Annotated Gel Markup Language, or AGML, is a language that has being proposed to markup data obtained by 2-D gel electrophorosis based on the XML language. The eXtensible Markup Language (XML) is particularly well suited to represent biological data and methods and, presently being the consensual choice in most areas. As such XML syntax notation was used to describe data acquired from 2-D gel electrophoresis and mass spectrometry. The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.

The AGML Central project is part of an wider XML data model to represent 2-D gel electrophoresis data. In this regard the aim is to faithfully represent both the data/results and experimental protocols/methods used in producing the data. The major advantage in this comes from the fact that when analysing 2-D gel electrophoresis data stored in AGML (an XML data structure), all the pertinent information can be found in one data file. AGML 2.0 data structure can store data, both gel and mass spectrometry, and experiemental methods through the use of MI2DG.

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