Format of the PDF article. The PDF mini summaries are composed of four pages. The first page features basic information such as the TF name, gene identifiers and classification, as well as author information. Also on the first page are the names and affiliations of the authors, an overview of the TF, an image of its active site protein structure accompanied by a brief commentary, and a featured TF binding profile selected by the author. The second and third pages contain a mixture of figures, paragraph text, and tables of genomic targets and protein as well as ligand interactors. The last page contains two brief paragraphs, a MeSH cloud, and selected references. These are the first two pages of a four-page PDF mini summary generated by the TFe system software. Our PDF creation tool, based on in-house code and the dompdf 0.5.1 open source module, is able to format a TFe article of any length and annotation depth as a standardized four-page PDF article. A fuzzy logic algorithm does all of the modifications necessary to make the conversion. These modifications may include changing the sizes of the figures, truncating excess text, reformatting the references, and calculating trade-offs between having larger figures and data tables at the expense of less text, or keeping more text at the expense of having fewer figures and smaller data tables.
Yusuf et al. Genome Biology 2012 13:R24 doi:10.1186/gb-2012-13-3-r24