PubMed Refresher
Updates for Research4Life users
23 August 2023
Kathy Kwan
Research4Life
Research4Life is a public-private partnership of five programmes
Outline
● What is PubMed and what is in it?
● Access to the full text from Research4Life publishers partners and other
free full text sources
● Noteworthy updates since the webinar “Re-introducing PubMed” in July
2020
● Proximity searching
● Automated Indexing for MEDLINE citations
● Filters updates
● and more ….
● Searching in PubMed – an overview
● Live demonstration, based on your feedback in registration
● Q&A
Recording and slides will be shared in the Research4Life webinars page:
https://www.research4life.org/training/webinars/
This work is licensed under Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
What is PubMed?
What is PubMed?
● PubMed, a premier and free database of citations for biomedical and life
sciences literature from peer reviewed journals and online books
○ over 36 millions records, may link to full text
○ around 3 and a half million unique users worldwide daily
○ significant amount of access through API calls and files downloaded
○ a program of the National Center for Biotechnology Information (NCBI) at the
US National Library of Medicine (NLM)
A rich history
MEDLINE (1971) PubMed (1997) -
Medical Literature freely available on
Index Medicus Internet, includes
Analysis and Retrieval
- dated back to 1879 citations besides
System (MEDLARS)
Online MEDLINE
Print Online Internet/WWW
(Mainframe
and CD ROM)
OLDMEDLINE data. “https://www.nlm.nih.gov/databases/databases_oldmedline.html ” Retrieved on 2023-08-16
Greenberg SJ, Gallagher PE. The great contribution: Index Medicus, Index-Catalogue, and IndexCat. J Med Libr Assoc. 2009 Apr;97(2):108-13. doi:
10.3163/1536-5050.97.2.007. PMID: 19404501; PMCID: PMC2670211.
Williamson PO, Minter CIJ. Exploring PubMed as a reliable resource for scholarly communications services. J Med Libr Assoc. 2019 Jan;107(1):16-29. doi:
10.5195/jmla.2019.433. Epub 2019 Jan 1. PMID: 30598645; PMCID: PMC6300231.
What is in PubMed?
What is in PubMed?
NNLM, July 2023. How PubMed Works: Selection. https://www.youtube.com/watch?v=7yzkBphAy-8 Retrieved on 2023-08-16
What is in PubMed?
● MEDLINE (30,678K, 85%)
○ journals selected by Literature Selection Technical Review
Committee (LSTRC)
● PubMed not MEDLINE (5,405K, 15%)
○ PMC journal articles
■ PMC journal selection process
○ Author manuscripts from PMC (103K, 0.3%)
■ repository of manuscripts to compile with funders’
public access policies
■ NIH, US government agencies and NGOs
■ International funders through Europe PMC
○ Preprint, a NIH pilot (12K, 0.03%)
○ Books (32K, 0.09%)
■ Selection process
Author manuscripts
US NLM, 2023, Author manuscripts in PMC. https://www.ncbi.nlm.nih.gov/pmc/about/authorms/ Retrieved on 2023-08-20
Preprints
See: US NLM, 2023. NIH Preprint Pilot. https://www.ncbi.nlm.nih.gov/pmc/about/nihpreprints/ Retrieved on 2023-08-20
Access full text from PubMed citations
as of 2023/08/17
Access full text from PubMed Ac
Access fullAccess
text forfor
Research4Life
Research4Life users
users as of 2022/03/16
as of 2023/08/17
Access PubMed via the Research4Life content portal
via the Research4Life content
Research4Life filter and icon in PubMed summary and
abstract displays Research4Life content portal
Updates since July 2020 - highlights
● Interface
○ Page navigation at top and bottom of search results
See https://www.nlm.nih.gov/pubs/techbull/nd21/nd21_pubmed_interface_update.html
○ “Sort by” button out of Display options
See https://www.nlm.nih.gov/pubs/techbull/ja23/brief/ja23_july_pubmed_updates.html
○ Author lists in summary display truncated after 1.2K characters
See https://
www.nlm.nih.gov/pubs/techbull/ma23/ma23_pubmed_update_usability_citations.html
○ Email up to 1K citations; Cite button remembers citation style
preference; Improved workflow for Save, Email and Send to
See https://www.nlm.nih.gov/pubs/techbull/ja21/ja21_pubmed_update.html
● Functionalities
○ Filters: “Journal” and “Subject” categories removed;
“Other” category includes MEDLINE and “Exclude preprints”
See https://www.nlm.nih.gov/pubs/techbull/so21/so21_pubmed_queries.html
○ Journal names can be searched with or without initial articles
See https://www.nlm.nih.gov/pubs/techbull/ja22/ja22_pubmed_journals_search.html
Noteworthy: Access to more free full
text and associated data
● US Office of Science and Technology Policy 2022 August memo
o All federal agencies to update their public access policies, with an effective date no later
than 2025-12-31
o To make publications and supporting data resulting from federally funded research
publicly accessible without an embargo
See https://www.whitehouse.gov/wp-content/uploads/2022/08/08-2022-OSTP-Public-Access-Memo.pdf
● 2023 NIH Data Management and Sharing Policy
o Effective 2023-01-25, researchers and institutions seeking NIH research funding are
expected to
● plan and budget for the managing and sharing of data
● submit a data management and sharing plan (DMS plan) for review when applying for funding
● comply with the approved DMS plan
See https://sharing.nih.gov/data-management-and-sharing-policy
Noteworthy: proximity search
● Supplement topical searches, e.g. searches not using MeSH
● Search for multiple terms in any order within a specified distance
● “search terms”[field:~N]
○ Search terms = two or more words enclosed in double quotes
○ Field = [Title], [Title/Abstract] or [Affiliation] ; [ti], [tiab] or [ad]
○ N = The maximum number of words that may appear between search terms; for
the affiliation field, N <= 1000
○ Example: “hip pain”[tiab:~2]
● Turn off Automatic Term Mapping; not compatible with term truncation
(*)
● Can combine proximity searches with other terms using Boolean
operators
Proximity search
For more information:
○ PubMed Update: Proximity Search Now Available in PubMed. NLM Tech Bull. 2022 Nov-Dec;
(449):e4. Available at: https://
www.nlm.nih.gov/pubs/techbull/nd22/nd22_pubmed_proximity_search_available.html
○ PubMed Update: Proximity Searching Now Available for Affiliation Search Field. NLM Tech Bull. 2023 Jul-
Aug;(453):e2. Available at:
https://www.nlm.nih.gov/pubs/techbull/ja23/ja23_pubmed_proximity_searching_affiliation.html
○ Try the Proximity Searching tutorial https://
www.nlm.nih.gov/oet/ed/pubmed/quicktours/proximity/index.html\
○ NLM Office Hours: Proximity Search (March 2023) https
://www.nlm.nih.gov/oet/ed/pubmed/nlm-office-hours_proximity_searching.html
○ PubMed User Guide: https://pubmed.ncbi.nlm.nih.gov/help/#proximity-searching
Noteworthy:
Transition to Automatic Indexing
Implemented to all incoming Medline citations since April
2022
Comments and questions to NLM support:
https://support.nlm.nih.gov/
MEDLINE 2022 Initiative: Transition to Automated Indexing. NLM Tech Bull. 2021 Nov-Dec;(443):e5. Available at
https://www.nlm.nih.gov/pubs/techbull/nd21/nd21_medline_2022.html
Automated Indexing
● Provide MeSH indexing to a MEDLINE citation within 24 hours after it
appears in PubMed
● Based on the title and abstract of an article; may expand to the full
text where possible in the future
● Use Medical Text Indexer-Auto (MTIA) algorithm which is pattern based,
and combines MeSH terms mapped from the title and abstract with the
MeSH terms from related PubMed records
● Human indexers performs quality assurance review of selected
indexing result
● Identified in PubMed XML as “IndexingMethod=“Automated”
See https://www.nlm.nih.gov/pubs/techbull/ja18/ja18_indexing_method.html
● Search PubMed for this type of citations: indexingmethod_automated
● Author can provide MeSH terms as keywords to publisher to be
included in their articles, such that those terms can be used in the
automated indexing
US NLM, 2023. Frequently Asked Questions about Indexing for MEDLINE. https://www.nlm.nih.gov/bsd/indexfaq.html retrieved on 2023-08-20
Search Tips from the US National
Library of Medicine
● Be specific
● No punctuation necessary
● No need for Boolean operators
● No need to capitalize
● PubMed can find phrases
● No need for search tags e.g. [tiab] [author]
● PubMed is smart!
NNLM , July 2023. How PubMed Works: Automatic Term Mapping. https://www.youtube.com/watch?v=XBRi0zy_B_g retrieved on 2023-
08-18
Frequently searched: a specific citation
AuthA
Frequently search: Author’s
3rd stop: Author Translation Table
work
● last name, 1st initial
○ example: fauci a
● last name, all initials
○ example: fauci as
● full name in natural and inverted order
○ example: anthony fauci
Author search - PubMed can help
AuthA
Author search - PubMed can help (cont’d)
AuthA
Canese K. PubMed and Computed Author Sorted Display NLM Tech Bull. 2012 May-Jun;(386):e2. https://
www.nlm.nih.gov/pubs/techbull/mj12/mj12_pm_author_ranking.html retrieved 2023-08-18
Computed Author Sort
AuthA
How PubMed
PubMed search details search?
Search Details
AutomaticAutomatic
Term Mapping (ATM): (ATM):
Term Mapping
Three translation tables tables
Three translation
NNLM , July 2023. How PubMed Works: Automatic Term Mapping. https://www.youtube.com/watch?v=XBRi0zy_B_g retrieved on 2023-
08-18
1st stop: Subject Translation
Table
● MeSH (Medical Subject Headings)
○ Headings, Subheadings, Supplementary Concepts
○ Entry Terms (synonyms)
○ Publication Types, a Mesh category
○ Pharmacologic actions, a Mesh category
● Singular and plural word forms
● British and American Spellings
● Drug brand name to generic name translation
● UMLS (Unified Medical Language System)
NNLM , July 2023. How PubMed Works: Automatic Term Mapping. https://www.youtube.com/watch?v=XBRi0zy_B_g retrieved on 2023-
08-18
MeSH term: COVID-19
Supplementary concept:
COVID-19 breakthrough infections
https://www.ncbi.nlm.nih.gov/mesh/2052179 https://www.ncbi.nlm.nih.gov/mesh/2100363
2nd stop: 2nd
Journal Translation
stop: Journal Translation Table
Table
● Full journal titles
○ example: The New England journal of medicine
● NLM title abbreviation
○ example: N Engl J Med
● ISSN with dashes
○ example: 0028-4793
For journal titles of all PubMed citations/NCBI
databases
NNLM, July 2023. How PubMed Works: Automatic Term Mapping. https://www.youtube.com/watch?v=XBRi0zy_B_g retrieved on 2023-
08-18
3rd stop: Author Translation Table
NNLM, July 2023. How PubMed Works: Automatic Term Mapping. https://www.youtube.com/watch?v=XBRi0zy_B_g retrieved on 2023-
08-18
How to turn off ATM
● Quotation marks
○ “chest pain” vs chest pain
● Search tags
○ chest pain [tiab] vs chest pain
● Advanced Search Builder
○ same as using search tag
○ explore the index related to a search field
NNLM, July 2023. How PubMed Works: Automatic Term Mapping. https://www.youtube.com/watch?v=XBRi0zy_B_g retrieved on 2023-
08-18
More
More on the PubMed PubMed
on thehome home page
page
PubMed New and Noteworthy and
NLM Technical Bulletin
https://www.nlm.nih.gov/pubs/techbull/
https://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews
Excellent resources from NLM and
NNLM (Network of the National Library of
Medicine)
● PubMed User Guide
○ https://pubmed.ncbi.nlm.nih.gov/help/
● How PubMed Works
○ https://nnlm.gov/training/class-catalog/how-pubmed-works
● PubMed Online Training
○ https://learn.nlm.nih.gov/documentation/training-packets/T00420
10P/
● PubMed Customer Support
○ https://support.nlm.nih.gov/
