FANTOM DB 2.0 & 2.1 release Notes
December5th, 2002

The FANTOM DB consists of functional annotations for the RIKEN full-length
cDNA clones. It provides not simply the gene functions themselves, but also many
other informative and useful data describing functional information about the clones. 
See FANTOM web site (http://fantom2.gsc.riken.go.jp/) for further information. 
 
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FANTOM DB 2.0 & 2.1(released on December5th, 2002) 

1. What is new?
1.1. The clone set and sequences. 
FANTOM DB 2.0 & 2.1 contains data for full length sequenced 60,770 RIKEN cDNA clones.
It consist of FANTOM1 21,076 clones and sequenced 39,694 clones.
ID information for all clones are shown in idtable2.0.txt at FANTOM web site (http://fantom2.gsc.riken.go.jp/fantom2/doc/release/idtable2.0-2.1.txt).


1.2. Annotation in FANTOM2
FANTOM DB 2.0 & 2.1 was outcome of the FANTOM2 collaborative research. 
Fanctional annotation for 60,770 cDNA clones were carried out at MATRICS (Mouse Annotation 
Teleconference for RIKEN cDNA sequences) via Internet with the web-based FANTOM using a secure server system.
See history page at FANTOM web site for further information.

Functional annotation was described using many qualifiers. See annotation strategy page at FANTOM web site.
The major advantages for annotation in FANTOM2 were as follows;
* Gene name were decided according to the improved pipeline for FANTOM2. 
The detailed evidence for gene name annotation were recorded in database.
* Coding sequence (CDS) region were determined by human curation. 
Not only start or stop position of CDS, but also status for clone problem were described.

1.2 Difference between FANTOM DB 2.0 and 2.1.
FANTOM DB 2.0 is a freezed data on October 4th, 2002 for the FANTOM2 article on Nature.
FANTOM DB 2.1 is updated version on November 27th, 2002.

2. Database access/Data Distribution

2.1. FANTOM annotation viewer
Each annotation results can be viewed through FANTOM viewer 
(http://fantom2.gsc.riken.go.jp/db/). 

2.2. FTP server
FANTOM data archive are available at FTP server (ftp://fantom2.gsc.riken.go.jp/)

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3. Copyright Notice

The RIKEN makes no representation about the suitability or accuracy of FANTOM data 
or software for any purpose and makes no warranties. Either express or implied, 
including merchantability and fitness for a particular purpose or that the use of 
FANTOM data or software will not infringe any third party patents, copyrights, 
trademarks, or other rights. The software and data are provided "as is".

This software is provided for non-commercial purpose in the scientific community.
Any reproduction or use for commercial purpose is prohibited without permissions of
the Institute of Physical and Chemical Research (RIKEN) and NTT Software Corporation. 

For further information, please contact: fantom-help@gsc.riken.go.jp 

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4. Citation
To cite resources available from the FANTOM web site in your publications, use a
following article. 

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team
Nature 420:563-573, 2002

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5. Acknowledgement
FANTOM DB 2.0 and 2.1 (released on December5th, 2002) were prepared by
The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team.

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6. Contact address

FANTOM-help
Genome Exploration Research Group
Genomic Sciences Center
RIKEN (The Institute of Physical and Chemical Research) 
Yokohama Institute
1-7-22,Suehiro-cho, Tsurumi-ku
YOKOHAMA, 230-0045 
Japan
Email: fantom-help@gsc.riken.go.jp 
FANTOM DB web site:http://fantom2.gsc.riken.go.jp/