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--- wiki:autolit:search:pubmed [2022/07/17 19:27]
kevinkallmes
+++ wiki:autolit:search:pubmed [2023/10/16 18:17]
kevinkallmes [Agreement and Acknowledgement of PubMed / National Library of Medicine]
@@ Line 1: / Line 1: @@
 ====== Searching PubMed ======
-This doc describes how to use Boolean search to retrieve records from PubMed via [[https://www.ncbi.nlm.nih.gov/home/develop/api/|Application Program Interface]] (API). See also our [[https://about.nested-knowledge.com/2022/04/22/create-a-great-literature-search/|blog]] on constructing a query from the start!
+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://www.ncbi.nlm.nih.gov/home/develop/api/|Application Program Interface]] (API). For advice on getting started, see also our [[https://about.nested-knowledge.com/2022/04/22/create-a-great-literature-search/|blog]] on constructing a query from the start!
 ===== Entering a Boolean Query =====
@@ Line 17: / Line 19: @@
 ''stroke AND (trevo OR solitaire) AND "modified Rankin Scale"''
-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 title, abstract, or keywords:
   * The word stroke or similar terms to stroke (using [[https://pubmed.ncbi.nlm.nih.gov/help/#automatic-term-mapping|Automatic Term Mapping]] [ATM])
   * The word trevo or the word solitaire and associated ATM
@@ Line 29: / Line 31: @@
 ''term[FIELD]'',
 using one of PubMed's pre-specified fields (or filters), which will narrow how that specific term is interpreted.
+Fields and filters generally follow the structure of ''term[FIELD]'', but if the field is incorrectly spelled or not recognized, it will be ignored by PubMed and the term will be searched as plain text.
 === MeSH Fields ===
@@ Line 34: / Line 38: @@
 PubMed indexes articles using the[[https://www.nlm.nih.gov/mesh/meshhome.html|MeSH controlled vocabulary]], which means that you can add this field to search for MeSH topics so long as your term of interest is in the MeSH hierarchy.
-  * [MESH] / [MEST TERMS]: Searches throughout the MeSH hierarchy.
+  * [mh] / [MESH] / [MESH TERMS]: Searches throughout the MeSH hierarchy.
   * [MESH MAJOR TOPIC]: Searches only for MeSH "[[https://www.nlm.nih.gov/bsd/disted/meshtutorial/principlesofmedlinesubjectindexing/majortopics/index.html|Major Topics]]" (which are indicated in the MeSH hierarchy by asterisks).
-  * [MESH SUBHEADING]: Searches for only non-Major Topics in the MeSH hierarchy.
+  * [MESH SUBHEADING]: Searches specific aspects or qualifiers of the MeSH heading. Learn more [[https://www.nlm.nih.gov/bsd/indexing/training/SUB_010.html|here.]]
 So, a search for ''stroke[MESH MAJOR TOPIC]'' will return only studies tagged with Major Topics at or under "stroke" in the MeSH hierarchy, while a search for ''stroke[MESH]'' will return any study tagged at or below "stroke" in the hierarchy.
-Note: MeSH field searches will still be mapped by ATM, but only across the relevant MeSH fields.
+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 ''name[AUTHOR]'';
+  * Journal, by searching ''name[JOURNAL]'';
+  * Publisher, by searching ''name[PUBLISHER]''
+  * Volume, by searching ''number[VOLUME]''
+  * Issue, by searching ''number[ISSUE]''.
 === Filter by Study Traits ===
 PubMed enables searches to be narrowed by the following [[https://pubmed.ncbi.nlm.nih.gov/help/#help-filters|study characteristics]]:
-  * Study type,
+  * Publication type, by searching for one of PubMed's supported [[https://pubmed.ncbi.nlm.nih.gov/help/#publication-types|publication types]] using, for example, ''review[PT]'';
-  * Text availability,
+  * Full Text available, by appending ''full text[SB]'';
-  * Publication date, by searching for ''YYYY-MM-DD[Date - Publication] : YYYY-MM-DD[Date - Publication]))''; only the Year is required.
+  * Publication date, by searching for ''(YYYY-MM-DD[Date - Publication] : YYYY-MM-DD[Date - Publication])'';
-  * Species,
+  * Language, by searching for the ''language[LANGUAGE]'';
-  * Language,
+  * And [[https://pubmed.ncbi.nlm.nih.gov/help/#help-filters|others]] (see full list here)
-  * Journal Category
+For Publication Date limits, only the Year is required for the filter to function, and PubMed uses the year "3000" to represent all publications through to the present. So, for example, to search for all studies published from January 1st, 2015 to Present, you can use the simplified ''(2015[Date - Publication] : 3000[Date - Publication])''
+=== Filter by Study Contents ===
+You can also narrow the section of the publication in question that your term will be searched within by specifying:
+  * Title only, ''term[TITLE]''
+  * Title or Abstract (TIAB), ''term[TITLE/ABSTRACT]''
+  * Text only, ''term[TEXT WORD]''
+Note: Text Words includes all words and numbers in the title, abstract, other abstract, MeSH terms, MeSH Subheadings, Publication Types, Substance Names, Personal Name as Subject, Corporate Author, Secondary Source, Comment/Correction Notes, and Other Terms (see Other Term [OT] above) typically non-MeSH subject terms (keywords), including NASA Space Flight Mission, assigned by an organization other than NLM. Learn more [[https://pubmed.ncbi.nlm.nih.gov/help/#tw|here.]]
 ===== Guidance on Search Creation =====
@@ Line 86: / Line 107: @@
 See also our guidance on [[wiki:autolit:search:optimize#number_of_records_when_to_stop|search size]].
-===== API vs. "New" PubMed Searches =====
-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 of [[https://www.nlm.nih.gov/oet/ed/pubmed/events/2019_09_faq.html|"New" PubMed]]. This **can lead to differences between the records pulled from the API compared to running the search directly on PubMed,** due to differences in [[https://pubmed.ncbi.nlm.nih.gov/help/#automatic-term-mapping|Automatic Term Mapping]] between New PubMed and the API.
+===== Sources and Copyright for PubMed Searches =====
+==== Source of Data for PubMed Searches; Copyright ====
+All data returned from PubMed searches on Nested Knowledge are sourced from the National Library of Medicine (NLM). The NLM assumes no responsibility or liability associated with use of copyrighted material, including transmitting, reproducing, redistributing, or making commercial use of the data. For full details, see [[https://www.nlm.nih.gov/web_policies.html#copyright|the NLM's Copyright Statement]].
+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/databases/download.html|the NLM's "Downloading NLM Data" guidance]].
+Nested Knowledge assumes no responsibility or liability associated with users' use of copyrighted material, including transmitting, reproducing, redistributing, or making commercial use of the data, and subject to Nested Knowledge's [[wiki:policies:copyright|Copyright Policy,]] Nested Knowledge may remove materials from users' projects.
-PubMed has recently released [[https://ncbiinsights.ncbi.nlm.nih.gov/2022/06/22/pubmed-api-launch-delayed/|estimates]] on the schedule to "match" the API to New PubMed.
-If you are interested in using New PubMed for Nested Knowledge, you still can do so! However, this involves running the search directly on PubMed, exporting an nBIB file, and [[wiki:autolit:search:import#using_nbib_files_instead_of_ris_files|importing it]]. This has the downside that there will be no automatic updating of your search.

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