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In a library, (and I'm not totally sure about this, but from experience) books are organized by category/theme into sections, and then they are given a number so that, globally, the numbers are ordered sequentially. This way you can easily just look up a number and go right to it, but then you can also browse entire sections by a common theme. I'm not sure how exactly they do this, but this is roughly what I've seen how it works.

So I'm wondering how biological specimens are organized in a gigantic specimen archive like at a large museum or university collection, with hundreds of thousands or millions of specimens. I'm wondering if they just give them a random number, and then place them wherever that number falls in the sequence. Or if they do like the libraries and group them by category/theme, then by number. Or something different.

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Biological specimens are ordered in museums phylogenetically. So all the birds are in one place, and the insects in another. Fossils are generally kept in their own place. Different museums may have their own standards, but most sort specimens phylogenetically as well. But alphabetical sorting also happens. So that all the members of a family are in one place, and then the genera within the family are organized alphabetically. So all the Trichoptera (Insecta), for example, at the Smithsonian are together on one of the floors with other insects, curated by a Trichoptera specialist. Within Trichoptera, the first drawers are Apatanaeidae, and the last are Xiphocentronidae. Individual specimens are often given a unique number, usually sequential, with the time of accession into the museum.

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As an addition to Karl Kjer's answer

Fossils specimens are usually ordered by locality(where it was collected) or phylogenetically, but size and shape is often more important as well. its hard to keep 3000lb sauropod pelvis in the same place as 3 ounce microraptors bones, but large sauropod bones and large pieces of petrified wood might be stored together. This is why good records are important in fossil collections, physical limitation often trump ideal cataloging. Fossil collections are often constantly growing as well which is why locality is often better than phylogeny, you don't know how many of anything you will end up with, but at least you can group things by where it came from.

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