Advanced Medline
Franklin Sayre
franklin.sayre@ubc.ca
Objectives
By the end of this session you should be able to:
1. Use MeSH scope notes to better focus your searching
2. Det...
Medline: Content & Scope
• Produced by the U.S. National Library of Medicine (NLM)
• 1946 to present
• ~20 million records...
Medline: Pubmed vs. Medline
Pubmed
MEDLINE (searchable
in Pubmed, OvidSP,
EBSCO, etc.)
• Some in-
process
citations
• Some...
Review: Medline - Organization
Medline contains bibliographic records not the full text of articles:
• A bibliographic rec...
Medical Subject Headings (MeSH)
MeSH are a system of Subject Headings (also called a “Controlled
Vocabulary”):
• Subject H...
Medical Subject Headings(MeSH): Examples
Two example MeSH:
•Pregnancy: http://www.ncbi.nlm.nih.gov/mesh/68011247
•Pregnant...
Medical Subject Headings (MeSH): Scope Notes
Parts of a Scope Note:
PREFERED TERM: The official term for that disease, pro...
Activity: Understanding MeSH Scope Notes (5
minutes)
• Search for a few different kinds of concepts, e.g.
• A disease or c...
Activity: Understand MeSH Scope Notes
(Wrap-up & Discussion)
Did you notice anything interesting?
•Definition: Notice how ...
Searching with MeSH: Three Questions
Explode, focus, subheadings
1. Should I explode?
2. Should I focus?
3. Should I use s...
Searching with MeSH: Do I want to explode?
Explode includes all narrower headings in the MeSH tree
• MeSH headings are org...
Medical Subject Headings (MeSH): Tree
A. Anatomic terms
B. Organisms
C. Diseases
D. Drugs and chemicals
E. Analytical,Diag...
Activity: Exploding vs. Not Exploding (5 minutes)
Take one or more of the MeSH headings you found earlier:
1.Find where it...
Searching with MeSH: Do I Want to Focus?
Focus designates the MeSH that are the main intellectual “focus” of
the article
•...
Activity: Using Focus (5 minutes)
Take one or more of the MeSH Headings you searched for
earlier:
1.Search for it again an...
Searching with MeSH: Do I want to use Subheadings?
Subheadings limit your search to particular aspects of a concept
• Subh...
Activity: Using Subheadings (5 minutes)
Take a MeSH you searched for earlier:
1.Search for it again, this time when you ge...
Keywords
• Keywords are words used in the title and abstract of the
article (and a number of other fields)
• Based on simp...
MeSH vs. Keywords
MeSH Keywords
• Established concepts
(Diabetes, Heart Disease)
• Core biomedical concepts
(diseases, dru...
Indexing Status and MeSH vs. Keywords
The delay in indexing articles means newer material can only be
found using keywords...
Tools for Keywords
Phrases: Find a specific phrase (more specific)
•“cultural deprivation”
Proximity: Find words within a ...
Activity: Search using keywords (10 minutes)
1. Try searching using:
1. An individual word (e.g. education)
2. A phrase (e...
Limits
Aspects of Study Design and Publication Type
• Always apply limits last
• Limits are not necessarily perfectly appl...
Activity: Applying Limits (5 minutes)
1. Try the following limits:
1. Publication Year
2. Age Groups (age of study populat...
Activity: Survey (3 minutes)
Your feedback helps us improve our current workshops and plan
services based on your needs. P...
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Advanced Medline for Health Researchers

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A 1.5 hour workshop on Medline meant for researchers who already have some experience with Medline. Built to be as interface neutral as possible and therefore usable for teaching Pubmed or OvidSP. Focus is on active learning and includes a worksheet where participants can record things they notice about MeSH headings and search results as they work through the activities. Feedback very welcome. Edited to remove section on filters and add an activity around limits.

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  • Who has searched medline? Via pubmed? Via ovidsp?
  • Review only if necessary
  • This often confuses people Medline is a database searchable through many different interfaces; Pubmed is an interface. Pubmed also searches some extra stuff like ebooks and out-of-scope articles MORE INFO IF PEOPLE ASK QUESTIONS: WHAT IS IN PUBMED NOT IN MEDLINE: The out-of- scope  citations (e.g., articles on plate tectonics or astrophysics) from certain MEDLINE journals, primarily general science and chemistry journals, for which the life sciences articles are indexed for MEDLINE. Citations that precede the date that a journal was selected for MEDLINE indexing. Some additional life science journals that submit full text to PubMed Central and receive a qualitative review by NLM. Citations for the NCBI Bookshelf collection.
  • The record is what you’re searching
  • Explain scope notes (parts of) and tree (importance of) in context of examples Then skip over next slide (there for handouts)
  • SKIP IF EXPLAINED IN EXAMPLES Each MeSH term has a scope note. Scope note tells you what that MeSH is about When to use it History Very important: e.g. AIDS, added in 1983, previously indexed as “i mmunologic Deficiency Syndromes (1979-1982)” so need to search that to get articles from before 1983
  • Quick demo using candy or lunch
  • Quick demo using candy or lunch
  • SKIP IF EXPLAINED IN EXAMPLES First 4 categories are the best indexed, most traditional parts of medicine Always look where you are; MeSH splits lots of hairs, i.e. disease vs. disease causing agent / practice of medicine vs. group that practices, etc. Also want to look around, see what is bellow you, what is above, ask is it relevent, do I need to include or exclude it
  • i.e. spelling mistakes in your search OR in the abstract
  • Generally: Searching using MeSH alone will result in a limited set of relevant results when the concepts are fairly established in the medical literature Searching with keywords alone will result in more results of varied quality but can work well for new and unusual concepts Combining the both is best to maximine recall, as in a systematic review, where you need to find as close to everything as possible
  • Skip over this
  • Advanced Medline for Health Researchers

    1. 1. Advanced Medline Franklin Sayre franklin.sayre@ubc.ca
    2. 2. Objectives By the end of this session you should be able to: 1. Use MeSH scope notes to better focus your searching 2. Determine when to use explode, focus, and subheadings 3. Determine when to use keywords 4. Use some advanced keyword search operators
    3. 3. Medline: Content & Scope • Produced by the U.S. National Library of Medicine (NLM) • 1946 to present • ~20 million records • US Based, 95% english • Citations from approximately 5,600 worldwide journals in 39 languages (careful review of journals for selection) • 2,000-4,000 records added per day
    4. 4. Medline: Pubmed vs. Medline Pubmed MEDLINE (searchable in Pubmed, OvidSP, EBSCO, etc.) • Some in- process citations • Some older material • Some eBooks • Medline is a database • Pubmed is an interface to Medline that includes some other material • Medline can be searched using different interfaces (OvidSP, EBSCO) *98% of what pubmed searches is searchable from other Medline is a database searchable through different interfaces
    5. 5. Review: Medline - Organization Medline contains bibliographic records not the full text of articles: • A bibliographic record contains: • Title • Authors • Abstract • MeSH Headings • Other descriptive information • Example Record: Mortality in relation to smoking: 50 years' observations on male British doctors: http://www.ncbi.nlm.nih.gov/pubmed/15213107
    6. 6. Medical Subject Headings (MeSH) MeSH are a system of Subject Headings (also called a “Controlled Vocabulary”): • Subject Headings are a system that designates a single authorized term or phrase for each unique concept • Helps control for variations in human language such as synonyms, spelling, and alternative phrasings • Similar to ICD9/10 Codes and other classification systems • Assigned to articles by indexers who apply the most appropriate headings to describe the content of the article
    7. 7. Medical Subject Headings(MeSH): Examples Two example MeSH: •Pregnancy: http://www.ncbi.nlm.nih.gov/mesh/68011247 •Pregnant Women: http://www.ncbi.nlm.nih.gov/mesh/68037841 Example Record with MeSH: •Mortality in relation to smoking: 50 years' observations on male British doctors: http://www.ncbi.nlm.nih.gov/pubmed/15213107 •See the MeSH headings applied to this article and how they describe various characteristics of the article
    8. 8. Medical Subject Headings (MeSH): Scope Notes Parts of a Scope Note: PREFERED TERM: The official term for that disease, process, etc. as assigned by NLM DEFINITION: The scope of the definition; what this MeSH covers. YEAR INTRODUCED: Important because articles indexed before this year will not be searchable using this MeSH. PREVIOUS INDEXING: The MeSH used to index this concept before the term was created. AVAILABLE SUBHEADINGS: Subheadings that can be applied ENTRY TERMS: Other terms for this concept (useful for building lists of keywords) SEE ALSO: Related MeSH terms MeSH TREE: Location within MeSH Tree
    9. 9. Activity: Understanding MeSH Scope Notes (5 minutes) • Search for a few different kinds of concepts, e.g. • A disease or condition • Something that causes a disease or condition • A therapy/test/intervention • An outcome • A social/cultural concept, group, geographic area • Record the name of the MeSH and anything interesting about the definition, year introduced, related terms, and available subheadings (don’t worry about writing everything down)
    10. 10. Activity: Understand MeSH Scope Notes (Wrap-up & Discussion) Did you notice anything interesting? •Definition: Notice how specific the definition is? •Year Introduced: Why then? How would this effect searching? •Previous Indexing: What would you need to do to find older material? •Way that MeSH split concepts up: E.G. Definition? Related Terms? Previous Indexing? •Available Subheadings: How do they compare with the subheadings available for other kinds of concepts?
    11. 11. Searching with MeSH: Three Questions Explode, focus, subheadings 1. Should I explode? 2. Should I focus? 3. Should I use subheadings?
    12. 12. Searching with MeSH: Do I want to explode? Explode includes all narrower headings in the MeSH tree • MeSH headings are organized in a hierarchy from broad to narrow concepts • Articles are indexed to the narrowest (most specific) level possible • Example: Canada (http://www.ncbi.nlm.nih.gov/mesh/68002170) • If an article is about Canada generally it will be indexed with “Canada” • If it is specifically about British Columbia it will be indexed with “British Columbia” but NOT with “Canada” • Explode includes all narrower concepts bellow that heading in the MeSH tree in your search
    13. 13. Medical Subject Headings (MeSH): Tree A. Anatomic terms B. Organisms C. Diseases D. Drugs and chemicals E. Analytical,Diagnostic &Therapeutic Techniques & equipment F. Psychiatry and Psychology G. Phenomena & Processes H. Disciplines & Occupations I. Anthropology,Education, Sociology and Social Phenomena G. Technology,Industry,Agriculture K. Humanities L. Information Science Named Groups N. Health Care M.Publication Characteristics P. Geographicals
    14. 14. Activity: Exploding vs. Not Exploding (5 minutes) Take one or more of the MeSH headings you found earlier: 1.Find where it is located in the MeSH tree 2.See if it has any narrower headings under it, if it doesn’t use another heading that does 3.Run a search with just the heading (not exploded) 4.Run a second search where you explode the heading 5.Notice the difference in search results NOTE: For now ignore both focus and subheadings
    15. 15. Searching with MeSH: Do I Want to Focus? Focus designates the MeSH that are the main intellectual “focus” of the article • Focus is given to 2-4 MeSH that reflect the main “focus” of an article, i.e. the concepts that the article is primarily about • Example: Mortality in relation to smoking: 50 years' observations on male British doctors (http://www.ncbi.nlm.nih.gov/pubmed/15213107) Focus was given to: • Neoplasms/mortality* • Physicians/statistics & numerical data* • Smoking/mortality* • Smoking Cessation/statistics & numerical data* • When you use “focus” you’re saying you only want to see articles where the concept that MeSH designates is a main focus of the article. • Should not be used with systematic reviews or if you need to be comprehensive.
    16. 16. Activity: Using Focus (5 minutes) Take one or more of the MeSH Headings you searched for earlier: 1.Search for it again and this time select the focus option 2.Run the search and compare how many results you received with the number you returned when you didn’t use focus 3.Scan through a few of the results and note how their content more closely centres around that concept. NOTE: For now ignore subheadings
    17. 17. Searching with MeSH: Do I want to use Subheadings? Subheadings limit your search to particular aspects of a concept • Subheadings get at particular aspects of a MeSH heading • Also called qualifiers • Example Record: Mortality in relation to smoking: • Neoplasms/mortality • Smoking Cessation/statistics & numerical data • 88 in total, including: Diagnosis, Drug Therapy, Drug Effects, Economics, Psychology, Rehabilitation, Trends, etc. • Specific subheadings are only available if relevant to that MeSH heading (not every subheading is applicable for every MeSH heading)
    18. 18. Activity: Using Subheadings (5 minutes) Take a MeSH you searched for earlier: 1.Search for it again, this time when you get to the subheadings screen select one of the subheadings 2.Look at the results and see how they differ from the results you found earlier in number and content 3.Search for a different kind of heading (e.g. if you already searched for a diseases try searching for a drug or social group) and note the different subheadings that are available NOTE: For now ignore subheadings
    19. 19. Keywords • Keywords are words used in the title and abstract of the article (and a number of other fields) • Based on simple character matching • Things to think about: • Language used by authors in your field • Synonyms • Alternative spellings (including British spellings) • Plural and other word root endings • Alternative phrasing • Abbreviations • etc.
    20. 20. MeSH vs. Keywords MeSH Keywords • Established concepts (Diabetes, Heart Disease) • Core biomedical concepts (diseases, drugs & chemicals, anatomy) • Traditional parts of medicine (Surgery, Immunology) • Newer concepts (eHealth) • Boundary-crossing topics (psychosocial and humanities concepts) • New parts of medicine (Rehabilitative Sciences, Population and Public Health, etc.) • New Articles (not yet indexed) • Errors in indexing Often you need to use a combination of MeSH and keywords
    21. 21. Indexing Status and MeSH vs. Keywords The delay in indexing articles means newer material can only be found using keywords Status What it Means Search using MeSH? PubMed - as supplied by publisher Citations recently added to PubMed via electronic submission from a publisher, and are soon to proceed to the next stage, PubMed - in process No PubMed - in process Citations bibliographic data will be reviewed and indexed, i.e., MeSH terms will be assigned (if the subject of the article is within the scope of MEDLINE). No PubMed - indexed for MEDLINE Citations that have been indexed with MeSH terms, Publication Types, Substance Names, etc., and bibliographic data have been reviewed. Yes
    22. 22. Tools for Keywords Phrases: Find a specific phrase (more specific) •“cultural deprivation” Proximity: Find words within a X words of each other (more flexible, increases the number of results) •needle ADJ2 exchange •Proximity searching is not available in every interface, see help Truncation: Find alternative word endings (increases results) $ OR * in OvidSP databases will search for multiple word endings •needle* – will search for needle or needles etc Wildcards: Find alternative spellings (more flexible, inceases results) •Colo*r
    23. 23. Activity: Search using keywords (10 minutes) 1. Try searching using: 1. An individual word (e.g. education) 2. A phrase (e.g. “medical education”) 3. Truncation (educat*) 4. Proximity searching (e.g. medical ADJ3 education)
    24. 24. Limits Aspects of Study Design and Publication Type • Always apply limits last • Limits are not necessarily perfectly applied and their application may not always be consistent. When doing systematic reviews speak to a librarian about using filters instead
    25. 25. Activity: Applying Limits (5 minutes) 1. Try the following limits: 1. Publication Year 2. Age Groups (age of study population) 3. Publication Types 1. Randomized Controlled Trial 2. Review 3. Systematic Review 4. Comparative Study
    26. 26. Activity: Survey (3 minutes) Your feedback helps us improve our current workshops and plan services based on your needs. Please take a moment to fill out the survey and give us your feedback.

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