Of course the metaphor of the bees and their honey is the biggest which we've all failed to mention! It's my favorite because of its age, its location within the tradition of rhetoric and sententiae/ars excerpendi, its prolific use through history, and the way it frames collecting and arranging for the use of creativity and writing.

In the his classic on rhetoric, Seneca gave an account of his ideas about note-taking in the 84th letter to Luculius ("On Gathering Ideas"). It begins from ut aiunt: "men say", that we should imitate the bees in our reading practice. For as they produce honey from the flowers they visit and then "assort in their cells all that they have brought in", so we should, "sift (separate) whatever we have gathered from a varied course of reading" because things keep better in isolation from one another, an idea which dovetails with ars memoria, the 4th canon of rhetoric.

"We should follow, men say, the example of the bees, who flit about and cull the flowers that are suitable for producing honey, and then arrange and assort in their cells all that they have brought in; these bees, as our Vergil says: 'pack close the flowering honey And swell their cells with nectar sweet.' "

Generations later in ~430 CE, Macrobius in his Saturnalia repeated the same idea (he assuredly read Seneca, though he obviously didn't acknowledge him):

"You should not count it a fault if I shall set out the borrowings from a miscellaneous reading in the authors' own words... sometimes set out plainly in my own words and sometimes faithfully recorded in the actual words of the old writers... We ought in some sort to imitate bees; and just as they, in their wandering to and fro, sip the flowers, then arrange their spoil and distribute it among the honeycombs, and transform the various juices to a single flavor by some mixing with them a property of their own being, so I too shall put into writing all that I have acquired in the varied course of my reading... For not only does arrangement help the memory, but the actual process of arrangement, accompanied by a kind of mental fermentation which serves to season the whole, blends the diverse extracts to make a single flavor; with the result that, even if the sources are evident, what we get in the end is still something clearly different from those known sources."

Often in manuscripts writers in the middle ages to the Renaissance would draw bees or write 'apes' (Latin for bees) in the margins of their books almost as bookmarks for things they wished to remember or excerpt for their own notes.

Of course, neither of these classical writers mentions the added benefit that the bees were simultaneously helping to pollenate the flowers, which also enhances the ecosystem.

• Seneca (2006) Epistles 66-92. With an English translation by Richard G. Gummere. Cambridge, MA: Harvard University Press (Loeb Classical Library), 277-285.
• Havens, Earle. Commonplace Books: A History of Manuscripts and Printed Books from Antiquity to the Twentieth Century. New Haven, CT: Beinecke Rare Book and Manuscript Library, 2001.

This general thought goes back to antiquity (and possibly earlier). In writing about classic rhetoric Seneca the Younger wrote in Epistulae morales

"We should follow, men say, the example of the bees, who flit about and cull the flowers that are suitable for producing honey, and then arrange and assort in their cells all that they have brought in; these bees, as our Vergil says, 'pack close the flowering honey | And swell their cells with nectar sweet.' "

(Sound a bit like he's one of the original digital gardeners, but in an analog world?)

He's essentially saying, read the best, take their thoughts and ideas, consume them, make them your own."

Generations later in ~430 CE, Macrobius in his Saturnalia repeated the same idea and even analogy (he assuredly read Seneca, though he obviously didn't acknowledge him):

"You should not count it a fault if I shall set out the borrowings from a miscellaneous reading in the authors' own words... sometimes set out plainly in my own words and sometimes faithfully recorded in the actual words of the old writers... We ought in some sort to imitate bees; and just as they, in their wandering to and fro, sip the flowers, then arrange their spoil and distribute it among the honeycombs, and transform the various juices to a single flavor by some mixing with them a property of their own being, so I too shall put into writing all that I have acquired in the varied course of my reading... For not only does arrangement help the memory, but the actual process of arrangement, accompanied by a kind of mental fermentation which serves to season the whole, blends the diverse extracts to make a single flavor; with the result that, even if the sources are evident, what we get in the end is still something clearly different from those known sources."

This is also related to the ideas of invention as well as the analogy of the bee in relation to commonplaces. Link this to the bee analogy of Seneca the Younger and Macrobius in Saturnalia.