PubMed - WV-INBRe

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PubMed

On
-
line access to searching the
Biomedical Literature

PubMed Tutorial


http://www.nlm.nih.gov/bsd/pubmed_
tutorial/m1001.html


This is an invaluable resource to
learning to use this tool.


You need to have the correct
download for the interactive
animations.

NCBI Entrez


Common retrieval
interface to many
databases


Controlled links between
databases


Maintained at the
National Center for
Biotechnology
Information (NCBI) in
the National Library of
Medicine (NLM)

Entrez 2004

PubMed vs. Google


PubMed


Peer reviewed journals


Multiple layers of
quality control


Edited and reviewed
text and grammar


Combines automated
and manual searching


Structured links to
other data sets
(nucleic acid and
protein sequences)


Google


The internet


Free, but you get
what you pay for


Variable document
structure and
grammar


Fully automated
search


Unstructured links

Entrez PubMed


Access

http://www.ncbi.nlm.nih.gov/entrez/



Coverage


Biomedical research broadly


Partial indexing of most recent couple months of journals


Lack of coverage in


CS and engineering


Physical chemistry


Plant science


Searchable content


Free text search


title, abstract, indexing, address


Controlled vocabulary


Mesh indexing, journal, dates, substance names,
secondary indices

Relationships between the Entrez
primary information resources

Searching the Biomedical
Literature


The PubMed literature is also in a flat file
format with various fields.


Knowledge of the fields in the file can
allow you to focus your search and find
what you are looking for more quickly.


For example, you can search by author and
journal if you are looking for a specific
person’s work and know where it was
published.

PubMed Search results


Search results for
PubMed include the
citation of the
articles that your
search has
returned.


Using Limits option
you can search for



Author/Keyword/
Title/ Journal


Language of pub


Date


Organism (human
or animal)


Sex (male or
female)


Type of publication

(Clinical, Review,
Editorial, etc.)

PubMed Entry


The
PubMed
Entry
includes:


Citation


Link to
paper
(maybe)


Abstract


PMID#


UID#

Uses and Limits of MeSH

Manually indexed


Major topics => intelligent filtering


Pick up things that are not in the title/abstract


Takes time to add new headings (no MeSH headings for
most recent ~couple of months)


People are fallible, so some misclassification occurs


Subheadings can be very useful, but are less reliable

Strong medical bias


Good for biomedical searches


Not as useful in technical areas, agriculture and plants

MeSH Vocabulary


The MeSH controlled vocabulary is a
distinctive feature of MEDLINE.


It imposes uniformity and consistency to
the indexing of biomedical literature.


MeSH terms are arranged in a hierarchical,
categorized system.


These MeSH Tree Structures are updated
annually.

MeSH Homepage


http://www.nlm.nih.gov/mesh/meshhome.ht
ml


MeSH is needed to help organize searching
for efficiency.


There are too many synonyms and
abbreviations in the biomedical literature.


Humans still help with the sorting of the
headings. This is called “curation.”




Structure of MeSH

Divisions

Anatomy [A]

Organisms [B]

Diseases [C]

Chemicals and Drugs [D]

Analytical, Diagnostic and Therapeutic
Techniques and Equipment [E]

Psychiatry and Psychology [F]

Biological Sciences [G]

Physical Sciences [H]

Anthropology, Education, Sociology and
Social Phenomena [I]

Technology and Food and Beverages [J]

Humanities [K]

Information Science [L]

Persons [M]

Health Care [N]

Geographic Locations [Z]



Hierarchy with Multiple
Inheritance


Amino Acids, Peptides, and Proteins [D12]


Proteins [D12.776]


DNA
-
Binding Proteins [D12.776.260]



NF
-
kappa B [D12.776.260.600]


Amino Acids, Peptides, and Proteins [D12]


Proteins [D12.776]



Nuclear Proteins [D12.776.
660
]


NF
-
kappa B [D12.776.
260
.600]


Amino Acids, Peptides, and Proteins [D12]


Proteins [D12.776]


Transcription Factors [D12.776.
930
]


NF
-
kappa B [D12.776.
260
.600]



MeSH Full Listing

NF
-
kappa B

Ubiquitous, inducible, nuclear transcriptional activator that binds
to enhancer elements in many different cell types and is
activated by pathogenic stimuli. The NF
-
kappa B complex is
a heterodimer composed of two DNA
-
binding subunits: NF
-
kappa B1 and relA.

Year introduced: 1991

Ssubheadings:

administration and dosage agonists analysis antagonists and
inhibitors biosynthesis blood cerebrospinal fluid chemistry
classification deficiency diagnostic use drug effects
genetics immunology isolation and purification metabolism
pharmacokinetics pharmacology physiology radiation effects
secretion therapeutic use toxicity ultrastructure

Restrict Search to

Major Topic headings only

Do Not Explode this term

(i.e., do not include MeSH terms found below
this term in the MeSH tree).

Entry Terms:

NF
-
kB

NF kB

Nuclear Factor kappa B

kappa B Enhancer Binding Protein

Immunoglobulin Enhancer
-
Binding Protein

Enhancer
-
Binding Protein, Immunoglobulin

Immunoglobulin Enhancer Binding Protein

Transcription Factor NF
-
kB

Factor NF
-
kB, Transcription

NF
-
kB, Transcription Factor

Transcription Factor NF kB

Ig
-
EBP
-
1

Ig EBP 1

Previous Indexing:

DNA
-
Binding Proteins (1987
-
1990)


Transcription Factors (1987
-
1990)


See Also:

I
-
kappa B


All MeSH Categories

Chemicals and Drugs Category

Amino Acids, Peptides, and Proteins

Proteins

DNA
-
Binding Proteins

NF
-
kappa B



All MeSH Categories

Chemicals and Drugs Category

Amino Acids, Peptides, and Proteins

Proteins

Nuclear Proteins

NF
-
kappa B



All MeSH Categories

Chemicals and Drugs Category

Amino Acids, Peptides, and Proteins

Proteins

Transcription Factors

NF
-
kappa B


Journals Database

Entrez
-
> Journals

A database of journal names and information

Entry structure:

Nature genetics.

pISSN: 1061
-
4036

MEDLINE Abbr: Nat Genet

ISO Abbr: Nat. Genet.

NLM ID: 9216904


See also: ISI databases

Boolean Logic


Boolean logic symbolically represents
relationships between entities. There are
three Boolean operators:


AND


Use the AND operator to retrieve a set in
which each citation contains ALL the search
terms. This operator places no condition on
where the terms are found in relation to one
another; the terms simply have to appear
somewhere in the same citation.

Boolean Logic


OR


Use the OR operator to retrieve documents
that contain at least one of the specified
search terms.


Use OR when you want to pull together articles
on similar subjects.


NOT


Use the NOT operator to exclude the retrieval
of terms from your search.


Be careful with NOT as you can exclude things
you might want

Boolean Logic in PubMed


Boolean operators
--

AND, OR, NOT
--

must be entered in uppercase letters.


Boolean operators are processed from left
to right.


Use parentheses to nest terms together so
they will be processed as a unit and then
incorporated into the overall strategy.

Boolean Logic in PubMed

Boolean Logic is revealed by clicking Details


Entrez attempts to intelligently parse your query

Query: dna binding transcription factor macrophage

Details => (((("dna"[MeSH Terms] OR dna[Text Word]) AND
(
("pharmacokinetics"[MeSH Subheading] OR "pharmacokinetics“
[MeSH Terms])

OR binding [Text Word]))

AND ("transcription factors“ [MeSH Terms] OR transcription
factor [Text Word]))

AND ("macrophages"[MeSH Terms] OR macrophage [Text
Word]))


You can force a Boolean search

Query: “dna binding” AND “transcription factor” AND
macrophage

Details => (("dna binding"[All Fields] AND "transcription
factor"[All Fields]) AND ("macrophages"[MeSH Terms] OR
macrophage[Text Word]))

Phrase Searching


Specify with quotes

“transcription factor” vs. “transcription” “factor”


Precomputed


Fast


Often mapped to synonyms and MeSH terms


Just because you get a “phrase not found”
message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)


Term usage similarity


Articles talking about the same thing are likely to use the
same words


Good recall (sensitivity)


Precomputed and fast

Limitations


Strictly algorithmic, no understanding


“Ras activates PI3K” vs. “PI3K activates Ras”


Historical and author biases in vocabulary


Poor precision (specificity)


Ranking can not satisfy everyone

Computational Issues in Statistical
Text Retrieval


Stop words


Simple words like “the” and “and” are not worth scoring


Term weights


We should weight matches of rare words more heavily than
matches of common words


Stemming and synonyms


Need to stem verbs and plural forms


May or may not be able to reduce to a normalized set of synonyms


Normalizing for length


Don’t want to exclude short articles or articles without an abstract


All vs. all comparison is not feasible


10
7

articles => 10
14

comparisons, not feasible


Compute demands of the task are growing faster than Moore’s law

Entrez Clipboard


The Clipboard gives you a place to collect selected
citations from one search or several searches.


After you add citations to the Clipboard, you may
then want to use the print, save, or order buttons.


The maximum number of items that can be placed
in the Clipboard is 500.


Once you have added items to the Clipboard, you
can click on Clipboard from the Features bar to
view your selections.


PubMed Central uses cookies to add your
selections to the Clipboard. To use this feature,
your web browser must be set to accept cookies.


Using Clipboard


Add to Clipboard



To place an item in the Clipboard, click on the
check box to the left of the citation.


Select Clipboard from the Send to pull
-
down
menu.


Then click the Send to button. Once you have
added a citation to the Clipboard, the record
number color will change to green. Send to
“clipboard”


You can save results collected from multiple
searches


The Clipboard will hold a maximum of 500 items.


Clipboard items will be lost after 1 hours of
inactivity.

Saving from the Clipboard



Citations are initially displayed in the summary
format in the relevancy order.


Use Sort to change the order. You can select all or
individual citations to display or save in one of the
citation display formats.


Select the desired format from the pull
-
down
menu, click Save to save your selections to a file,
or use the Print feature of your web browser to
print the citations.


Printing from your web browser will only print the
information and citations listed on the web page.


You may also display citations as plain text without
the sidebar menu and toolbars by clicking the
Text button.

Document Display in PubMed


PubMed Central displays your search results in
relevancy order by batches
-

the default is 20
citations per page.


The Show pull
-
down menu allows you to change the
number of citations displayed on a single page up
to a maximum of 500 items. To do this:


From the Summary Page, click on the Show pull
-
down menu and select a number. To have all of the
citations displayed on a single page, select a
number higher than the total number of your
search results.


Click the Display button to redisplay your citations
according to your selection.

Modifying the Display


PubMed Central citations are initially
displayed in a summary format. You can
choose to display other formats:


Click on the Abstract, Full Text, PDF or PubLink
hyperlink for a specific citation.


All Citations
-
Select a display format from the
Display pull
-
down menu and then click Display to
view a different display or Links for all
citations on the page.


Selected Citations
-

Click on the boxes to the
left of each author to select specific citations
and then select a format or Links from the
Display pull
-
down menu and click Display.


Entrez History


Retrieve and use your search history


Boolean combinations of search results. To
combine searches use # before search number,
e.g., #2 AND #6.


Filtering of previous search results


This can help you on big searches to remember
and build on your terms


Search History will be lost after eight hours of
inactivity

Address Fields

Find a local expert in PubMed

“Marshall University” AND (25755) [ad] OR “West Virginia”
[ad] NOT WVU [ad])

Need to think about all the ways people write
addresses

“Joan C. Edwards” fails to pick up “MUSOM.” Zip codes are
very specific, but only get about 70%, since they might not
list all authors zips

Won’t catch co
-
authored articles with a remote
collaborator

Secondary Indexes

Find articles about a Genbank entry


Query: “L44140 [si]”

1: Robertson SP, Twigg SR, Sutherland
-
Smith AJ, Biancalana V, Gorlin
RJ, Horn D, Kenwrick SJ, Kim CA, Morava E, Newbury
-
Ecob R,
Orstavik KH, Quarrell OW,Schwartz CE, Shears DJ, Suri M,
Kendrick
-
Jones J, Wilkie AO; OPD
-
spectrum Disorders Clinical
Collaborative Group. Localized mutations in the gene encoding the
cytoskeletal protein filamin A cause diverse malformations in
humans. Nat Genet. 2003 Apr;33(4):487
-
91.

2: Rivella S, Palermo B, Pelizon C, Sala C, Arrigo G, Toniolo D.
Selection and mapping of replication origins from a 500
-
kb region of
the human X chromosome and their relationship to gene expression.
Genomics. 1999 Nov 15;62(1):11
-
20.

3: Small K, Iber J, Warren ST. Emerin deletion reveals a common X
-
chromosome inversion mediated by inverted repeats. Nat Genet.
1997 May;16(1):96
-
9.

4: Chen EY, Zollo M, Mazzarella R, Ciccodicola A, Chen CN, Zuo L,
Heiner C, Burough F, Repetto M, Schlessinger D, D'Urso M. Long
-
range sequence analysis in Xq28: thirteen known and six candidate
genes in 219.4 kb of high GC DNA between the RCP/GCP and G6PD
loci. Hum Mol Genet. 1996 May;5(5):659
-
68
.

PubMedCentral


U.S. National Library of Medicine's digital
archive of life sciences journal literature


Full text of many journal archives


Not the most recent issues


Limited journal collection


Access to PMC is free and unrestricted

http://www.pubmedcentral.nih.gov/about/faq.html

Related Articles


PubMed uses a powerful word
-
weighted
algorithm to compare words from the Title
and Abstract of each citation, as well as
the MeSH headings assigned. The best
matches for each citation are pre
-
calculated and stored as a set.


You may see a few citations without the
Related Articles link. These citations have
not yet gone through the algorithm, which
takes several days.





Links


The Links pull
-
down menu provides
access to the links between records
in the Entrez databases. All links,
except for Related Articles, are
included in the pull down menu.


LinkOut


LinkOut provides links from PubMed and
other Entrez databases to a wide variety
of relevant web
-
accessible online resources
including full
-
text publications.


To see the full list of web
-
accessible online
resources for an item, select LinkOut from
the Links pull
-
down menu.


View the Abstract or Citation display
formats to see if there is an icon link to
full
-
text.

PubMed Link

NCBI Bookshelf


The Bookshelf is a growing collection of
biomedical books that can be searched
directly


Accessible as in text annotations on many
PubMed abstracts


“Links” => “Books”


Automated phrase indices hyperlinked to text
books

OnlineBooks

Example of Books Links

J Biol Chem. 2003 Aug 28 [Epub ahead of print].





Phosphorylation of
serine

S337 of
NF
-
kappa B

p50

is critical for
DNA binding
.


Hou S, Guan H, Ricciardi RP.


Microbiology Biochemistry, University of Pennsylvania, Philadelphia, PA 19342.


It has been demonstrated that phosphorylation of the
p50

subunit of
NF
-
kappa B

is required for efficient
DNA binding
, yet the specific phospho
-
residues of
p50

have not been determined. In this study, we substituted all of the
serine

and
conserved threonine residues in the
p50

Rel

homology

domain and identified three
serine residues
, S65, S337 and S342, as critical for
DNA binding

without
affecting
dimerization
. While substitution with negatively charged
aspartic acid

at
each of these positions failed to restore
DNA binding
, substitution with
threonine
,
a potential phospho
-
acceptor, retained
DNA binding

for residues 65 and 337. In
particular, S337, in a consensus site for PKA and other
kinases
, was shown to be
phosphorylated both in vitro and
in vivo
. Importantly, phosphorylation of S337 by
PKA in vitro dramatically increased
DNA binding

of
p50
. This study shows for the
first time that
DNA binding

ability of
NF
-
kB

p50

subunit is regulated through
phosphorylation of residue S337 and has implications f o r both positive and
negative control of
NF
-
kappa B

transcription
.t


PMID: 12947093 [PubMed
-

as supplied by publisher]

NCBI Handbook