RT Journal
A1 Kasukawa, Takeya
A1 Furuno, Masaaki
A1 Nikaido, Itoshi
A1 Bono, Hidemasa
A1 Hume, David A.
A1 Bult, Carol
A1 Hill, David P.
A1 Baldarelli, Richard
A1 Gough, Julian
A1 Kanapin, Alexander
A1 Matsuda, Hideo
A1 Schriml, Lynn M.
A1 Hayashizaki, Yoshihide
A1 Okazaki, Yasushi
A1 Quackenbush, John
T1 Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6b 
SP 1542 
OP 1551 
DO 10.1101/gr.992803 
UL http://genome.cshlp.org/content/13/6b/1542.abstract 
AB Manual curation has long been held to be the “gold standard”  for functional annotation of DNA sequence. Our experience with the annotation  of more than 20,000 full-length cDNA sequences revealed problems with this  approach, including inaccurate and inconsistent assignment of gene names, as  well as many good assignments that were difficult to reproduce using only  computational methods. For the FANTOM2 annotation of more than 60,000 cDNA  clones, we developed a number of methods and tools to circumvent some of these  problems, including an automated annotation pipeline that provides  high-quality preliminary annotation for each sequence by introducing an  “uninformative filter” that eliminates uninformative annotations,  controlled vocabularies to accurately reflect both the functional assignments  and the evidence supporting them, and a highly refined, Web-based manual  annotation tool that allows users to view a wide array of sequence analyses  and to assign gene names and putative functions using a consistent  nomenclature. The ultimate utility of our approach is reflected in the low  rate of reassignment of automated assignments by manual curation. Based on  these results, we propose a new standard for large-scale annotation, in which  the initial automated annotations are manually investigated and then  computational methods are iteratively modified and improved based on the  results of manual curation.