MeSH : A Thesaurus for PubMed

Transcription

1 Scuola di dottorato di ricerca in Scienze Molecolari Resources and tools for bibliographic research MeSH : A Thesaurus for PubMed

2 What is MeSH? Who uses MeSH? Why use MeSH? Searching by using the MeSH Database

3 What is MeSH? Acronym for Medical Subject Headings The U.S. National Library of Medicine's controlled vocabulary (thesaurus), created in 1960 Gives uniformity and consistency to the indexing and cataloging of biomedical literature and is a distinctive feature of MEDLINE Similar to keywords on other systems Arranged in a hierarchical manner called the MeSH Tree Structures Updated annually to reflect changes in medicine and medical terminology

4 Who uses MeSH? Searchers of MEDLINE/PubMed, library catalogs, and other databases -- to assist with subject searching National Library of Medicine (NLM) Indexers -- to describe subject content of journal articles for MEDLINE Catalogers -- to describe books and audiovisuals in the NLM and other medical library collections

5 2014 MeSH Vocabulary includes four types of terms (1): Headings over 27,149 headings (descriptors) represent concepts found in the biomedical literature (e.g. kidney, radioactive waste, self-medication). MeSH headings used to describe the group or a person being studied are called check tags (human,animal, female, male etc.) Subheadings (also called qualifiers) attached to MeSH headings to describe a specific aspect of a concept (e.g. drug therapy, epidemiology, etiology) Supplementary Concept Records over 219,000 terms (in a separate thesaurus). These are primarily substance terms, but also include some protocols and rare disease terms. These terms are updated weekly (e.g. cordycepin, tacrolimus binding protein 4, Snyder Robinson syndrome)

6 2014 MeSH Vocabulary includes four types of terms (2): Publication Characteristics (Publication Types) describe the type of publication being indexed, i.e. what the item is, not what the article is about (letter, review, randomized controlled trial) Also over 218,000 Entry terms that assist in finding the most appropriate MeSH Heading

7 The MeSH Tree Structures MeSH headings are organized in a "tree" with 16 main branches (i.e. Anatomy, Diseases, Chemical and Drugs etc.) Each branch has many levels of sub-branches, and each heading has a position in the hierarchy (subheadings are arranged hierachically too!) Some terms appear in more than one branch of the tree (e.g. Ear in Anatomy-Body Regions and Ear in Anatomy-Sense Organs) The hierarchy allows a MEDLINE/PubMed search of a broader term to include the narrower terms in all branches automatically. This is known as exploding

8 MeSH - Major Topics Asterisks on MeSH headings and subheadings designate that they are the major topics of the article, usually obtained from the title and/or statement of purpose e.g. Wound Healing/radiation effects* Non-major (non-asterisked) headings and subheadings are usually additional topics substantively discussed within the article, terms added to qualify a major topic, or check tags. Check tags are never major topics

9 The MeSH Database allows you to: locate and select MeSH terms (Headings, Subheadings, Supplementary Concept terms, Publication Types) see the definition and other helpful information for a MeSH term see the position of MeSH terms in the hierarchy select MeSH heading/subheading combinations to build a PubMed search limit MeSH terms to a major concept for a search

10 More about the MeSH Database Note 1: Searching with MeSH subject terms excludes in process and publishersupplied citations, as well as other PubMed citations that are not indexed for MEDLINE (e.g., citations that are out of scope for MEDLINE, such as a volcanology article in Science) and Oldmedline records. These records do not (or do not yet) include MeSH subject terms Note 2: Filters are MeSH term! Deactivate the function Filters activated, before searching article in press, publisher-supplied articles and older MEDLINE records

11 PubMed coverage [PubMed as supplied by publisher] [PubMed - in process] Citations received electronically from publishers. Records providing basic citation information and abstracts before the citations are indexed with NLM MeSH Terms and added to MEDLINE. Daily updated No MeSH term No MeSH term [PubMed indexed for MEDLINE] New citations that have been indexed with MeSH terms, publication types, GenBank accession numbers, and other indexing data. Daily updated MeSH terms available [PubMed] The out-of-scope citations from certain MEDLINE journals, (not biomedical science journals) for which the life sciences articles are indexed for MEDLINE. No MeSH term [PubMed OLDMEDLINE] OLDMEDLINE records ( ) MeSH terms -Not for all records

12 More about the MeSH Database Autocomplete feature available from the search box Relevance-ranked order display of Search results When a user s search exactly matches a MeSH Term, that Term is displayed first Year Introduced is the year the term was added to MeSH If more than one year is shown, the term was available for indexing back to the earliest year noted

13 Untagged terms that are entered in the PubMed Search box are matched (in this order) against : a MeSH (Medical Subject Headings) translation table a Journals translation table the Full Author translation table Author index PubMed Automatic Term Mapping and MeSH Translation Table the Full Investigator (Collaborator) translation table and an Investigator (Collaborator) index

14 The MeSH Translation Table contains: MeSH terms (i.e. liver, scoliosis, amiodarone etc.) The See-Reference mappings (also known as entry terms) for MeSH terms MeSH Subheadings (diagnosis, drug therapy, etiology etc.) Publication Types (review, guideline, historical article etc.) Pharmacologic action terms (from 1996-) Terms derived from the Unified Medical Language System (ULMS) that have equivalent synonyms or lexical variants in English Supplementary concept (substance) names and their synonyms (CAS numbers, chemical names etc.)

15 PubMed Automatic Term Mapping and MeSH Translation Table If a match is found in this Translation table, the term will be searched as MeSH (that includes the MeSH term and any specific terms indented under that term in the MeSH hierarchy, i.e. Explosion of the MeSH term), and in all fields Important! Use of a field tag (i.e. Title [TI]) or use of asterisk * for truncation and use of quotes for a phrase searching will turn off the Automatic Search Mapping and bypass a search of MeSH! Try your search without tags, quotes and truncation first!

16 PubMed Automatic Term Mapping and MeSH Translation Table - Example 1. Search: ebola virus Search Details : "ebolavirus"[mesh Terms] OR "ebolavirus"[all Fields] OR ("ebola"[all Fields] AND "virus"[all Fields]) OR "ebola virus"[all Fields] (1803 results) 2. Search: ebola virus Search Details: "ebola virus"[all Fields] (1167 results)

17 MeSH terms and Databases You can find MeSH terms in the following database records SCOPUS WEB OF SCIENCE - ALL DATABASES (MEDLINE)

18 Web Tutorials and Training Resources (1) Basics of MeSH Branching out: The MeSH Vocabulary (11 min video) Medical Subject Headings Homepage MeSH Browser Online vocabulary look-up aid designed to help quickly locate descriptors of possible interest (From September 4, 2014 daily update) Inforamtion literacy in Chemistry

19 Web Tutorials and Training Resources (2) Introduction to MeSH ISS - MeSH 2014 (Traduzione italiana) PubMed Online Training For all the NLM electronic resources follows this link cfm Gquery - NCBI Global Cross-database Search

20 The on Demand tool analyzes chunks of text (up to characters) and identifies potentially related MeSH terms. It is currently a viable tool for brainstorming MeSH terms to help build a PubMed query.

21 PubMed Commons New in PubMed 2014! Social media icons (for Facebook, Twitter, and Google+) have been added to the PubMed Abstract display Daily updates (seven days a week) New tutorial Searching Drugs or Chemicals in PubMed

22 PubMed Commons enables authors to share opinions and information about scientific publications in PubMed. To be eligible to use PubMed Commons: you must be an author of a publication in PubMed you will need an My NCBI account (free of charge) you will need an invitation to join PubMed Commons (free of charge)

23 BIBLIOGRAFIA PubMed Help: NCBI Help Manual. Bethesda (MD): National Center for Biotechnology Information (US), Information literacy in chemistry