Taxonbridge

Taxonbridge provides an R package that merges the GBIF Backbone Taxonomy and the NCBI Taxonomy to generate unified, deduplicated, and disambiguated taxonomies covering extant and extinct species for biodiversity and evolutionary analyses.

Key Features:

• Integration of Major Taxonomies: Merges taxonomic records from the GBIF Backbone Taxonomy and the NCBI Taxonomy into a consolidated dataset.
• Deduplication and Disambiguation: Identifies and resolves duplicated and erroneous entries and disambiguates ambiguous scientific names.
• Conflict Resolution: Resolves conflicts between databases, including differing scientific names and hierarchical structures.
• Extant and Extinct Coverage: Supports taxonomic entries for both extant and extinct species.
• Customizable Outputs: Produces custom taxonomies scoped to specific taxonomic neighborhoods (e.g., arthropods, vertebrates) or study contexts.

Scientific Applications:

• Biodiversity research: Provides unified taxonomies for analyses of species diversity and distribution.
• Evolutionary biology: Supplies reconciled taxonomic frameworks for phylogenetic and comparative studies.
• Ecological modeling: Delivers consistent species lists for ecological and environmental models.
• Species identification and classification: Produces cleaned taxonomic references for accurate species identification and systematic comparisons.

Methodology:

Implements algorithms to merge taxonomic data from GBIF and NCBI that resolve conflicts in scientific names and hierarchical structures and handle ambiguities and duplicates.