Genome Informatics 11: 219–221 (2000)
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FANTOM+: The Interface for Functional Annotation of Mouse cDNA Hidemasa Bono1
Takeya Kasukawa1,
Toshihisa Okido1
[email protected]
[email protected]
[email protected]
Katsunaga
Sakai1
[email protected]
Kiyoshi
Yoshida1
[email protected] 1
2 3
Masaaki
Furuno1
[email protected]
Yasushi
Okazaki1,2
[email protected]
Shotaro Kohtsuki3
[email protected]
Yoshihide Hayashizaki1,2
[email protected]
Genome Exploration Research Group, Genomic Sciences Center (GSC) RIKEN (The Institute of Physical and Chemical Research) 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Genome Science Laboratory, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan Multimedia Development Center, Advanced Technology Development, Department, NTT Software Corporation, 223-1 Yamashita-Cho, Naka-ku, Yokohama-shi, Kanagawa 231-8554, Japan
Keywords: annotation, cDNA, mouse, interface
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Introduction
RIKEN has been working on the mouse full-length cDNA encyclopedia since 1995. We have been focusing on the collection and sequencing of more than one million mouse cDNAs, Phase I of the project. In Phase II, we have re-arrayed the non-redundant clones and produced full-length sequence for about 20,000 clones. In order to assign functional annotation to the uncharacterized cDNA sequences by human effort effectively, we developed a semi-automatic annotation tool called FANTOM+, which can present analysis results graphically on the web browser and store annotation results in RDBMS (Sybase). Recently, we held an annotation meeting, named FANTOM (Functional ANnoTation Of Mouse) meeting, from 28th August to 8th September in Tsukuba and annotated all of the clones, using the annotation tool, with experts in the fields of bioinformatics, genome science, biology and other fields [1, 2, 3].
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Overview of FANTOM+
FANTOM+ has following features; i) simple interface with HTML and JavaScript, ii) Graphical User Interface, iii) Controlled system of annotation records, and iv) Parser for XML output (MaXML). The top page of FANTOM+ has FANTOM menu (login/logout, annotate, search, database search, statistics and MaXML), discussion boards and other Interfaces. The editing (annotating) page of FANTOM+ contains three frames. The top (summary) frame is to show summary of the current object (riken clone, database record or protein motif etc...). The middle (reference) frame is to graphically display precomputed sequence similarity and motif search results. By clicking the buttons in each reference, the definition of corresponding database hits can be copied to the form in the following (annotation) frame as a template of the definition (RIKEN definition; riken def). The bottom frame is to edit the annotation of current cDNA clone. For
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Figure 1: Snapshot of Web Interface of FANTOM+
Figure 2: Flowchart of determining riken definition
example, in FASTA search, the top black thin line and numbers above the line represent a sequence and nucleotide numbers of a cDNA clone, respectively, the middle red line represents CDS predicted by DECODER program, and the bottom blue thin line, blue-colored box, and the number in the bluecolored box represent non-homology region, homology region, and % identity of homology, respectively. The result of alignment for homology search can also be browsed by following the link (’align’) (Figure 1).
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Annotation
Annotation effort by curators is focused on mainly on describing riken def, which is the essence of functional annotation. Curators can modify preliminary annotated text by referring precomputed results in the upper frame. Some Qualifiers, including riken def suppl, status, note, and comment are optionally placed by curators’ evaluation. Currently other Qualifiers are automatically retrieved from existing database. Furthermore, Gene Ontology (GO) [4] terms are used in order to functionally annotate genes, which are classified into three categories (molecular function, biological process and cellular component) consisting of authorized vocabularies by the GO Consortium. During the FANTOM meeting, we discussed strategy of functional annotation for the mouse full length cDNAs and decided how to describe riken def. The flowchart in Figure 2 summarizes our current functional annotation strategy. Based on the rules shown in Figure 2, curators can annotate riken def, data source and source key of data used for annotation by using the FANTOM+ system. Annotation for RIKEN cDNA clones are designed to be updated automatically when reference data used for annotation of the cDNA clones are updated.
Acknowledgement This study has been supported by Special Coordination Funds and a Research Grant for the RIKEN Genome Exploration Research Project, and ACT-JST (Research and Development for Applying Advanced Computational Science and Technology) of Japan Science and Technology Corporation (JST). These are funds from the Science Technology Agency of the Japanese Government to YH. This work was also supported by a Grant-in-Aid for Scientific Research on Priority Areas and Human Genome Program, from the Ministry of Education, Science and Culture, to YH.
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References [1] TOUCHINGbase, Nature Genetics, 25(4):371, 2000. [2] Cyranoski, D., Japan opens access to mouse cDNA data, Nature, 407:279. 2000. [3] http://genome.rtc.riken.go.jp/FANTOM/ [4] Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G., The Gene Ontology Consortium The Gene ontology: tool for the unification of biology, Nature Genetics, 25(1):25–29, 2000.
