PubMed

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PubMed More

• Annette M. Nahin
• National Library of Medicine
• Woods Hole Biomedical Informatics
• September 2009

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• Produced by the National Center for Biotechnology
  Information (NCBI).
• NLMs free web interface for searching
  biomedical/life science citation data.
• Over 19 million citations.
• PubMed provides links to NCBIs integrated
  molecular biology databases and to publishers for
  full text.
• It is easy to create links to PubMed searches for
  hospital, library, or personal web sites. 

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PubMed Daily Statistics

• 10 million page hits
• 3 million searches
• 550,000 Google referrals
• 3.5 million Abstract views
• 10 of all Abstract views use a link to Related
  Articles

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Related Articles
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Why Are We So Popular?

• Fast and Current
• Strength of MEDLINE
• Power of PubMed
• Available anytime/anywhere
• Free

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PubMed 19 million
MEDLINE 17.6 million
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Publisher
LinkOut
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Publisher-Supplied Data

• Electronic Submission of Data
• means
• PubMed can link back to full-text at publishers
  site..LinkOut

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Indexing with MeSH Vocabulary
5-20 MeSH Headings
50K/month!
/subheading
Asterisk major concept.
Index to the specific
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MeSH

• The backbone of MEDLINE
• Controlled Vocabulary
• 25K Headings
• 80 subheadings
• 100K Substances (Chemicals drugs)
• Headings in a hierarchy

Mitochondrial Myopathies
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PubMed Redesign Goals

• Make PubMed easier to use
• Simplify the interface
• Refresh the look
• Organize information
• Expose features better
• Promote scientific discovery

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Searching with PubMed
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Searching Automatic Term Mapping (ATM)

• Recognizes Subject Terms
• MeSH example drooling maps to Sialorrhea
• UMLS example heart attack maps to
  Myocardial Infarction
• Recognizes Journal Titles
• Pediatr Transplant -gt Pediatric Transplantation
• Recognizes Names
• Author (Fauci AS)
• Full Author (Anthony Fauci - 2002)
• Collaborators (2008)

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PubMed Parsing

• prostate cancer treatment with estrogen

stop word
MeSH translation
MeSH translation
MeSH translation

• public health reports alexander lk continuing
  education

MeSH translation
Journal
Author name
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PubMed - Enter terms
gene therapy macular degeneration
and click Search.
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Auto Suggest
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katayama cell
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Gene Sensor
brca1
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Structure Sensor
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Structure
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Sequence Sensor
nm_000125
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Advanced Search
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History
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Search by Author, Journal, Publication Date, and
more
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Advanced Seach (contd)
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Limit by Topics, Languages, and Journal Groups
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Subject Subsets for Limits

• AIDS
• Bioethics
• Cancer
• Complementary Medicine
• History of Medicine
• Space Life Sciences
• Systematic Reviews
• Toxicology

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Advanced Search (contd)
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Advanced Search (contd)
Med Educ 2009 43 6 533
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Clinical Queries
myasthenia gravis
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Results of Clinical Study Category Search
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Collaborators
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RSS Feed
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Coming from Google
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Linking from Search Engines
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PubMed Links to PubMed Central
paralytic shellfish poisoning
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PubMed Central Icon Links
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PMC includes over 1.8 million free full-text
articles from 700 journals!
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What is the NIH Public Access Policy?

• If NIH funds your work (whole or part), deposit
  your article in PMC
• Submit final, peer-reviewed manuscripts accepted
  for publication
• Not covered book chapters, editorials, or
  conference proceedings

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NIH Public Access Policy Compliance
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Manuscripts in PubMed Central
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NIH Manuscript Submission Help

• Submission tutorials available at
  NIHMShttp//www.nihms.nih.gov/web-help
• FAQs on Public Access Policy and
  NIHMShttp//publicaccess.nih.gov/policy.htm
• NIHMS Help Deskhttp//www.nihms.nih.gov

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Need PMCIDs?
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Converter
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PMID/PMCID Converter
Converter
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E-Utilities
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Leasing MEDLINE(no charge)

• We will search MEDLINE for data associated to
  stem cells mainly of genes and proteins specific
  of several types of stem cells.
• We will be extracting taxonomic and phenotypic
  information from titles and abstracts of MEDLINE.
  
• We are using MEDLINE and UMLS to perform text
  and data mining on textual data to support drug
  discovery and development efforts.
• We intend to use MEDLINE/PubMed to develop
  automatic methods to check for certain facts,
  i.e. whether malignant hypertension is a medical
  emergency, or asthma is a lung disease.

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• Save Searches (strategies)
• Create automatic e-mail updates
• Save citations in Collections My
  Bibliography and share with others
• Select filters to group retrieval by topics
• Create customized filters.
• Highlight search terms
• Libraries create accounts with preferences
  selected for your patrons.

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Automatic E-mail Update
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My NCBI Features
Filters are activated
handheld computerized medical records
Highlighting is turned on
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My NCBI E-mail Updates
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Six Months of Recent Activity
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Recent Activity
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Sharing Your My NCBI Collections
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My NCBI Preferences
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My NCBI Filters
handheld computerized medical records
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My NCBI Custom Filters
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LinkOut to full text

• Over 10 million citations from over 7 thousand
  journals include full-text article links
• Over 2.7 million links to free full text
• 2,225 libraries participate in LinkOut (646
  international)
• PubMed can display a librarys print electronic
  icons - usage data are available for these links

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NLM Mobile
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• Introduced in August 2009
• an archival service to support research shared
  through new venues for rapid communication (e.g.,
  online forums) enabled by the internet.
• allows users to access and cite research that is
  provided through participating publisher programs
  designed for immediate communication.
• prompted in part by the 2009 worldwide outbreak
  of H1N1 influenza and the call for a means to
  quickly share research information about this
  emergent public health threat.
• PLoS Currents Influenza, the first collection
  being archived in RRN.

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NCBI Homepage
www.ncbi.nlm.nih.gov
brca2
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Entrez All Databases
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smallpox
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Hands On Lab Time

• Register for My NCBI
• Create an automatic e-mail update
• Create a Collection share it
• Add some new or customized filters
• Create a Web link to record in PubMed
  pubmed.gov/PMID
• Search PubMeds Clinical Queries
• Create a PubMed RSS feed