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KEGG as a self-sustaining database

As we start Fiscal Year 2022, I would first like to thank the NBDC Program of the Japan Science and Technology Agency for providing me with another five-year grant supporting KEGG MEDICUS. I would also like to thank the Institute for Chemical Research, Kyoto University and the Human Genome Center, the Institute of Medical Science, the University of Tokyo for their continued supports of the KEGG project.

KEGG is now 27 years old. It was fully funded by grants up until our 16th year. Currently, public funding accounts for only about one tenth of our total operational cost. KEGG is essentially a self-sustaining database project based on the community funding model, whereby the user community contributes financially to the development and maintenance of the project. I am especially grateful to all the commercial users who recognize the value provided by KEGG and honor our request to obtain a license.

Minoru Kanehisa

Posted on April 1, 2022

Thank You from KEGG

Fiscal Year 2017 just started in Japan. I would like to thank the National Bioscience Database Center of the Japan Science and Technology Agency for a five-year grant and the Institute for Chemical Research of Kyoto University for hosting KEGG in its supercomputer facility. Public funding now constitutes only one tenth of the total operation cost, but we are able to maintain and expand KEGG as a freely available web resource, thanks to your support through our licensing and subscription mechanisms.

We will develop a new database component named KEGG NETWORK for "perturbed" molecular networks involving human diseases and drugs. KEGG NETWORK will be a collection of network variants, such as variants of signaling pathways, caused by gene variants and other factors. We hope this will become another reference knowledge base for interpretation of personal genome sequences.

Minoru Kanehisa

Posted on April 3, 2017

Renewed Plea to Support KEGG

During the past three years we have been able to maintain and expand the KEGG database by successfully converting our operation from a fully government-funded project to a more community-supported project. We thank all the academic organizations and academic users who have obtained FTP subscriptions as well as all the commercial organizations who have obtained license agreements.

I was recently awarded a new three-year grant from the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency. The Institute for Chemical Research, Kyoto University has allowed me to continue to use the supercomputer facility and lab space for KEGG database development. However, since the NBDC funding covers only KEGG MEDICUS and amounts to only one-third of the entire operational cost, I must ask for your continued support of our academic FTP subscription and commercial licensing mechanisms.

The KEGG database will continue to be made freely available on the web. We are encouraged with the increasing popularity of the KEGG web service – the number of unique visitors per month has now reached 400 to 500 thousand and has more than doubled over the last three years. With your support KEGG will be sustainable as a most advanced, high-quality database meeting the changing needs of biological science.

Thank you again.

Minoru Kanehisa

Posted on April 1, 2014

Plea to Support KEGG

Since 1995 the KEGG database has been developed in my laboratories (Kanehisa Laboratories) at Kyoto University and the University of Tokyo thanks to funding from the Japanese Ministry of Education and its agencies. Contrary to popular perception, KEGG has never been a public database, as there has never been an official long-term commitment from any government agency. Although I have managed over the years to obtain multiple and overlapping short-term research grants to support KEGG, this has become more difficult now that I am reaching the mandatory retirement age. Foreseeing this eventuality, together with my colleagues, I started a non-profit organization, NPO Bioinformatics Japan, as a vehicle to raise funds for the service that we have been delivering.

For the last ten years our major source of funding has come from the Institute for Bioinformatics Research and Development (BIRD) of the Japan Science and Technology Agency (JST). As of April 1, 2011 BIRD has been converted to the National Bioscience Database Center (NBDC) in JST. The newly established NBDC focuses on the integration of various databases, and does not support the development of individual databases as BIRD did. The good news is that I was awarded a three-year grant from NBDC for integration of KEGG MEDICUS with disease and drug information used in practice and in society. However, the bad news is that this grant is not sufficient to continue to hire my talented crew of KEGG curators and software developers.

KEGG is now one of the most widely used biological databases in the world as indicated by the web access statistics (150 to 200 thousand unique visitors per month) and the number of KEGG paper citations (one thousand per year). I intend to ensure that KEGG remains a freely available web resource. However, this will be possible only with your support. First, I would like to ask all of you who have benefited from KEGG to write, email, tweet, and blog about your support for KEGG. I hope, in the long run, your voices will increase our chances of getting more stable funding. Second, we will continue to ask commercial organizations to obtain a license to use KEGG from Pathway Solutions Inc. I am very grateful to all the companies who have so far supported KEGG by obtaining license agreements. This licensing revenue is fully reinvested to further the development of KEGG. Unfortunately though, this is still insufficient to maintain the high-quality service that we strive to accomplish. Consequently, I would like to introduce the following mechanism.

Starting on July 1, 2011 the KEGG FTP site for academic users will be transferred from GenomeNet at Kyoto University to NPO Bioinformatics Japan, and it will be available only to paid subscribers. The publicly funded portion, the medicus directory, will continue to be freely accessible at GenomeNet. The KEGG FTP site for commercial customers managed by Pathway Solutions will remain unchanged. The new FTP site is available for free trial until the end of June.

Please register to learn more about the KEGG FTP subscription.

Thank you!

Minoru Kanehisa

Posted on May 16, 2011

Thank you for your immediate responses to this plea. I would like to emphasize that the KEGG web services, including the KEGG API, will be unaffected by the new mechanism to be introduced on July 1, 2011. Our policy for the use of the KEGG web site will remain unchanged. The only change will be to FTP access. We have already introduced a "Download KGML" link for the KGML files that used to be available only by FTP, and will continue to improve the functionality of KEGG API. I would be very grateful if you could consider obtaining a KEGG FTP subscription as your contribution to the KEGG project.


Minoru Kanehisa

Posted on May 21, 2011

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