Class 2: Taxonomy

Bioinformatics

Andrés Aravena

September 29, 2022

What is Taxonomy?

According to Oxford Dictionary

tax·on·o·my | takˈsänəmē |
noun mainly Biology
the branch of science concerned with classification, especially of organisms; systematics.

  • the classification of something, especially organisms: the taxonomy of these fossils.
  • a system of classification: a taxonomy of smells.

From Greek taxis “arrangement” + -nomia “method”

Example: Book classification

This is why library books look like this

More details: List of Dewey Decimal classes at Wikipedia

Each class has subclasses

Our definition of Taxonomy

“A nested hierarchical classification system”

  • What does “hierarchical” mean?
  • What does “classification” mean?
  • What does “nested” mean?

Classification

“arrange in a class or classes, arrange according to common characteristics”

Assigning each object to a class

Every object is in one and only in one class

  • There is always a class for each object
  • There is no object that is in two or more classes

Example of classification

Dictionary definition of “Hierarchy”

hi·er·ar·chy | ˈhī(ə)ˌrärkē |

noun (plural hierarchies)

a system or organization in which people or groups are ranked one above the other according to status or authority

Dictionary instances of “Hierarchy”

  • the clergy of the Catholic or Episcopal Church; the religious authorities
  • the upper echelons of a hierarchical system; those in authority
  • an arrangement or classification of things according to relative importance or inclusiveness: a taxonomic hierarchy of phyla, classes, orders, families, genera, and species.
  • Theology the traditional system of orders of angels and other heavenly beings: the heavenly hierarchy.

Etymology of “Hierarchy”

From Greek hieros “sacred” + arkhein “to lead, rule”

Question

  • Which other words derive from hieros?

  • Which other words use the suffix archy?

Example of hierarchy

How to draw a Taxonomy

Yahoo began as a taxonomy

Can also be a tesselation

like this

One from my research

Sideways rectangles

Usually we draw them as trees

Treebolic

Some fishes

Craniates

All pictures from this book

What do all trees have in common?

Abstract trees

  • All classes are represented by points that we call nodes

  • Nodes are connected with arrows that we call arcs

  • Each has a single arrow pointing to another node

  • We say that each node points to its parent

Extra details

  • There are no loops

  • One node has no parent. We call it root

  • we usually describe relationships using “family” names

Family relationships

Biological Taxonomy

Invented by Carl Linnaeus
(Latin Carolus Linnæus)

This is why we say lineage

He decided that scientific names have two words
(i.e. binomial nomenclature)

He defined the ranks of the hierarchy

  • Kingdom (Regnum Animale, R. Vegetabile, R.Lapideum)
  • Phylum
  • Class
  • Order
  • Family
  • Genus
  • Species

Genus and Species

Genus
What all objects share in general
Species
What makes the object distinct from the others
What makes the object special

Example:

  • Acidithiobacillus thiooxidans
  • Acidithiobacillus ferroxidans

NCBI Taxonomy

NCBI has an unofficial taxonomy tree
(because there is no official one)

Nodes are called taxa (singular: taxon)

Each taxon has a numeric ID, called taxid

Each taxon has several attributes

  • Taxid of the parent node
  • Scientific name
  • Common name
  • Alternative names: old names, misspellings
  • History of the classification

Searching into NCBI Taxonomy

Use Taxonomy Browser

You can search by phonetic name if you are not sure of the spelling

Take a look at the taxon page

You can see the taxon attributes, and a table of related Entrez records

Using Taxonomy in Entrez searches

There are two columns titled “links”: Subtree and Direct

Click on “Nucleotide, Subtree links” and in “Nucleotide, Direct links”

What is the difference?

Practice