Chemical libraries are usually generated for a specific goal and larger chemical libraries could be made of several groups of smaller libraries stored in the same location.  In the drug discovery process for instance, a wide range of organic chemicals are needed to test against models of disease in high-throughput screening. Therefore, most of the chemical synthesis needed to generate chemical libraries in drug discovery is based on organic chemistry. A company that is interested in screening for kinase inhibitors in cancer may limit their chemical libraries and synthesis to just those types of chemicals known to have affinity for ATP binding sites or allosteric sites.
Generally, however, most chemical libraries focus on large groups of varied organic chemical series where an organic chemist can make many variations on the same molecular scaffold or molecular backbone. Sometimes chemicals can be purchased from outside vendors as well and included into an internal chemical library.
Depending upon their scope and design, chemical libraries can also be classified as diverse oriented, Drug-like, Lead-like, peptide-mimetic, Natural Product-like, Targeted against a specific family of biological targets such Kinases, GPCRs, Proteases, PPI etc. These chemical libraries are often used in target based drug discovery (reverse pharmacology). Among the compound libraries should be annotated the Fragment Compound Libraries, which are mainly used for Fragment-based lead discovery.