Identifying all of the relevant research on a particular topic for literature reviews involving non-human primates (NHPs) can be difficult and time consuming. filterNHP automatizes the creation of search filters for the taxonomic levels of NHPs for three bibliographic sources (PubMed, PsycINFO via EBSCOhost, and Web of Science). These search filters can be combined with topic search strings using the Boolean operator 'AND' to facilitate the retrieval of all publications related to NHPs and the topic within the specified database/platform.
We encourage users to review the search filters and adapt them to their own needs. For further details, please see Cassidy et al., (2021). To report a bug or request a new feature, please use the GitHub repository.
Please cite: Cassidy LC, Leenaars CHC, Rincon AV, & Pfefferle D. (2021). Comprehensive search filters for retrieving publications on non-human primates for literature reviews (filterNHP). American Journal of Primatology, 83(7), e23287. https://doi.org/10.1002/ajp.23287
|Strepsirrhini||Lemuriformes||Lemuridae||Eulemur, Hapalemur, Lemur, Prolemur, Varecia|
|Cheirogaleidae||Allocebus, Cheirogaleus, Microcebus, Mirza, Phaner|
|Indriidae||Avahi, Indri, Propithecus|
|Galagidae||Euoticus, Galago, Galagoides, Otolemur, Paragalago, Sciurocheirus|
|Haplorhini||Tarsiiformes||Tarsiidae||Carlito, Cephalopachus, Tarsius|
|Simiiformes||Platyrrhini||Cebidae||Callitrichinae||Callibella, Callimico, Callithrix, Cebuella, Leontocebus, Leontopithecus, Mico, Saguinus|
|Atelinae||Ateles, Brachyteles, Lagothrix|
|Pitheciidae||Pitheciinae||Cacajao, Chiropotes, Pithecia|
|Callicebinae||Callicebus, Cheracebus, Plecturocebus|
|Catarrhini||Cercopithecoidea||Cercopithecidae||Cercopithecinae||Cercopithecini||Allenopithecus, Cercopithecus, Chlorocebus, Erythrocebus, Miopithecus|
|Papionini||Cercocebus, Lophocebus, Macaca, Mandrillus, Papio, Rungwecebus, Theropithecus|
|Colobinae||Colobini||Colobus, Piliocolobus, Procolobus|
|Presbytini||Nasalis, Presbytis, Pygathrix, Rhinopithecus, Semnopithecus, Simias, Trachypithecus|
|Hominoidea||Hylobatidae||Hoolock, Hylobates, Nomascus, Symphalangus|
Taxonomic structure referencing Perelman et al., (2011).
Each bibliographic database queries its library of scientific articles in different ways. We have formatted the NHP search filters to take these differences into account and search publications by their associated index terms (i.e., standardized database terminology labelled as topic-relevant) and other aspects (i.e., title, abstract, author keywords) that ensure that new relevant publications are detected. Below are the definitions of each syntax used.
|*||Indicates that the adjacent word is followed by any group of characters, including no character (e.g., the term 'galagid*' detects publications referencing 'galagid', 'galagids', and 'galagidae').|
|[mh]||Indicates the search term is an index term and that the search includes all nested index terms.|
|[mh:noexp]||Indicates the search term is an index term and that the search does not include nested index terms.|
|[tiab]||Indicates the search term should be searched for in the title and abstract of database publications.|
|DE()||Listed search terms are searched for in the 'Subjects [exact]' database field (i.e., index terms).|
|TX()||Listed search terms are searched for in the 'All Text' database field.|
|TS=()||Listed search terms are searched for in the 'Topic' database field (searches by title, abstract, author keywords, and Keywords Plusa).|
aNote: Keywords Plus is an algorithm developed by Web of Science that retrieves publications that are broadly related, but lack the original search terms (e.g., detects publications with terms of other mammal species, but no NHP terms). Please note that this algorithm may increase the time necessary to filter search results for directly topic-relevant publications.
Index terms are topic-relevant standardized search terms that are tagged (i.e., indexed) as topic-relevant by each bibliographic source. These terms are found at the beginning of search filters created by filterNHP if they are relevant to the taxonomic group you are interested in. PubMed uses MeSH terms (i.e., Medical Subject Headers) created by the National Library of Medicine (NLM) and are searched using the syntax '[mh]' or '[mh:noexp]'. Similarly, PsycINFO uses the American Psychological Association (APA) Thesaurus of Psychological Index Terms and are searched for via EBSCOhost within the syntax 'DE()'. Web of Science does not have an associated thesaurus. Each bibliographic source organizes index terms into a hierarchical structure by subject category so that more specific terms (i.e., narrow) are nested under more general terms (i.e., broad). Including index terms expands the scope of literature searches and may result in the retrieval of publications that may have gone undetected otherwise.
We created search filters that maximize the number of potentially relevant publications because literature reviews may reach biased conclusions if they are missing relevant publications. Therefore, we included terms that are commonly used to refer to NHPs, but may also reference other nouns. For example, we include the term 'monkey' in the comprehensive NHP search filter, although it may also be used to refer to a 'monkey wrench' or the 'monkey orchid'. As a result, publications unrelated to NHPs may be retrieved. Publications irrelevant to the topic you are interested in can be filtered out during search result screening phase. We encourage users to review the search filters created by filterNHP and adapt them to their own specific needs.
Before combining an NHP filter with a topic search string, researchers must thoughtfully determine and test what topic-relevant terms are necessary to include. Searches conducted in PubMed and PsycINFO should include relevant index terms that can be identified from the Medical Subject Headers (MeSH) database or the APA Thesaurus of Psychological Index Terms, respectively. The topic search string should also include any topic-relevant terms to be searched in the title and abstract of publications (TIAB terms), which primarily retrieve publications that have not received an index term yet. Index terms and TIAB terms are formatted using the syntax of the corresponding source and combined with the Boolean operator 'OR'.
Below we provide an example for a topic search strings on cortisol related studies (index terms are indicated in italics). Note that Web of Science does not have index terms as this platform has no associated thesaurus.
|hydrocortisone[mh] OR cortiso*[tiab] OR hydrocortiso*[tiab] OR epicortiso*[tiab] OR glucocortico*[tiab]|
|DE(hydrocortisone) OR TX(cortiso* OR hydrocortiso* OR epicortiso* OR glucocortico*)|
|TS=(cortiso* OR hydrocortiso* OR epicortiso* OR glucocortico*)|
To find publications involving NHPs on a particular topic, search filters from filterNHP and the topic search string should each be surrounded by parentheses and combined together with the Boolean operator 'AND'. Below are examples of an NHP search filter for the genus Macaca combined with the topic search strings for cortisol related studies (see above). Green text indicates the NHP search filter and purple text indicates the topic search string; index terms are indicated in italics.
|("macaca"[mh] OR "cynomolgus"[tiab] OR "macaca"[tiab] OR "macaque's"[tiab] OR "macaque"[tiab] OR "macaques"[tiab] OR "rhesus monkey*"[tiab]) AND (hydrocortisone[mh] OR cortiso*[tiab] OR hydrocortiso*[tiab] OR epicortiso*[tiab] OR glucocortico*[tiab])|
|(TS=("cynomolgus" OR "macaca" OR "macaque's" OR "macaque" OR "macaques" OR "rhesus monkey*")) AND (TS=(cortiso* OR hydrocortiso* OR epicortiso* OR glucocortico*))|