PlutoF

PlutoF provides data management and molecular-analysis services for biological research, enabling storage and annotation of taxon occurrences, metabarcoding datasets, taxonomic classifications, traits, laboratory data, and DNA sequences to support molecular identification and species discovery from environmental samples such as eDNA.

Key Features:

• Data Management: Manages taxon occurrences, metabarcoding data, taxonomic classifications, traits, laboratory data, and DNA sequences.
• Annotation Module: Supports third-party annotations on collection specimens, living cultures, and DNA sequences, including material source, geolocation, habitat, taxonomic identifications, and interactions.
• Analysis Module: Provides molecular sequence identification and species discovery from eDNA and environmental samples, optimized for environmental Internal Transcribed Spacer (ITS) sequences in fungi and adaptable to other genetic markers and organism groups.
• Standardized Terminology: Implements internationally standardized terminology for precise annotation and linking of interacting specimens and species.
• Relational Database and Data Integration: Built on a relational database and supports submission, retrieval, and analysis of study, specimen, and sequence data from public databases such as the International Nucleotide Sequence Databases (INSD) and private datasets.

Scientific Applications:

• Taxonomic curation and annotation: Enables precise taxonomic curation by linking standardized annotations to specimens, living cultures, and sequences.
• Metabarcoding and eDNA community profiling: Facilitates metabarcoding analyses and species discovery from eDNA, including fungal ITS-based community profiling.
• Molecular identification: Performs molecular sequence identification using sequence data aggregated from INSD and private collections.
• Ecological and taxonomic meta-analysis: Supports integration of occurrence, trait, and sequence data for ecological and taxonomic meta-analyses and for improving metadata quality in downstream studies.

Methodology:

PlutoF employs a relational database backend, integrates internationally standardized terminologies, provides annotation linking among specimens, cultures, and sequences, performs molecular sequence identification and species discovery from eDNA, and includes sequence analysis workflows optimized for environmental ITS sequences in fungi; it also supports retrieval and analysis of sequence data from the International Nucleotide Sequence Databases (INSD) and private datasets.