Biblioteca Centrale P. Arduino – CIS Agripolis
Edited by the Group for Training in Library Resources
Course
“Access to bibliographic resources”
for post graduate Schools of Agripolis
10-14 ottobre 2011
(15 hours)
3° PART –12 october - 9.30-12.30
Terachers: Micaela De Col, Federico Fogo
• Bibliographic searches through Scifinder
(presented by Federico Fogo)
• Bibliographic searches through free data
banks as PUB MED, AGRICOLA, AGRIS
etc.
Bibliographic search
Basic 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
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
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
TE TOOLS - Logical operators (or Boolean
operators) AND, OR, NOT
AND
WORD 1 AND WORD 2 You will retrieve documents
that contain both words. As a
result, you limit your search
OR
You will retrieve documents
WORD 1 OR WORD 2
that contain word 1 or either
word 2 or both. As a result,
you expand your search
NOT
You will retrieve documents
WORD 1 NOT WORD 2 that contains word 1 but not
word 2.
As a result, you refine your
search
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
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 …
Ricerca
bibliografica
(motore di
ricerca,banch
e dati, Aire,
etc.)
Organizzazione della ricerca
Individuazione
bibliografica documento
Aire/
Opac di Ateneo : E-journals
Cerca SBN – MAI :
periodici, ACNP : ricerca
a citazione : monografie,
monografie, periodici (Capere,
periodici, periodici
etc Aire, etc.)
libri, articoli
Localizza Accesso al Localizza Accesso
Localizza
il documento full-text il documento al full-text
il documento Localizza Localizza
nelle e in biblioteche e
nelle biblioteche il documento il documento
biblioteche stampa di altre stampa
di Ateneo
di Ateneob documento città o stati documento
Recupero Recupero
di un testo di un testo Recupero Servizio DD Servizio DD Servizio ILL
o o del documento
fotocopie fotocopie tramite DD/ILL (articoli) (articoli) (libri)
di un articolo di un articolo
BIBLIOGRAPHIC SEARCH
To do a bibliographic search we can:
– To look up journals with their
indexes
– To search databanks
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.)
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
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.)
ACCESS TO UNIVERSITY OF PADOVA
DATA BANKS:
HOW 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
Bibliographic searches through
Scifinder
Scifinder
(dott. Federico Fogo)
Bibliographic searches through
free data banks:
PubMed,
Treesearch,
AGRICOLA,
AGRIS/CARIS
(Dott.ssa Micaela De Col)
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
PubMed Bibliographic Search
PubMed Content
PubMed comprehends over 20 million citations of
biomedical literature from MEDLINE, life science journals,
and online books.
•MEDLINE®: NLM’s 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
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
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.
How do I search PubMed?
Search
You can get:
1. by subject lists of bibliographic
2. by author citations from articles
3. by journal Link to the full-text (if present)
or to related articles
4. Other search
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)
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.
Esempio:
• Animal Diseases [C22]
Abortion, Veterinary[C22.021]
+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
Mesh Browser
http://www.nlm.nih.gov/mesh/MBrowser.html
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 m[AU], Liver
diseases[MH]
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)"
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] = Crabs[mh]).
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.
Seach field descriptions and
Tag
Searching for a phrase
USING 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.
Link
PubMed is available
free on the Internet at :
http://www.ncbi.nlm.nih
.gov/pubmed
Esempi
1. Search for records in Javma Journal that
contain the term cancer in text
2. Records that contain liver in general, but not
studies on humans
3. Records on neoplasia in cats and dogs
indifferently
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.
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
• Con:not all the words used in natural language
are key words
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.
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.
Simple search: Text word
PubMed displays a list of results in Summary format in
batches of 20 citations.
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.
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 .
Searching by author
First
authir or
co-author
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
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
author’s 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.
Combining more authors with
Boolean operator AND
Combining more authors
with Boolean operator OR
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..
Search by journal
Advanced search
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.
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.
.
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)
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.
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.”.
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
Understanding Your Search Results –
Display formats
PubMed Citation Display Formats
• Summary: default (Authors, Title, Journal
source, etc.)
Understanding Your Search Results –
Display formats
• Abstract: include abstract, but the Abstract (text) format does
not include MeSH data.
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.
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.
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.
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)
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
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
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.
1. AGRIS/CARIS (FAO)
• http://www.fao.org/Agris/
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.
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.
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.
2. AGRICOLA
http://agricola.nal.usda.gov/
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.
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).
3. TREESEARCH
http://www.treesearch.fs.fed.us
THANK FOR YOUR ATTENTION
AND GOOD WORK!!!!!!!
If you have any requests, suggestions or you need
further information please contact:
•micaela.decol@unipd.it
•gabry.leon@unipd.it