Great Link for PubMed
Help
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
1. Create a Cubby to store your search
strategies.
o
Saving
Entire Search Results:
§
The
default for the Save feature is to save the entire retrieval, up to 10,000
items, unless you specifically select citations. For example, if you use the
Send to File on a screen displaying 1-20 items of 30,
your saved file will contain all 30 citations.
§
Use
the Display pull-down menu to select a format.
§
Click
Send to File and your items will be saved in this format as plain text.
o
Saving
Selected Citations from a Single Search:
§
Use
the Display pull-down menu to select a format.
§
Click
in the check boxes next to each citation you want to save.
§
You
can move to other pages within the search results to make more selections.
§
Click
Send to File and your selected items will be saved in the Display format as
plain text.
o
Saving
Citations from Multiple Searches:
§
Use
the Send to Clipboard selection to add either entire search results or selected
items to the Clipboard.
§
The
Clipboard can contain up to 500 items.
§
After
adding citations to the Clipboard, click on the Clipboard link to go to that
screen.
§
Use
the Display pull-down menu to select a format.
§
Choose
File and click Send to and your items will be saved in
this format as plain text.
2. For this part of the assignment, do your
searches and then bring down the History menu and use the clipboard to
summarize your efforts.
o
Write
a simple term search to find articles about HIV RNA dependent DNA
polymerase. What search terms did you
select?
o
Select
the first 10 articles published in 2004 and send them to the clipboard. Save them as text. Score each for relevance (e.g. highly
relevant, somewhat relevant or irrelevant).
o
Try
your search delimited by quotation marks around “RNA dependant” “DNA
polymerase” and “human immunodeficiency virus”.
Try hyphens too. What are some
differences and why?
o
What
description do you get of your search when you click “Details”? Is this what you expected?
o
Search
using all three of the Boolean operators (AND, OR, NOT).
o
Demonstrate
that you can search in PubMed using the parentheses to
make an ordered series of searches.
3. Read the section on MeSH
terms. http://www.nlm.nih.gov/mesh/introduction2004.html.
o
What
is a descriptor?
o
A
qualifier?
o
An
entry term?
4. Write a search strategy for the same
search using MeSH headings related to the term on the
Main Heading.
o
What
is a MeSH tree?
Where on a MeSH tree is your term?
o
What
happens with Find Exact Term?
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What
happens with “Find terms with ALL fragments”?
o
Find
terms with ANY fragment.”
o
How
many articles do you find using the MeSH terms
instead of the terms you thought of?
o
Score
the first 10 articles published in 2003 for relevance as above.
5. Use “Related Articles” to find articles
similar to those retrieved in #4.
o
How
many articles do you find?
o
Score
the first 10 articles in 2003 for relevance as above.
o
Use
the History function and combine two searches.
o
Select
the “links for one or more of your articles.
Can you locate a “linkout” resource for HIV?
6. Use “limits” focus your searches.
o
Find
review articles on HIV RNA
dependent DNA polymerase. Export 10
articles and rank for relevance as above.
o
Find
clinical trials on food allergies limited to human infants. Export 10 articles
and rank for relevance as above.
7. Compare the precision and recall of these
searches. What are some issues in
assessing performance of the searches?
8. Try Google with the same search
term. What are some of the differences
in what you hit? Number of hits?
9. Try using some of the subfields in PubMed listed below.
o
Find
local or regional experts on HIV (Marshall, WVU, Ohio State etc.?
What was your search strategy?
o
Search
for a paper written by someone with your last name.
o
Search
for a method used in a paper, such as rtPCR or PCR?
o
Find
a free full text article on HIV.
o
Find
a paper on Canis familiaris
published in Proceedings of the National
Academy of Science USA
10. Create a search strategy for a topic you
are interested in. Tell me the topic, describe
you strategy and save it in your cubby.
Exercise your search more than once during the course of the class to
look for new papers.
Search
Field Descriptions and Tags (in alphabetical order)
- Affiliation [ad] - Includes the institutional
affiliation and address (including email address) of the authors of the
article as it appears in the journal. This field can be used to search for
work done at specific institutions (e.g., "cleveland [ad] AND clinic [ad]").
- All Fields [all] - Includes all searchable PubMed Central fields. However, only terms where there
is no match found in one of the Translation tables or Indexes via the
Automatic Term Mapping process will be searched in All Fields. PubMed Central ignores stopwords
from search queries.
- Abstract [ab]
- Includes all words and numbers in the abstract of an article.
- Accession [accn] - Accession
numbers from the GenBank sequence database that
are cited in PMC articles.
- Author [au] - PubMed
Central citations do not list the full author name. The format to search
for an author 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. PubMed
Central 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 qualify with [au] in brackets, e.g., "o'brien
j" [au] to retrieve just o'brien
j.
- Body - All Words [articlebody]
- Includes all words and numbers in the body of a
article except for the Abstract and References.
- Body - Key Terms [body
- key terms] - Key
terms from the article body.
- EC/RN Number [rn]
- Number assigned by the Enzyme Commission to designate a particular
enzyme or by the Chemical Abstracts Service (CAS) for Registry Numbers.
- Electronic Publication
Date [epubdat] - The date of the electronic publication. Dates or
date ranges must be entered using the format YYYY/MM/DD [edat], e.g. 1998/04/06 [edat] . The month and day are optional (e.g., 1998 [edat] or 1998/03 [epubdat]).
To enter a date range, insert a colon (:) between each date (e.g.,
1996:1997 [epubdat] or 1998/01:1998/04 [epubdat])
- Figure/Table Caption
[figure/table caption]
- Includes all words and numbers in the figure and table captions of an
article.
- Filter [filter] - Technical tags used by PubMed Central to qualify citations.
- Issue [ip]
- The number of the journal issue in which the article is published.
- Journal [ta]
- The journal title abbreviation, full journal title, or ISSN number
(e.g., J Biol Chem,
Journal of Biological Chemistry, 0021-9258). The Journal Database is also
available to look up the full name, abbreviation, and ISSN number of a
journal. If a journal title contains parentheses or brackets,
enter the name without the parentheses or brackets, e.g., enter J Hand Surg [Am] as j hand surg am.
- MeSH
Major Topic [majr] - A MeSH
term that is one of the main topics discussed in the article..
- MeSH
Subheadings [sh] - MeSH
Subheadings are used with MeSH terms to help
describe more completely a particular aspect of a subject. For example,
the drug therapy of asthma is displayed as asthma/drug therapy, see MeSH/Subheading Combinations. The MeSH
Subheading field allows users to "free float" Subheadings, e.g.,
"hypertension [mh] AND toxicity [sh]". MeSH Subheadings
automatically include the more specific Subheading terms under the term in
a search. To turn off this automatic feature, use the search syntax [sh:noexp], e.g.,
"therapy [sh:noexp]". In addition, you
can enter the MEDLINE two-letter MeSH Subheading
abbreviations rather than spelling out the Subheading, e.g., "dh [sh] = diet therapy [sh]".
- MeSH
Terms [mh] - NLM's Medical Subject
Headings controlled vocabulary of biomedical terms is used to describe the
subject of each journal article in MEDLINE. MeSH
contains more than 19,000 terms and is updated annually to reflect changes
in medicine and medical terminology. MeSH terms
are arranged hierarchically by subject categories with more specific terms
arranged beneath broader terms.
- Methods - Key Terms
[methods - key terms] -
Key terms from the "methods" section of the article abstract.
- Organism [orgn]
- Contains the scientific and common names for the organisms in the NCBI
taxonomy database that are found in PMC articles. The NCBI taxonomy
database only includes species that are represented in the public sequence
databases, so many of the organisms mentioned in PMC articles will not be
found in this index. To cut down on false hits, matches to scientific
names are required to add PMC articles to this index - common names in
this field will only retrieve articles that mention the corresponding
scientific name. By default the PMC organism index is 'unexploded' - the
query "Mammalia[orgn]" will only
retrieve articles that explicitly mention the Mammalia.
The query "Mammalia[orgn:exp]" will
retrieve articles that mention any of the species of mammals.
- Organism Unsynonymized [orgn_nosyn] - Organism names that are
identified as Synonyms in the NCBI taxonomy database will retrieve the
same set of articles in the PMC Organism index (e.g
"Danio rerio[orgn]" = "Brachydanio
rerio[orgn]").
The Organism unsynonymized index will only
retrieve articles that use the name in question.
- NLM Unique ID [JID] The alpha-numeric identifier for
the cited journal that was assigned by NLM's
Integrated Library System LOCATORplus, e.g.,
0375267 [jid].
- Other Term [OT] Mostly non-MeSH
subject terms (keywords), including NASA Space Flight Mission, assigned by
an organization other than NLM. The Other Term data may be marked with an
asterisk to indicate a major concept, however
asterisks are for display only. You cannot search Other Terms with a major
concept tag. The OT field is searchable with the Text Word [tw] and Other Term [ot] search tags.
- Owner Acronym that identifies the organization
that supplied the citation data. Search using owner + the owner acronym,
e.g. ownernasa.
- Pagination [PG] Enter only the first page number
that the article appears on. The citation will display the full pagination
of the article but this field is searchable using only the first page
number. See Single Citation Matcher.
- Personal Name as
Subject [PS] Use
this search field tag to limit retrieval to where the name is the subject
of the article, e.g., varmus
h [ps]. Search names following the Author field
format, e.g., varmus h[ps].
- Pharmacologic Action MeSH Terms [PA]
Substances
known to have a particular pharmacologic action. Each pharmacologic action
term index is created with the drug/substance terms known to have that
affect. This includes both MeSH terms and terms
for Supplementary Concept Records.
- Place of Publication
[PL] Indicates the
cited journal's country of publication. Geographic Place of Publication regions are not
searchable. In order to retrieve records for all countries in a region
(e.g., North
America)
it is necessary to OR together the countries of interest. Note: This field
is not included in All Fields or Text Word retrieval.
- PMC Live Date [pmcdat]
- Date the citation was first available in PubMed
Central. Dates or date ranges must be entered using the format YYYY/MM/DD,
e.g. "1998/04/06 [pmcdat]". The month
and day are optional (e.g., "1998 [pmcdat]"
or "1998/03 [pmcdat]"). To enter a
date range, insert a colon (:) between each date (e.g., "1996:1997 [pmcdat]" or "1998/01:1998/04 [pmcdat]").
- Publication Date [dp] - The date that the article was
published. Dates or date ranges must be searched using the format
YYYY/MM/DD, e.g. "1998/03/06 [dp]".
The month and day are optional (e.g., "1998 [dp]" or "1998/03 [dp]").
To enter a date range, insert a colon (:) between each date (e.g.,
"1996:1998 [dp]"
or "1998/01:1998/04 [dp]").
- Publication Type [PT] Describes the type of material the
article represents (e.g., Review, Clinical Trial, Retracted Publication,
Letter); see full listing, e.g., review[pt].
- Secondary Source ID
[SI] The SI field
identifies secondary source databanks and accession numbers of molecular
sequences discussed in MEDLINE articles.
The field is composed of the source followed by a slash followed by
an accession number and can be searched with one or both components, e.g.,
genbank [si], AF001892
[si], genbank/AF001892 [si].
The SI field and the Entrez sequence database
links are not related. The PubMed links to these
databases are created from the reference field of the GenBank
or GenPept flatfile.
These references include citations that discuss the specific sequence
presented in these flatfiles.
- Subset [SB] Method of restricting retrieval by
Subject Subsets and Citation Status Subsets. Searchable with [SB]. Other
Subsets are available for searching that do not
use this search tag. See also Limits and LinkOut.
- Substance Name [NM] The name of a chemical discussed in
the article. Synonyms to the Supplementary Concept Substance Name will
automatically map when qualified with [nm]. This field was implemented in
mid-1980. Many chemical names are searchable as MeSH
terms before that date.
- Text Words [TW] Includes all words and numbers in
the title, abstract, other abstract, MeSH terms,
MeSH Subheadings, chemical substance names,
personal name as subject, MEDLINE Secondary Source, and Other Terms
typically non-MeSH subject terms (keywords),
including NASA Space Flight Mission, assigned by an organization other
than NLM.
- Title [TI] Words and numbers included in the
title of a citation.
- Title/Abstract [TIAB] Words and numbers included in the
title, abstract, and other abstract of a citation.
- Unique Identifier [UID] PubMed Unique Identifier PMID. To search
for the PMID type in the number with or without the search field tag [uid]. You can search for several ID numbers by
entering each number in the query box separated by a space (e.g., 95091318
97465762); PubMed will OR the terms together. To
search in combination with other terms, you must enter the search field
tag, e.g., smith [au] AND (10403340 [uid] OR
vaccines [mh]).
- Volume [VI] The number of the journal volume in
which an article is published. See Single Citation Matcher.