{"access":"The tool is open access","capabilities":"ID-TaxER provides an interface to explore potential soil habitat preferences of bacterial taxa derived from 16S rRNA gene sequencing.  Query sequences are blasted against a database of representative sequences of 97% OTUs obtained from a large soil survey conducted across Britain (the Countryside Survey). Each sequence in the database is linked to an additional trait matrix containing taxonomic assignments as well as environmentally derived information about that OTU (e.g pH or habitat preference). Results are displayed as an interactive table of hits with percentage match to a CS sequence, and associated taxonomy (greengenes). Upon selecting a hit, a plot of model fit to soil parameters is displayed indicating for example the pH optima of that taxon, as well as habitat preferences and spatial distribution (currently Britain only).","description":"The purpose of the ID-TaxER is to provide a data explorer for potential soil habitat preferences of bacterial taxa derived from 16S rRNA gene sequencing. Users need to enter a 16s rRNA gene sequence","id":"3da8144d-519f-4b93-b375-60dd49257cc9","infrastructureCategory":{"value":"data","description":"Environmental data and information","infrastructureClass":"Digital infrastructures","uri":"http://vocabs.ceh.ac.uk/ri/data"},"lifecycle":"The database was constructed from sequences obtained from the 2007 Countryside Survey (CS), a randomly stratified sampling of most soil types and habitats across Great Britain. The web application was developed using Shiny package2 which enables users to BLAST a 16S query sequence against the countryside survey representative sequences, subsequently allowing visualization of key environmental information including HOF model outputs, relevant to individual matched sequences. The GUI was implemented in R (3.4.1) using the Shiny package alongside ShinyJS to execute JavaScript functions from R3. BLASTn commands are executed from R using the users query sequence, e-value of 0.01, and the reference sequence database of CS representative sequences. To facilitate batch processing of query sequences the sequence database, taxonomy and trait matrix are released via github (github.com/brijon/ID-TaxER-flat-files) for integration into bioinformatics pipelines.","metadataDate":"2025-04-09T09:24:56","onlineResources":[{"url":"https://connect-apps.ceh.ac.uk/ID-TaxER/","function":"website","type":"OTHER"}],"owners":[{"familyName":"Jones","givenName":"Briony","displayName":"Briony Jones","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"pointOfContact","email":"enquiries@ceh.ac.uk","address":{"city":"Bangor"},"fullName":"Briony Jones","pointOfContact":"UK Centre for Ecology & Hydrology"}],"resourceIdentifiers":[{"code":"https://catalogue.ceh.ac.uk/id/3da8144d-519f-4b93-b375-60dd49257cc9"}],"scienceArea":"Soils and Land Use","title":"Identification of Taxa & Environment Responses  (ID-TaxER)","type":"infrastructureRecord","uniqueness":"The tool provides an interface to explore potential soil habitat preferences of bacterial taxa derived from 16S rRNA gene sequencing (currently limited to Britain)","uri":"https://catalogue.ceh.ac.uk/id/3da8144d-519f-4b93-b375-60dd49257cc9","users":["The app is predominantly aimed at researchers but is available to members of the public."]}