Environmental yeasts isolated in Colombia, a dataset
Description
This dataset contains the absolute frequency of environmental yeasts (clinical isolates were not included) isolated in different substrates in Colombia. The TSV file contains the structured version, available to analyze inmediatly in Python packages, or to import in different Data visualizers. This TSV file is almost identical (without first and last column, without last row) to the first sheet of the Excel file. The Excel file contains all unstructured information, but organized in different manners. The first sheet is organized by author (row) and the species (column). The second sheet shows the species (or genus) in rows, and the contributor in columns. The third and fourth sheets show the frequency for yeasts identified only to taxonomic level of species or genus, respectively. The last sheet includes the merged frequency between species and their genera. This dataset was updated until June 2023 (first sheet and TSV file). The publication is located at https://www.researchgate.net/publication/364382939_Chapter_7_Diversity_of_Environmental_Yeasts_of_Colombia_A_Systematic_Review
Files
Steps to reproduce
Literature searches were carried out in English and Spanish,comprising studies from January 2000 to December 2020,in the following databases: Google Scholar, Pubmed, Scielo,Science Direct, Scopus, Springer, and Web of Science.In addition, institutional repositories from universitiesand editorials were also consulted. Specific keywords,connectors, and possible combinations were establishedas shown in Figure 1. Finally, we also included the officialdatabase of biological collections from Colombia. Data selection We used Mendeley v1.19.8 to organise all the literature data, includingauthor information, journal or publisher, year, andkeywords. For the analysis of information, we screened alldownloaded databases by title, keywords, and abstract.We applied the following inclusion and exclusion criteria toselect final reports Inclusion criteria a. Original papers and documents. b. Papers and documents in English and Spanish. c. Papers and documents that have isolated yeasts fromColombia and identified it, at least to the genus level. Exclusion criteria a. Papers without any yeast identification or only metabar-coding results. b. Review papers and documents. c. Duplicate papers and documents in different databasesor repositories. d. Theses already published as papers or books. e. Papers with clinical isolates. f. Papers that do not involve yeast diversity assessments. Data analyses Selected papers were organised, standardised usingMendeley, and exported to the RIS format in a plaintext file. This file was importedinto VOSviewer v1.6.17. Twotypes of analyses were performed: 1. a co-occurrencenetwork, where the field “keywords” was updated with thegenera found in each paper; and 2. a co-author network. Weshowed all keywords or authors in the generated map. Thenodes in the reconstructed network represent the genera,whereas the edges (i.e., connections) correspond to a strongand significant correlation between nodes. The clusteringcoefficient was defined as how nodes are embedded intheir neighbourhood and, thus, the degree to which theytend to cluster together. Several characteristics, such asregion, category, and specific substrate where yeasts wereisolated, were extracted from each report for analysis. Wealso updated the taxonomy and nomenclature of all recordsusing Mycobank or Index Fungorum and computed thefrequency of inclusion for each genus or species.For example, Cryptococcus was updated and separated intothe segregated Vanrija, Papiliotrema, Cutaneotrichosporon,Solicoccozyma, among others. In addition, we organisedthe richness and abundance of species in a spreadsheetaccording to paper, and we classified reports according to thesubstrate wherever available. Finally, we included additionalfields, such as region and year of publication.