Etymology
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onto- 

word-forming element meaning "a being, individual; being, existence," from stem of Greek on (genitive ontos) "being," neuter present participle of einai "to be" (from PIE root *es- "to be").

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oo- 

word-forming element meaning "egg, eggs," from Greek ōon "egg," cognate with Latin ovum, Old Norse egg,from PIE *ōwyo‑, *ōyyo‑ "egg," which perhaps is a derivative of the root *awi- "bird."

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op- 
assimilated form of ob- before -p-.
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oro- 
word-forming element meaning "mountain," from Greek oros "mountain" (see oread).
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ortho- 

before vowels orth-, word-forming element meaning "straight, upright, rectangular, regular; true, correct, proper," now mostly in scientific and technical compounds, from Greek orthos "straight, true, correct, regular," from PIE *eredh- "high" (source also of Sanskrit urdhvah "high, lofty, steep," Latin arduus "high, steep," Old Irish ard "high").

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os- 
frequent form of ob- before -c- and -t- in words from Latin.
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osteo- 
before vowels oste-, word-forming element meaning "bone, bones," from Greek osteon "bone," from PIE root *ost- "bone."
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over- 

word-forming element meaning variously "above; highest; across; higher in power or authority; too much; above normal; outer; beyond in time, too long," from Old English ofer (from PIE root *uper "over"). Over and its Germanic relations were widely used as prefixes, and sometimes could be used with negative force. This is rare in Modern English, but compare Gothic ufarmunnon "to forget," ufar-swaran "to swear falsely;" Old English ofercræft "fraud."

In some of its uses, moreover, over is a movable element, which can be prefixed at will to almost any verb or adjective of suitable sense, as freely as an adjective can be placed before a substantive or an adverb before an adjective. [OED]

Among the old words not now existing are Old English oferlufu (Middle English oferlufe), literally "over-love," hence "excessive or immoderate love." Over- in Middle English also could carry a sense of "too little, below normal," as in over-lyght "of too little weight" (c. 1400), overlitel "too small" (mid-14c.), overshort, etc.

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