There have been recent improvements in document technologies like the standardization of object interfaces to access and manipulate the properties of web documents. There has also been significant progress in pen based computing for recognition of digital ink in desktops, tablets and handheld devices. These have necessitated a need for further research on annotation architectures for digital documents, specifically pen-based annotation systems. This paper presents an attempt to leverage the new standards of DHTML and W3C DOM that are being gradually implemented by popular browsers, to build a prototype of an ink annotation system with common components across browsers. One of the primary goals in this study is to semantically link ink data with underlying document elements like text and images. The system has three components: a) Ink capture and rendering b) Ink Understanding, which recognizes and associates ink with the underlying document and c) Ink storage and retrieval.