe publications and resources
  encompassing all aspects of agriculture and
  allied disciplines, including animal and
  veterinary sciences, entomology, plant sciences,
  forestry, aquaculture and fisheries, farming and
  farming systems, agricultural economics,
  extension and education, food and human
  nutrition, and earth and environmental sciences.
• Although the NAL Catalog (AGRICOLA) does not
  contain the text of the materials it cites,
  thousands of its records are linked to full-text
  documents online, with new links added daily.

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2. AGRICOLA

• The NAL Catalog (AGRICOLA) is organized into two
  bibliographic data sets
• The NAL Online Public Access Catalog contains
  citations to books, audiovisuals, serials, and
  other materials, most of which are in the
  Library's collection. (The Catalog does contain
  some records for items not held at NAL.)
• The Article Citation Database includes citations,
  many with abstracts, to journal articles, book
  chapters, reports, and reprints, selected
  primarily from the materials found in the NAL
  Catalog.

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2. AGRICOLA
http//agricola.nal.usda.gov/
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3. TREESEARCH

• Treesearch is an online system for locating and
  delivering publications by Research and
  Development scientists in the US Forest Service.
• Publications in the collection include research
  monographs published by the agency as well as
  papers written by our scientists but published by
  other organizations in their journals, conference
  proceedings, or books.
• Research results behind these publications have
  been peer reviewed to ensure the best quality
  science.
• Treesearch make available all new books,
  chapters, and articles beginning January 2004,
  and to add older publications as rapidly as
  possible. At the start of 2004 the collection
  contained over 7,000 publications, making it the
  largest freely available collection of online
  forestry research in the world.

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3. TREESEARCH

• Treesearch lets you search listings by author,
  keyword, originating Station or date . Keyword
  searches examine both the title and abstract.
• Once you have selected a publication, you can
  view and print the entire publication online.
  That's because all publications listed in
  Treesearch have their full text available online,
  usually in Adobe's Portable Document Format
  (PDF).

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3. TREESEARCH
http//www.treesearch.fs.fed.us
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THANK FOR YOUR ATTENTION AND GOOD WORK!!!!!!!

• If you have any requests, suggestions or you need
  further information please contact
• micaela.decol_at_unipd.it
• biblio.agripolis_at_unipd.it