About RAP


History of the Rice Annotation Project

The Rice Annotation Project (RAP) was conceptualized upon the completion of the rice genome sequencing in 2004 with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. One of the major activities of RAP is to hold jamboree-style annotation meetings on a regular basis to facilitate the manual curation of all gene structures and functions in rice. Also part of the overall objective is to facilitate a comprehensive analysis of the sequence based on the results of annotation and the construction of a public database. These activities have jointly been organized by the National Institute of Agrobiological Sciences (NIAS) and the International Rice Genome Sequencing Project (IRGSP) in collaboration with the Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST) and the DNA Data Bank of Japan (DDBJ), National Institute of Genetics (NIG), and supported in part by a grant from the Ministry of Education, Culture, Sports, Science and Technology (MEXT).





RAP9 in Chiang Mai

The Ninth Rice Annotation Project Meeting (RAP9) was held in Chiang Mai, Thailand on October 28th, 2012, as a concurrent session of 10th International Symposium on Rice Functional Genomics. There were five presentations, who gave talks about new databases and application of bioinformatics to future experiments in rice. In this RAP meeting, we discussed how to utilize new data derived from next-generation sequencers, and how to apply bioinformatics to the new green revolution. For the detailed program of the RAP9 session, please click on here (PDF file, 19KB).





RAP8 in Taipei

The Eighth Rice Annotation Project Meeting (RAP8) was held in Taipei, Taiwan on November 9th, 2011, as a workshop of 9th International Symposium on Rice Functional Genomics. In this year, a unified Oryza sativa (japonica group, cv. Nipponbare) genome, Os-Nipponbare-Reference-IRGSP-1.0, was created in collaboration with MSU's rice annotation group and an overview of this assembly was presented by Dr. Takuji Sasaki, a former co-chair of the International Rice Genome Sequencing Project. In addition, to cope with emerging massive data generated by next-generation sequence technologies, a new browser for genome-wide sequencing data was introduced.





RAP7 in Tokyo

The Seventh Rice Annotation Project Meeting (RAP7) was held in Tokyo, Japan on October 14th, 2010, as a satellite meeting of Biocuration 2010. We had about 40 researchers with expertise in genome analyses of rice and other cereals. During this meeting, discussed were various issues such as updating the rice genome annotation, new computational tools, efficient access to annotation data and topics about genome annotation of other cereal crops. Detailed information including the program and abstract is available from the RAP7 website.





RAP6 in Manila

The Sixth Rice Annotation Project Meeting (RAP6) was held in Manila, Philippines on November 15th, 2009 as a satellite meeting of the 6th International Rice Genetics Symposium and the 7th International Symposium of Rice Functional Genomics. The workshop-discussion meeting was participated by a total of about 70 researchers including rice researchers as well as researchers of other cereal crops and other plants involved in genome analysis and comparative genomics. The major rice annotation groups, namely, RAP-DB, MSU Rice Genome Annotation, and Gramene presented the current status of their annotation projects. In addition, members of the IRGSP also gave an update on their respective projects on rice genomics. The wrap-up discussion focused on constructing a consensus Nipponbare rice genome assembly. For a detailed program of the RAP6 workshop, please refer here (PDF file, 80KB).





RAP5 in Odaiba

The Fifth Rice Annotation Project (RAP5) Meeting was held in Odaiba, Tokyo on November 14-15, 2008. It was a workshop-discussion meeting. In addition to the rice researchers, distinguished researchers with expertise in genome analyses of other cereals were also invited. Through RAP5, we discussed various issues on updating the annotation, new computational tools, efficient access to annotation data, as well as issues relevant in genome annotation of other cereal crops.

RAP5 participants





RAP4 in Tsukuba

The Fourth Rice Annotation Project Meeting (RAP4) was held in Tsukuba, as a part of the Fifth International Symposium of Rice Functional Genomics (ISRFG) held on October 15-17. In the RAP4 workshop, seven researchers presented their research progresses on rice genome analyses using RAP annotation data. In addition, how we promote researches on the rice genome and how we deal with increasingly accumulating genomic data in the future were also discussed. For the detailed program of the RAP4 workshop, please see here (PDF file, 20KB).




RAP3 in Tsukuba

The Third Rice Annotation Project Meeting (RAP3) was organized with the aim of annotating the rice genome in a topic-specific manner so that detailed analyses of the rice genes and genome would be facilitated. The meeting was held on December 9-10, 2006 in Tsukuba. Experts in various field of rice genomics with their own projects using the RAP2 annotation data participated on this 2-day discussion meeting. Among the projects presented cover the following topics:

RAP3 participants

Genome annotatio

  • Transposon
  • Small RNA, microRNA
  • Structure and functional motif

Genome analysis

  • Functional domain
  • Gene duplication
  • Natural variation

Gene family annotation

  • LEA protein
  • F-Box protein
  • Cytokinin
  • Kinase
  • Stress response gene

Functional annotation

  • Cell wall
  • Metabolism
  • Development



RAP2 in Manila/Tsukuba

An update on the annotation has become necessary with the release of the build 4 assembly of the rice genome. Thus the Second Rice Annotation Project Meeting (RAP2) was organized again in two parts. Instead of holding the meeting in one venue, the discussion part was held in Manila on November 18-19, 2005 in conjunction with the 5th International Rice Functional Genomics Symposium and the annotation part followed in Tsukuba on Feb 1-3, 2006. The discussion part was participated mainly by researchers who were using the rice genome sequence in more advanced research on rice genomics and therefore aimed to identify the areas that must be addressed for further analysis of the genome sequence. The annotation part focused on the manual curation of function descriptions and gene structures based on the build 4 assembly, and was participated mainly by annotators from the IRGSP member countries, BIRC/JBIRC, DDBJ, NCBI, EMBL, etc.

RAP2 participants




RAP1 in Tsukuba

The First Rice Annotation Project Meeting (RAP1) was held in Tsukuba, Japan on December 13-18, 2004. The meeting was modeled on the H-Invitational human annotation workshop (Imanishi et al. PLoS Biol. 2:856-875) and focused on the manual curation of gene structures and functions using rice full-length cDNA sequences and the build 3 assembly of the rice genome. RAP1 consisted of two parts: (1) annotation part participated by annotators from the IRGSP member countries, BIRC/JBIRC, DDBJ, NCBI, EMBL, etc. and (2) discussion-workshop participated by rice researchers, bioinformatics specialists and other potential users of the rice genome sequence. The results derived from RAP1 were released from the RAP-DB and described in detail in the papers published in Nucleic Acids Research and Genome Research.

RAP1 participants