ChemXSeer is a digital library and a data repository for the chemistry domain. The data deposited into our repository is linked with digital documents to create aggregates of resources representing the links between the data and the articles in which the data is reported. ChemXSeer enables the user to annotate the data using a metadata capturing tool. The metadata is indexed and searched to return relevant datasets to the user. ChemXSeer extracts chemical formulae and chemical names, disambiguates them and indexes them to allow for domain-knowledge enhanced search capabilities. As search engines mature, we foresee such vertical search engines, employing domain-specific knowledge to perform information extraction and indexing, especially for scientific domains, become more popular. Though substantial research has been pursued on information extraction from text, extracting information from tables and figures has received little attention. In the ChemXSeer project, we are building tools that allow automatic extraction of tables and figures.