These general requirements were our main interest in developing an annotation interface because most curation systems currently available solve very specific problems and few of them can be used for multiple annotation tasks (14 16).
This returned a single annotation for 9,863 isogroups (43%), and multiple annotations for 199 isogroups that we excluded from further portions of this analysis.
'Unknown' annotations are often present as the sole annotation for a GO aspect for a gene, but non-'unknown' annotations are typically part of a set containing multiple annotations for a gene.
However, the over-representation analysis at the functional level that we applied here allows multiple annotations for a single gene and, therefore, inherently overcomes this type of problems.
Also it is common, from a single article, to identify multiple annotations identified for one aspect and to annotate to different levels of granularity in the same branch of the ontology.
For each identified human lincRNA, multiple annotations are grouped as three sheets in the "Entry detail" tab: 1) "Basic Information" sheet contains its genomic location, original accession number and the source link, as well as the functional and evolutionary annotations.
GATE is distributed with a number of its own language processing tools, such as part-of-speech taggers, gazetteers and an interface to the Weka machine learning tools [ 14], plus it contains useful facilities for keeping track of corpora, multiple annotations, and interactive visualization and mark-up of text.
We believe that BEACON may help improve the quality of bacterial genome annotations deposited in public databases when multiple annotations are available for the same bacterial genome.
