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wiki:autolit:search:pubmed [2022/07/17 19:03] kevinkallmes |
wiki:autolit:search:pubmed [2023/10/16 18:17] kevinkallmes [Source of Data for PubMed Searches; Copyright] |
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====== Searching PubMed ====== | ====== Searching PubMed ====== | ||
- | This doc describes how to use Boolean search to retrieve records from PubMed via [[https:// | + | PubMed searches on Nested Knowledge source information from the National Library of Medicine. |
+ | |||
+ | This doc describes how to use Boolean search to retrieve records from PubMed via [[https:// | ||
===== Entering a Boolean Query ===== | ===== Entering a Boolean Query ===== | ||
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'' | '' | ||
- | will retrieve all PubMed-indexed publications that contain **all of the following** in their title, abstract, or keywords: | + | will retrieve all PubMed-indexed publications that contain **all of the following** in all PubMed fields including |
* The word stroke or similar terms to stroke (using [[https:// | * The word stroke or similar terms to stroke (using [[https:// | ||
* The word trevo or the word solitaire and associated ATM | * The word trevo or the word solitaire and associated ATM | ||
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If you want to specify how a term will be interpreted by PubMed, specify the field in the following manner: | If you want to specify how a term will be interpreted by PubMed, specify the field in the following manner: | ||
'' | '' | ||
- | using one of PubMed' | + | using one of PubMed' |
- | === MeSH === | + | Fields and filters generally follow the structure of '' |
+ | |||
+ | === MeSH Fields | ||
PubMed indexes articles using the[[https:// | PubMed indexes articles using the[[https:// | ||
- | * [MESH] / [MEST TERMS]: Searches throughout the MeSH hierarchy. | + | * [mh] / [MESH] / [MESH TERMS]: Searches throughout the MeSH hierarchy. |
* [MESH MAJOR TOPIC]: Searches only for MeSH " | * [MESH MAJOR TOPIC]: Searches only for MeSH " | ||
- | * [MESH SUBHEADING]: | + | * [MESH SUBHEADING]: |
+ | |||
+ | So, a search | ||
+ | |||
+ | Note: Use of field tags turns off Automatic Term Mapping (ATM). | ||
+ | |||
+ | === Field-limited Search Terms (Author, Journal, etc.) === | ||
+ | |||
+ | PubMed enables you to specify whether one of your terms of interest is one of the following: | ||
+ | * Author, by searching '' | ||
+ | * Journal, by searching '' | ||
+ | * Publisher, by searching '' | ||
+ | * Volume, by searching '' | ||
+ | * Issue, by searching '' | ||
+ | |||
+ | === Filter by Study Traits === | ||
+ | |||
+ | PubMed enables searches to be narrowed by the following [[https:// | ||
+ | * Publication type, by searching for one of PubMed' | ||
+ | * Full Text available, by appending '' | ||
+ | * Publication date, by searching for '' | ||
+ | * Language, by searching for the '' | ||
+ | * And [[https:// | ||
+ | |||
+ | For Publication Date limits, only the Year is required for the filter to function, and PubMed uses the year " | ||
+ | |||
+ | === Filter by Study Contents === | ||
- | Note: MeSH field searches | + | You can also narrow the section of the publication in question that your term will be searched within |
+ | * Title only, '' | ||
+ | * Title or Abstract (TIAB), '' | ||
+ | * Text only, '' | ||
+ | Note: Text Words includes all words and numbers in the title, abstract, other abstract, MeSH terms, MeSH Subheadings, | ||
===== Guidance on Search Creation ===== | ===== Guidance on Search Creation ===== | ||
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If you are searching for clinical studies and are seeking a framework for building out your search, you may consider using [[wiki: | If you are searching for clinical studies and are seeking a framework for building out your search, you may consider using [[wiki: | ||
+ | ==== Automatic Term Mapping ==== | ||
+ | When you search on PubMed, it will search not only for your term of interest but also use [[https:// | ||
+ | * A Subject translation table (including MeSH (Medical Subject Headings)), | ||
+ | * A Journals translation table, | ||
+ | * The Author index, and | ||
+ | * An Investigator (Collaborator) index. | ||
- | ===== Testing your Search | + | In effect, ATM expands your search' |
- | You may wish to inspect the quality | + | ==== Expanding |
- | | + | If your search was too narrow (and did not return the records you want to include), consider: |
- | * For [[https:// | + | |
+ | * Removing extraneous and highly specific terms | ||
+ | * Removing quotation marks. | ||
- | {{: | + | If your search |
+ | * Removing general terms in favor of more specific ones, | ||
+ | * Appending more " | ||
+ | * Adding quotation marks, where appropriate. | ||
- | ===== AREAs ===== | + | See also our guidance on [[wiki: |
- | ClinicalTrials.gov publishes a full list of AREAs that may be searched & which fields are included in that AREA [[https:// | ||
- | '' | + | ===== Sources and Copyright for PubMed Searches ===== |
- | ===== Operators ===== | + | ==== Source of Data for PubMed Searches; Copyright |
- | A full listing | + | All data returned from PubMed searches on Nested Knowledge are sourced from the National Library |
- | '' | + | Users of PubMed, including users of Nested Knowledge accessing PubMed via API, must comply with any relevant NLM policies, including attributing search results to PubMed or the National Library of Medicine, or otherwise acknowledge NLM as the source of the data in a clear and conspicuous manner. For details on use of data from PubMed, see [[https://www.nlm.nih.gov/ |
- | ===== API vs. " | + | Nested Knowledge assumes no responsibility or liability associated with users' use of copyrighted material, including transmitting, |
- | When you run your PubMed search on Nested Knowledge, you are plugging into the PubMed API. The API still uses the search from before the launch | + | ==== Agreement and Acknowledgement |
- | PubMed | + | By using the API with PubMed, you agree to certain terms of use related to resources provided by the [[https://www.nlm.nih.gov/ |
- | If you are interested in using New PubMed for Nested Knowledge, you still can do so! However, this involves running | + | * As applicable, you agree to perform |
+ | * attribute your search | ||
+ | * not indicate or imply that NLM has endorsed any findings. |