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The general idea comes from like Lewis and Clark I guess. What would their collection of knowledge on the animals they discovered be called? I guess it could just be called their journals but is there a more specific term for something like a collection of knowledge of animals, like a bestiary or something along those lines?

To expand on that is there a word for the collective knowledge they had on plants as well?

"Lewis and Clark's "bestiary" contained knowledge from how big the average boar was to how the behaviors of geese during mating season."

"Lewis and Clark's "plant bestiary" contained knowledge on how certain flowers could be grown but also had information on how flowers could be made into tea for healing attributes."

Something like that.

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    "Botanical notes." "Bestiary" is OK for anecdotal info on animals but not plants.. – Mark Hubbard Mar 6 '17 at 16:35
  • Natural history (covers plants and animals). – aparente001 Mar 7 '17 at 6:15
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Zoography

A description of animals, their forms, and habits; descriptive zoology. (Wiktionary)

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Bestiary does nicely for animals. For plants:

Botanary
The word does not seem to have found its way into dictionaries-yet. However, this from RMIT University in Australia RMIT University.
The term botanary is in use, as many references to this term, meaning a collection of plant names, may be had in the internet. Dave's Garden
Illinois Farm Bureau Partners

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The notes that Lewis and Clark made during their travels could be called fieldnotes.

Fieldnotes are defined as follows in this Wikipedia article:

Fieldnotes refer to qualitative notes recorded by scientists or researchers in the course of field research, during or after their observation of a specific phenomenon they are studying... There are two components of fieldnotes: descriptive information and reflective information... Fieldnotes can also include sketches, diagrams, and other drawings.

If the fieldnotes are then published, they could be in the form of a field guide or an atlas.

The Wikipedia article on Field Guide, states the following:

A field guide is a book designed to help the reader identify wildlife (plants or animals) or other objects of natural occurrence (e.g. minerals). It is generally designed to be brought into the 'field' or local area where such objects exist to help distinguish between similar objects. Field guides are often designed to help users distinguish animals and plants that may be similar in appearance but are not necessarily closely related.

It will typically include a description of the objects covered, together with paintings or photographs and an index. More serious and scientific field identification books, including those intended for students, will probably include identification keys to assist with identification, but the publicly accessible field guide is more often a browsable picture guide organized by family, colour, shape, location or other descriptors.

An atlas in this case would be defined more broadly than a book of maps:

A volume of tables, charts, or plates that systematically illustrates a particular subject

There are a lot of animal atlas books, if you search for that term.

For your two sentences, I think you could rewrite them to say something like this:

"Lewis and Clark's fieldnotes on the flora and fauna they encountered contained details from how big the average boar was to how geese behaved during mating season, as well as information on how certain flowers could be grown and how those flowers could be made into tea with certain healing attributes."

(If you're not familiar with the term "flora and fauna," see this definition.)

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