liminfoTaxonomy Database
Free reference guide: Taxonomy Database
About Taxonomy Database
The Biological Taxonomy Database is a comprehensive reference covering the hierarchical classification of life across 3 domains and 6 kingdoms. It includes detailed entries for Domain Bacteria (peptidoglycan cell walls, 70S ribosomes, binary fission, major phyla: Proteobacteria, Firmicutes, Actinobacteria), Domain Archaea (ether-linked lipids, extremophiles, Euryarchaeota, Crenarchaeota, Thaumarchaeota), and Domain Eukarya with its four kingdoms: Animalia, Plantae, Fungi, and Protista.
The classification system section covers the 7-level taxonomic rank hierarchy (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species), Linnaeus's binomial nomenclature rules, cladistics with key concepts like synapomorphy and monophyly, and phylogenetic tree construction methods including Neighbor-Joining, Maximum Parsimony, Maximum Likelihood, and Bayesian inference using tools like MEGA, RAxML, and IQ-TREE.
The reference also includes classification examples for 6 model organisms with NCBI Taxonomy IDs (Homo sapiens #9606, E. coli #562, S. cerevisiae #4932, A. thaliana #3702, M. musculus #10090, D. melanogaster #7227), major databases (NCBI Taxonomy, ITIS, GBIF), molecular markers (16S/18S rRNA primers), the SILVA rRNA database, and the Baltimore virus classification system with all 7 groups.
Key Features
- 3 domains and 6 kingdoms with detailed characteristics: cell wall composition, DNA structure, metabolic pathways
- Complete 7-level taxonomic hierarchy with the "Dear King Philip" mnemonic for memorization
- Binomial nomenclature rules: genus capitalization, species lowercase, italics, author citation conventions
- 6 model organism classifications with NCBI Taxonomy IDs, genome sizes, and chromosome counts
- Phylogenetic tree methods: NJ, UPGMA, Maximum Parsimony, Maximum Likelihood, Bayesian (MrBayes, BEAST)
- 16S/18S rRNA primer sequences (27F/1492R) and SILVA database for classifier training
- Major taxonomy databases: NCBI Taxonomy API, ITIS with TSN, GBIF with Darwin Core and Species API
- Baltimore virus classification: 7 groups from dsDNA to dsDNA-RT with representative virus families
Frequently Asked Questions
What are the 3 domains and 6 kingdoms of life?
The 3 domains are Bacteria (prokaryotes with peptidoglycan), Archaea (prokaryotes with ether-linked lipids), and Eukarya (eukaryotes with membrane-bound organelles). The 6 kingdoms within these domains are Eubacteria, Archaebacteria, Protista, Fungi (chitin cell walls), Plantae (cellulose cell walls, photosynthesis), and Animalia (multicellular heterotrophs). This reference covers each with specific features like ribosome type, DNA structure, and reproduction methods.
What is binomial nomenclature and how does it work?
Binomial nomenclature is Linnaeus's system for naming species using two Latin terms: Genus (capitalized) + species (lowercase), both italicized. For example, Homo sapiens for humans or Camellia sinensis for the tea plant. The original describer is cited after the name (e.g., Linnaeus, 1758). This reference includes rules for proper formatting and examples across all kingdoms.
How do I look up a species in the NCBI Taxonomy database?
Search by scientific name or Taxonomy ID at https://www.ncbi.nlm.nih.gov/taxonomy. The API endpoint is efetch.fcgi?db=taxonomy&id=9606 (for humans). This reference includes NCBI TaxIDs for 6 model organisms: Homo sapiens (9606), E. coli (562), S. cerevisiae (4932), A. thaliana (3702), M. musculus (10090), and D. melanogaster (7227). Full database downloads are available via FTP.
What is 16S rRNA and why is it used as a taxonomic marker?
16S rRNA is a ribosomal RNA gene (~1,500 bp) found in all prokaryotes. It contains both conserved regions (for universal primer binding) and variable regions (for species differentiation). The standard primers are 27F (AGAGTTTGATCMTGGCTCAG) and 1492R (TACGGYTACCTTGTTACGACTT). For eukaryotes, 18S rRNA (~1,800 bp) serves the same purpose. These markers have low horizontal transfer rates, making them reliable for phylogenetic analysis.
What methods are used to build phylogenetic trees?
The reference covers four main methods: Distance-based methods (Neighbor-Joining, UPGMA), Maximum Parsimony (fewest evolutionary changes), Maximum Likelihood (statistically most probable tree), and Bayesian inference (posterior probability using MrBayes, BEAST). Tools include MEGA, RAxML, IQ-TREE, and PhyML. Bootstrap analysis evaluates branch confidence. Choice of method depends on dataset size and computational resources.
What is the Baltimore virus classification system?
The Baltimore classification divides viruses into 7 groups based on genome type and replication strategy: I (dsDNA: Herpes, Adenovirus), II (ssDNA: Parvovirus), III (dsRNA: Reovirus), IV (+ssRNA: Coronavirus, Flavivirus), V (-ssRNA: Influenza, Ebola), VI (ssRNA-RT: HIV), VII (dsDNA-RT: Hepadnavirus). The ICTV (International Committee on Taxonomy of Viruses) oversees formal virus taxonomy.
What is the difference between monophyletic, paraphyletic, and polyphyletic groups?
In cladistics, a monophyletic group (clade) includes an ancestor and all its descendants. A paraphyletic group includes an ancestor but excludes some descendants. A polyphyletic group includes organisms from multiple ancestors. Cladistics aims to identify monophyletic groups using shared derived characters (synapomorphies) rather than ancestral traits (plesiomorphies). This is fundamental to modern phylogenetic classification.
What is GBIF and how can I access its species data?
GBIF (Global Biodiversity Information Facility) at gbif.org provides worldwide biodiversity occurrence data using the Darwin Core standard. Access species data via the API: https://api.gbif.org/v1/species?name=Homo+sapiens. GBIF complements NCBI Taxonomy (sequence-focused) and ITIS (North American species) by providing global distribution records and occurrence data for ecological research.