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--- wiki:autolit:search:europepmc [2022/07/17 21:03]
kevinkallmes created
+++ wiki:autolit:search:europepmc [2022/07/22 23:48] (current)
kevinkallmes
@@ 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]'';
+  * Language, by searching for the ''(LANG:language)'';
+  * Open-access-only, by searching for ''(OPEN_ACCESS)''
+For Publication Date limits, only the Year is required for the filter to function, and for a specific year, you can also search ''PUB_YEAR:YYYY'' instead of identifying the whole range.
+EuropePMC 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 ''FIRST_PDATE:[2015 TO 3000]''
 === 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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