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Thus, we first asked which processes tend to be rhythmic by identifying GO terms with an overrepresented number of cycling genes.
An executable program for identifying GO and DO annotations in Wikipedia articles according to the protocol described above as well as all relevant source code may be accessed at the open source Gene Wiki code repository [ 37].
Through collaboration with professional GO curators from five different MODs, we created the BC4GO corpus for the development and evaluation of automated methods for identifying GO terms from full-text articles in BioCreative IV (48).
Sequences with no BLAST hits were then searched against NCBI nr database with an E-value threshold of 10−30 and classified functionally by identifying GO terms of molecular function, cellular component, and biological process using the software Blast2GO [ 59].
Our first experiment was to check that our tools for identifying GO categories from a set of genes produce results comparable to the published results (the authors used custom computer scripts, which they make freely available).
However, they are limited by the complex nature of the GO terms; indeed, identifying GO terms in text is highly challenging, as they often do not appear literally or approximately in text (e.g. 'regulation of transcription, DNA-dependent', which is one of the most frequent GO terms assigned by curators).
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