Binomial nomenclature

Binomial nomenclature; also known as binomial designation, scientific name, or Latin name; was a system of naming organisms in which each species received a formal name of two terms. Subspecies were given a third term. (PROSE: The Pirate Loop)

At the gardens on the Scientifica colony, Adric saw each plant had a nameplate that included their common and scientific names. (PROSE: Cold Fusion)

Earth species
The I-Spyder Book of Earth Creatures included the binomial nomenclature for each listed species: (PROSE: The Last Dodo)
 * Ankylosaurus (Ankylosaurus magniventris)
 * Aye-aye (Daubentonia madagascariensis)
 * Chinese three-striped box turtle (Cuora trifasciata)
 * Diplodocus (Diplodocus longus)
 * Dodo (Raphus cucullatus)
 * Dromaeosaurus (Dromaeosaurus albertensis)
 * Eastern black rhinoceros (Diceros bicornis michaeli)
 * Great Auk (Pinguinus impennis)
 * Human (Homo sapiens sapiens) (PROSE: The Pirate Loop)
 * Ilin Island cloudrunner (Crateromys paulus)
 * Kakapo (Strigops habroptilus)
 * Megalosaurus (Megalosaurus buckland)
 * Mountain gorilla (Gorilla beringei beringei)
 * Paradise parrot (Psephotus pulcherrimus)
 * Phorusrhacos (Phorusrhacos longissimus)
 * Quagga (Equus quagga quagga)
 * Sabre-toothed tiger (Smilodon fatalis)
 * Steller's sea cow (Hydrodamalis gigas)
 * Tasmanian tiger (Thylacinus cynocephalus)

Others binomial names include:
 * Black rat (Rattus rattus) (PROSE: All-Consuming Fire, Antidote to Oblivion)
 * Brown rat (Rattus norvegicus) (PROSE: All-Consuming Fire, Times Squared)
 * Bubonic plague (Yersinia pestis) (COMIC: Black Death White Life, Antidote to Oblivion)
 * Recombinant yersinia pestis (COMIC: A Fairytale Life)
 * Blue whale (Balaenoptera musculus) (PROSE: Doctor Who and the Ark in Space)
 * Cat (Felis silvestra catus or Felis catus) (PROSE: Outstanding Balance, Resurrection of the Daleks)
 * Dog (Canis familiaris) (PROSE: Cat's Cradle: Witch Mark)
 * Deadly nightshade (Atropa belladonna) (TV: The Sensorites)
 * E. coli (PROSE: Deadfall)
 * Earthworm (Lumbricus terrestris) (PROSE: Lucy Wilson & the Bledoe Cadets)
 * Guinea pig (Cavia porcellus) (PROSE: Artificial Intelligence)
 * Homo erectus (PROSE: Beige Planet Mars, Sometime Never...)
 * Homo habilis (PROSE: Genocide, The Taking of Planet 5, AUDIO: Interstitial)
 * Lion (Felis leo) (PROSE: The Romans)
 * Mimic octopus (Thaumoctopus mimicus) (PROSE: T.memeticus: A Morphology)
 * Silurian (Homo reptilia or Homo Reptilicus) (PROSE: Doctor Who and the Cave-Monsters, TV: The Hungry Earth, PROSE: First Frontier)
 * Sumatran bamboo rat (Rhizomys sumatrensis) (PROSE: All-Consuming Fire)
 * Tiger (Panthera tigris) (PROSE: The Year of Intelligent Tigers)
 * Tyrannosaurus rex (TV: Invasion of the Dinosaurs, et al.)
 * Western European badger (Meles meles meles) (PROSE: The Pirate Loop)
 * Wolf (Canis lupus) (PROSE: Cat's Cradle: Witch Mark)
 * Indian wolf (Canis lupus pallipes) (AUDIO: The Emerald Tiger)

35 million years in Earth's future, the common mouse evolved into Mus musculus sapiens, the smartest creature on the planet. (PROSE: Omegamorphosis)

Gallifreyan species
The I-Spyder Book of Earth Creatures gave Time Lords the binomial nomenclature of Dominus temporis. (PROSE: The Last Dodo)

Madevinia aridosa was the name of a Gallifreyan flower. (PROSE: Cat's Cradle: Time's Crucible)

Other species
The Mecrim (Singropoda mecrimus) were a genetically engineered species used as weapons in the Human-Draconian War. (PROSE: The Menagerie)

The Dreamweaver was also known as Somnifax vehementi. (AUDIO: The Lovecraft Invasion)

An aspect of the Enemy was called Thaumoctopus memeticus. (PROSE: T.memeticus: A Morphology)

Blowfish were also known as Homoformatus piscis. (PROSE: The Baby Farmers)

Rusty looked like a giant squirrel and was given the "long Sci-latin name" of Para sciurus vulgaris. (PROSE: Shadowmind)

A stuffed Venusaurus erectus of Venus was an exibit at Mildeo Twisknadine's Museum of Things That Don't Exist. (PROSE: The Taking of Planet 5)