Binomial nomenclature

Binomial nomenclature; also known as binomial designation, scientific name, or Latin name; was a system of naming organisms with a formal name of two terms: genus and species. (PROSE: The Menagerie) 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)

Animals
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 or Didus ineptus) (PROSE: Cat's Cradle: Time's Crucible)
 * 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)
 * 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)
 * 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)
 * Homo naledi (PROSE: Interlude from a Civil War)
 * Jellyfish (Turritopsis nutricula) (TV: End of the Road)
 * Lion (Felis leo) (PROSE: The Romans)
 * Mimic octopus (Thaumoctopus mimicus) (PROSE: T.memeticus: A Morphology)
 * Neanderthal (Homo neanderthalis) (PROSE: Predating the Predators)
 * Polar bear (Ursus maritimus) (AUDIO: The Wreck of the Titan)
 * Pterodactylus antiquus (PROSE: Something Borrowed)
 * 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)

The Silurians and their "underwater cousins" the Sea Devil were known as Homo reptilia. (PROSE: Doctor Who and the Cave-Monsters, Doctor Who and the Sea-Devils, TV: The Hungry Earth) Both groups of Earth Reptiles were also known as Homo Reptilicus. (PROSE: First Frontier) Alternatively, Petronella Osgood referred to both Silurians and Sea Devils as Reptilia sapiens. (AUDIO: Tidal Wave)

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

Variations of humanity
Josiah Samuel Smith classified some humans as Homo Victorianus Ineptus. (TV: Ghost Light)

Homo peculiar were an advanced mutation of homo sapiens that began emerging through telepathic youth in the 20th century. (PROSE: Peculiar Lives)

Steve and Val Ross taught that the destiny of the human race was to mate with alien species and become the Homo stellar. (AUDIO: Believe)

The Homo superior were a group of children on Earth that did missions for the Galactic Federation. (PROSE: The Blue Angel)

Homo solarians were a posthuman species who lived inside the Sun after it destroyed Earth. (PROSE: The Brakespeare Voyage)

Plants

 * Amyris elemifera (PROSE: Another Life)
 * Deadly nightshade (Atropa belladonna) (TV: The Sensorites)
 * Lily of the valley (Convallaria majalis) (PROSE: The Secret in Vault 13)
 * Oak (Quercus robur) (PROSE: The Secret in Vault 13)
 * Parsley (Petroselinum crispum) (PROSE: The Secret in Vault 13)
 * Tea (Camellia sinesis) (AUDIO: A Small Semblance of Home)
 * Valeriana officinalis centiculare europea (TV: Castrovalva, The Mark of the Rani)
 * Willow (Salix fragilis) (PROSE: The Secret in Vault 13)
 * Wolfsbane (Aconitum napellus) (PROSE: Wolfsbane)

Fungi

 * Psilocybe mexicana (PROSE: The Left-Handed Hummingbird)

Microorganisms

 * Bubonic plague (Yersinia pestis) (COMIC: Black Death White Life, Antidote to Oblivion)
 * Recombinant yersinia pestis (COMIC: A Fairytale Life)
 * E. coli (PROSE: Deadfall)

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
Originally a hoax created by the First Doctor, (AUDIO: The Suffering) Tim Connolly used remembrance tanks in City of the Saved to turn the Piltdown Man (Homo piltdownensis) into a real species. (PROSE: The Adventure of the Piltdown Prelate)

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)

The weed planet of Necros was known as Herbabaculum vitae, which was Latin for "staff of life". (TV: Revelation of the Daleks, PROSE: Revelation of the Daleks)

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)

faries were also known as Homo fata vulgaris. (PROSE: The Shining Man)

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

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