Editing Cheminformatics (section)

===Storage and retrieval===
{{unreferenced section|date=February 2020}}
{{main|Chemical database}}
A primary application of cheminformatics is the storage, indexing, and search of information relating to chemical compounds.{{cn|date=March 2025}} The efficient search of such stored information includes topics that are dealt with in computer science, such as data mining, information retrieval, [[information extraction]], and [[machine learning]].{{citation needed|date=February 2020}} Related research topics include:{{citation needed|date=February 2020}}
{{div col}}
* [[Digital libraries]]
* [[Unstructured data]]
* [[Structured data mining]] and mining of [[structured data]]
**[[Database mining]]
**[[Graph mining]]
**[[Molecule mining]]
**[[Sequence mining]]
**[[Tree mining]]
{{div col end}}

==== File formats ====
{{main|Chemical file format}}
The ''in silico'' representation of chemical structures uses specialized formats such as the [[Simplified molecular input line entry specification]]s (SMILES)<ref>{{cite journal|title=SMILES, a Chemical Language and Information System: 1: Introduction to Methodology and Encoding Rules|author=Weininger, David|journal=Journal of Chemical Information and Modeling|year=1988|volume=28|issue=1|pages=31–36|doi=10.1021/ci00057a005|s2cid=5445756 }}</ref> or the [[XML]]-based [[Chemical Markup Language]].<ref>{{cite journal|title=Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles|author=Murray-Rust, Peter|author2=Rzepa, Henry S.|journal=Journal of Chemical Information and Computer Sciences|year=1999|volume=39|issue=6|pages=928–942|doi=10.1021/ci990052b}}</ref>  These representations are often used for storage in large [[chemical database]]s.{{citation needed|date=February 2020}} While some formats are suited for visual representations in two- or three-dimensions, others are more suited for studying physical interactions, modeling and docking studies.{{citation needed|date=February 2020}}