PubMedPubMed

On-line access to searching the Biomedical Literature

PubMed TutorialPubMed Tutorialhttp://www.nlm.nih.gov/bsd/pubmed

_tutorial/m1001.htmlThis is a useful tool.You need to have the correct

download for the interactive animations.

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp

Another useful tool with lots of Quick Start hints.

I have summarized some in this lecture

NCBI EntrezNCBI Entrez

Entrez links between databases

It is a life sciences search engine

http://www.ncbi.nlm.nih.gov/sites/gquery

Interrelationships

PubMed vs. GooglePubMed 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 PubMedEntrez PubMedAccess http://www.ncbi.nlm.nih.gov/entrez/ Entrez covers the Biomedical research

broadly. Even recent journals are indexed. 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

PubMedCentralPubMedCentralU.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 unrestrictedhttp://www.pubmedcentral.nih.gov/about/faq.html

PubMed EntryPubMed EntryThe

PubMed Entry includes:◦ Citation◦ Link to

paper (maybe)

◦ Abstract◦ PMID#◦ UID#

Searching the Biomedical Searching the Biomedical LiteratureLiteratureThe 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.

Uses and Limits of MeSHUses and Limits of MeSHManually 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 several months)◦ People are fallible, so some misclassification

occurs◦ Subheadings can be very useful, but are less

reliable

Strong medical focus◦ Good for biomedical searches◦ Not as useful in technical areas, agriculture

and plants

MeSH VocabularyMeSH VocabularyThe 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.

Curating-Not in a MuseumCurating-Not in a MuseumCurating in Bioinformatics is an action

taken by someone (often a scientist trained in technical areas) to regularize the language of Science.

Science uses too many synonyms- word that mean roughly the same thing.

Curating makes that regular so we can search for things.

MESH is a form of curation.

MeSH HomepageMeSH Homepagehttp://www.nlm.nih.gov/mesh/meshho

me.htmlMeSH is needed to help organize

searching for efficiency. This reduces the synonyms and

abbreviations in the biomedical literature.

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

Structure of MeSHStructure of MeSH

DivisionsAnatomy [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 ListingMeSH Full ListingNF-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: 1991Ssubheadings:

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 DatabaseJournals Database

Entrez -> JournalsA database of journal names and

informationEntry structure:

Nature genetics. pISSN: 1061-4036MEDLINE Abbr: Nat GenetISO Abbr: Nat. Genet.NLM ID: 9216904

Boolean LogicBoolean LogicBoolean 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 LogicBoolean LogicOR

◦ 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 PubMedBoolean Logic in PubMedBoolean 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 is revealed by clicking Details

Boolean Logic in PubMedBoolean Logic in PubMed

Phrase SearchingPhrase SearchingSpecify 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 NeighboringText NeighboringRelated 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 Computational Issues in Statistical Text RetrievalText Retrieval

Stop words◦Simple words like “the” and “and” are

not worth scoringTerm 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

Computational Issues in Statistical Computational Issues in Statistical Text RetrievalText Retrieval

Normalizing for length◦Don’t want to exclude short articles

or articles without an abstract

All vs. all comparison is not feasible◦107 articles => 1014 comparisons,

not feasible◦Compute demands of the task are

growing faster than Moore’s law

Entrez ClipboardEntrez 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.

Entrez ClipboardEntrez Clipboard

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 ClipboardUsing 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 8 hours of

inactivity.

Saving from the Clipboard 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.

Saving from the Clipboard Saving from the Clipboard

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.

Saving from the Clipboard Saving from the Clipboard

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.

Modifying the DisplayModifying the DisplayPubMed 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.

◦ You can also use the link-out function in the display menu which can be handy.

Entrez HistoryEntrez HistoryRetrieve 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 FieldsAddress FieldsFind 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

Related ArticlesRelated 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.

THIS MAKES IT FAST.You may see a few citations without

the Related Articles link. These citations have not yet gone through the algorithm, which takes several days.    

OnlineBookOnlineBookss

NCBI HandbookNCBI Handbook