In just one year, we have successfully obtained over 1,114 manually curated genes (57 families) from members of the rice and plant community at large, incorporated this annotation into our annual update, and displayed all of the CA annotation on individualized web pages.
We also incorporated published annotation corrections based on proteomic evidence [ 71, 72].
Our algorithm measured the robustness of evidence provided by the spliced EST annotations and incorporated evidence from annotations of UCSC Known Genes and GenBank mRNA.
Between February 2008 and August 2011, we incorporated 20 601 community annotations into TAIR, including11 870 GO annotations, 8517 PO annotations and 214 annotations of protein interactions.
To determine gene structure (introns and exons), cDNAs were mapped onto the BAC contigs containing the respective gene using est2genome incorporated in the annotation software MAKER [ 50].
ST11 included several tasks: GE11, an extension of GE09, incorporated full text annotations in addition to abstracts, EPI [EPIgenetics and post-translational modifications (PTM ] concerned events relating to epigenetic change, and ID dealt with infectious diseases in full texts.
The incorporated genes were annotated using a variety of methods including Swiss-Prot annotation, TrEMBL annotation, KEGG annotation, InterPro domain annotation and Gene Ontology annotation.
The gene prediction program Prodigal [ 11] was developed at Oak Ridge National Laboratory (ORNL; Oak Ridge, TN, USA) and incorporated into the JGI annotation pipeline after the initial ATCC 27405 genome annotation.
For example, synthetic polymers consisting of an undefined number of monomers were detected during the annotation and incorporated to this class.
Consistent with this evidence-based annotation, we incorporated published results from genome-wide association studies of a wide array of chemotherapeutic agents, as cataloged in a public resource PACdb [ 29] we created.
