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--- wiki:autolit:search:europepmc [2022/07/17 21:03]
kevinkallmes created
+++ wiki:autolit:search:europepmc [2022/07/18 18:24]
jthurnham [Using Search Fields and Filters]
@@ Line 2: / Line 2: @@
 This doc describes how to use Boolean search to retrieve records from EuropePMC via [[https://europepmc.org/RestfulWebService|Application Program Interface]] (API).
+===== Databases Covered =====
+EuropePMC combines results from the following databases:
+  * [[https://www.nlm.nih.gov/bsd/difference.html|PubMed and PMC]],
+  * The [[https://agricola.nal.usda.gov/|Agricola]] agricultural library,
+  * [[https://europepmc.org/Preprints#preprint-servers|Preprints]] from 24 different life-sciences-related preprint databases.
 ===== Entering a Boolean Query =====
@@ Line 18: / Line 25: @@
 will retrieve all EuropePMC-indexed publications that contain **all of the following** in their 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 stroke
-  * The word trevo or the word solitaire and associated ATM
+  * The word trevo or the word solitaire
   * The exact phrase "modified Rankin Scale."
-Note: Asterisks are also Boolean operators and can be used for [[wiki:autolit:search:optimize#truncation|truncation]],
 ==== Using Search Fields and Filters ====
-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 EuropePMC, specify the field in the following manner: ''(FIELD:term)'', using one of EuropePMC's pre-specified fields (or filters), which will narrow how that specific term is interpreted. See the [[https://europepmc.org/searchsyntax#field-search|full set of fields/filters enabled on EuropePMC]].
-''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.
+<WRAP center round important 60%> Note that this structure is different from that used by PubMed, meaning that a query must be altered before being copied over from one database to the other! </WRAP>
 === MeSH Fields ===
-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.
+Use of MeSH terms in EuropePMC is not automatic but you can limit your search to MeSH or other attached keywords:
-  * [MESH] / [MEST TERMS]: Searches throughout the MeSH hierarchy.
+  * Search for ''(KW:term)''
-  * [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.
-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.
+=== Searching Fields such as Author, Journal, etc. ===
-Note: MeSH field searches will still be mapped by ATM, but only across the relevant MeSH fields.
+EuropePMC enables you to specify whether one of your terms is:
+  * Author, by searching for ''(AUTH:name)'',
+  * Journal, by searching for ''(JOUR:name)'',
+  * Volume, by searching for ''(VOLUME:number)''
+  * Issue, by searching for ''(ISSUE:number)''
 === Filter by Study Traits ===
-PubMed enables searches to be narrowed by the following [[https://pubmed.ncbi.nlm.nih.gov/help/#help-filters|study characteristics]]:
+EuropePMC enables searches to be narrowed by the following [[https://pubmed.ncbi.nlm.nih.gov/help/#help-filters|study characteristics]]:
-  * 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]'';
-  * Full Text available, by appending ''full text[SB]'';
+  * Publication type, by searching for one of EuropePMC's supported[[https://pubmed.ncbi.nlm.nih.gov/help/#publication-types|publication types]] using, for example, (PUB_TYPE:review);
-  * Publication date, by searching for ''YYYY-MM-DD[Date - Publication] : YYYY-MM-DD[Date - Publication]))'' (only the Year is required for the filter to function);
+  * Abstract available, by appending ''(HAS_ABSTRACT)'';
-  * Language, by searching for the ''language[LANGUAGE]'';
+  * PDF Full Text available, by appending ''(HAS_PDF)'';
-  * And [[https://pubmed.ncbi.nlm.nih.gov/help/#help-filters|others]] (see full list here)
+  * Publication date, by searching for ''FIRST_PDATE:[YYYY-MM-DD TO YYYY-MM-DD]''  (only the Year is required for the filter to function), and for a specific year, you can also search ''PUB_YEAR:YYYY'';
+  * Language, by searching for the ''(LANG:language)'';
+  * Open-access-only, by searching for ''(OPEN_ACCESS)''
 === 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]''
+  * Title only, ''(TITLE:text)''
-  * Text only, ''term[TEXT WORD]''
+  * Abstract only, ''(ABSTRACT:text)''
+  * Body of the text only, ''(BODY:text)''
 ===== Guidance on Search Creation =====

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