Canonical is an adjective derived from canon. Canon comes from the Arabic word "Qanuun" which essentially means "rule", "law", "standard", and has come to mean "generally accepted" or "authoritatively correct."
basic, canonic, canonical: reduced to the simplest and most significant form possible without loss of generality, e.g. "a basic story line"; "a canonical syllable pattern"
Some circles in the field of computer science have borrowed this usage from mathematicians. It has come to mean "the usual or standard state or manner of something"; for example, "the canonical way to organize a file system is as a hierarchy, with extensions to make it a directed graph". XML Signature defines canonicalization as the process of converting XML content to a canonical form, to take into account changes that can invalidate a signature over that data (from JWSDP 1.6).
For an illuminating story about the word's use among computer scientists, see the Jargon File's entry for the word[1].
Some people have been known to use the noun canonicality; others use canonicity. In fields other than computer science, canonicity is this word's canonical form.
The company Canonical Ltd. is named jocularly referencing this usage.
Hackers invest this term with a playfulness that makes an ironic contrast with its historical meaning. A true story: One Bob Sjoberg, new at the MIT AI Lab, expressed some annoyance at the incessant use of jargon. Over his loud objections, GLS and RMS made a point of using as much of it as possible in his presence, and eventually it began to sink in. Finally, in one conversation, he used the word canonical in jargon-like fashion without thinking. Steele: "Aha! We've finally got you talking jargon too!" Stallman: "What did he say?" Steele: "Bob just used ‘canonical’ in the canonical way."
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