NLMMBL BioMedical Informatics

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PubMed, LinkOut, Gateway, and moreAnnette M.
NahinNational Library of Medicine

• NLM/MBL BioMedical Informatics
• Fall 2008
• Woods Hole, MA

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Who Does What?

• National Institutes of Health (NIH)
• National Library of Medicine
• NLM creates MEDLINE
• National Center for Biotechnology Information
• NCBI creates PubMed
• Lister Hill National Center for Biomedical
  Communications
• LHNCBC creates the NLM Gateway
  ClinicalTrials.gov

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Entrez All Databases
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PubMed
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• Supplied by publisher (epub ahead of
  print)
• In process (indexing)
• Indexed for MEDLINE

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Why Are We So Popular?

• Fast
• Strength of MEDLINE
• Power of PubMed
• Free

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Publisher-Supplied Data

• Electronic Submission of Data
• Links back to full-text at publishers site
• (LinkOut)

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MEDLINE
Asterisk major concept.
/subheading
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Searching PubMeds Automatic Term Mapping (ATM)

• Recognizes Subject Terms
• MeSH (maps drooling -gt sialorrhea)
• UMLS (maps heart attack -gt myocardial
  infarction)
• Recognizes Journal Titles
• Pediatr Transplant -gt Pediatric Transplantation
• Recognizes Names
• Author (Fauci AS)
• Full Author (2002)
• Collaborators (2008)

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Parsing PubMed Queries

• use of vitamin c for treating the common cold
• clinical trial knee replacement

stop words
stop word
stop word
MeSH mapping
MeSH mapping
subheading mapping
publication type
simple phrase -gt automatic term mapping
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Enter Your Search
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Mapping!

• ("anti-hiv agents"MeSH Terms OR ("anti-hiv"All
  Fields AND "agents"All Fields) OR "anti-hiv
  agents"All Fields OR ("aids"All Fields AND
  "drugs"All Fields) OR "aids drugs"All Fields
  OR "anti-hiv agents"Pharmacological Action)
• AND
• ("maternal foetal transmission"All Fields OR
  "disease transmission, vertical"MeSH Terms OR
  ("disease"All Fields AND "transmission"All
  Fields AND "vertical"All Fields) OR "vertical
  disease transmission"All Fields OR
  ("maternal"All Fields AND "fetal"All Fields
  AND "transmission"All Fields) OR "maternal
  fetal transmission"All Fields)

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Mapping Expanded

• gill "gills"MeSH Terms OR "gills"All
  Fields OR "gill"All Fields
• gene therapy "gene therapy"MeSH Terms OR
  ("gene"All Fields AND "therapy"All
  Fields) OR "gene therapy"All Fields

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ATM (contd)
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AbstractPlus
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Mouseover to see Journal Title
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Title Searching

• Competitive swimmers with allergic asthma show a
  mixed type of airway inflammation.

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Advanced Search Beta!
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Advanced Search
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History
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Combining searches in 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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Ads
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Our version - Discovery
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Drug Sensor
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Clinical Queries
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Clinical Queries (contd)
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Special Queries
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HSR Search Tool
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Linking from Web Search Engines
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PubMed Offers More
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Cant Spell?
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Spelling Corrections
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Full Author Searching
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Full Author Searching (contd)
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Search Links Author
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Search Links MeSH, Trial, Grant Numbers
PubMeds Citation format
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ClinicalTrials.gov

• A registry of federally and privately supported
  clinical trials conducted in the United States
  and around the world.
• ClinicalTrials.gov gives you information about a
  trial's purpose, who may participate, locations,
  and phone numbers.
• This information should be used in conjunction
  with advice from health care professionals.
• Recently Redesigned - New User Interface.
• New options to display results and study
  information.
• Search terms and synonyms are now highlighted.

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Search Link -gt ClinicalTrials.gov
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Display, Show, Sort by, Send to
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Sample RSS Feed
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My NCBI
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Over 1.4 million registered users!
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Want Updates? Use Save Search
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Selecting Options for Auto Updates
Over 1 million updates sent out each month.
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Sample E-mail Update
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Sample E-mail Update
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Viewing Update Items in PubMed
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Review Filter
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Saved Searches (strategies)
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Collections (of citations)
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Add to a Collection
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Append to Existing Collection
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Collection was Updated
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My NCBI Preferences
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Filters Up to 5
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Filter for Your Library
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Filter for Your Library
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Filter Tabs in Action
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Filter Tabs
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Your library may provide a special link to PubMed
that can display icon links.
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LinkOut

• 6,100 journals with LinkOut links.
• 8.9 million citations
• Activity 29 million hits/month
• LinkOut for Libraries program
• 1,934 Libraries participating
• 500 participate with Outside Tool (e.g., SFX,
  FindIt)

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PubMed Central

• NIHs digital archive of biomedical journal
  literature.
• Provides free access to the full text of
  articles.
• Journals are encouraged to deposit all their
  content.
• A journal may delay release of its full text in
  PMC for some period of time after publication.

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PubMed Links to PubMed Central
detection carriers BRCA1 BRCA2
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PubMed Links to PubMed Central
detection carriers BRCA1 BRCA2
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NIH Public Access Policy
publicaccess.nih.gov
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PubMed Central ID

• PMC ID unique ID for articles in PubMed
  Central.
• Researchers must provide the PMC ID for articles
  cited in grant applications, proposals, progress
  reports
• Find PMC ID in PMC, in PubMed, or use PMC ID
  Converter

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PubMed Central ID
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PubMed Central ID in PubMed
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PMC ID Converter
http//www.ncbi.nlm.nih.gov/sites/pmctopmid
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Mobile PubMed
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Get the Data

• E-Utilities tools that provide access to Entrez
  data outside of the regular web query interface
  and may be helpful for retrieving search results
  for future use in another environment.

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Leasing MEDLINE sample uses

• 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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Creating a Web link to search PubMed

• http//www.ncbi.nlm.nih.gov/pubmed/18276894,182768
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• http//www.ncbi.nlm.nih.gov/pubmed?termantioxidan
  tchocolate

create web link
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Tutorials Location, Location, Location
10K page views per month!
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• An NIH/NCBI database of Genotype and Phenotype
• Developed to archive and distribute the results
  of studies that have investigated the interaction
  of genotype and phenotype.

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• This Web site brings together information on
  genetic disorders from multiple sources.
• www.geneticalliance.org

Prader-Willi Syndrome example
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NLM Gateway
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Archival collections of leaders in biomedical
research and public health.
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Francis Cricks ready-made reply post card to
refuse invitations.
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NLM Catalog Books Monographs
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Hands On Lab Time

• Register for a My NCBI account.
• Create an automatic e-mail update.
• Change the default filter settings.
• Create an RSS feed.
• Create a Web Link to PubMed (see bookmarks).
• Search PubMeds Clinical Queries using your
  handheld.
• Create a Collection.
• Try the PMC ID Converter.