Request for Letters of Support for Renewing the Protege project in 2016

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Request for Letters of Support for Renewing the Protege project in 2016

Tania Tudorache

Dear community,

This month, the Protégé team is very busy writing a renewal grant to ensure the continuation of the Protégé project.

We would be extremely grateful if you could join with us to help us secure the next round of funding by writing us a letter of support.

Please find all the details in the original email from Prof. Mark Musen, the PI of the Protégé project, at the end of this email, or online at:


Please send your letters to Prof. Mark Musen at the address [hidden email] by January 15, 2016.

Your letter will make an enormous difference to ensure that Protégé doesn’t go away!

Much appreciated!

The Protégé Team


Email from Prof. Mark Musen, Principal Investigator of the Protege project

Dear Colleagues,

I apologize for the cross-postings, and for the length of this e-mail, but this posting is very important. This message is about the future of the Protégé system.

As most of you know, Stanford is able to make Protégé available as a freely downloadable, supported, open-source platform only because we receive a generous grant from the United States National Institutes of Health (NIH). The NIH funding supports bug fixes and feature enhancements requested by the community. Each new release of the Protégé and WebProtégé systems is a direct result of our NIH funding.

We have received ongoing funding for the Protégé resource since 2003, and it is now time to prepare our next grant application so that we can continue to evolve the software (the rich client, WebProtégé, and a wide range of plug-ins) and to answer questions posted to our mailing lists. For those of you who have benefitted from the availability of Protégé over the years, we would be extremely grateful if you could join with us to help us secure the next round of funding so that you can continue to receive these benefits.

I am asking for something very simple: A letter of support that we can include in our grant application.

When our request for grant funding will be reviewed by the NIH, the testimonials that we receive from our user community will have a major role in determining whether we will receive future funding and, if so, whether we will be funded at the level that we request in our proposal. Letters from people who rely on Protégé technology will go a long way in ensuring uninterrupted user support and many exciting new features in the years ahead. Your letter will make an enormous difference to ensure that Protégé doesn’t go away.

It would be best if you could send me a signed letter on letterhead (either a hardcopy or, preferably, a PDF) that I can include in the grant application. Sending me plain e-mail is OK, but a letter on formal letterhead with a real signature will have maximum impact on the reviewers. Regardless of whether you send a real letter or e-mail, it would be best not to quote this message or to appear prompted in your comments; reviewers prefer testimonials that appear to spring from the heart.

Every letter should provide a brief description of the project or projects for which you are using Protégé or have used Protégé. If a project is the result of federally sponsored research, please include a reference to the agency that is funding the work and the corresponding grant or contract number, if possible. Grant numbers are particularly important to the National Institutes of Health.

Although there is no required format for your letter—and indeed it should not appear that your letter is following a specific template—it would be wonderful if you could comment on the following kinds of things:

  • How are you using Protégé? Please describe the project or projects with which you are using the system.
  • How have you benefitted from the Protégé resource? Have you or your team used our mailing lists? Have you communicated with the Protégé development group directly? Have you attended any of our short courses?
  • If the availability of an open-source product such as Protégé is important to you, you might comment on why this is the case.
  • There are now several research tools and commercial products on the market that allow users to create and edit ontologies and knowledge bases. If you believe that Protégé, its plug-ins, or the Protégé user community offer advantages that are important to you that are not associated with these other systems, you might want to comment on why you are using Protégé. Do you see a tangible advantage to the development and enhancement of a tool such as Protégé by a research group such as ours? Simply put, the government will want to know why it should continue to invest in the Protégé system and in its ongoing evolution.
  • In sum, how has the availability of the Protégé resource made a difference to you and your work?

As I have indicated, formal letters are best, but, if it is impractical to write a letter, a brief e-mail message will be greatly appreciated. Fundamentally, the continued existence of the Protégé resource depends on our ability to demonstrate the importance of our work to the community of users whom we support. Without your enthusiastic letters, NIH will not see evidence for continuing to fund us.

I know that this request imposes on your time. The entire Protégé team will be grateful for any statement of support that we can include in our grant application. One of the most exciting aspects of the Protégé project has been the ability to serve and support a user community that believes in our work and in what we are trying to do. All of us who work on the Protégé system are grateful to all of you who have contributed your support, your suggestions, and your code to the Protégé project.

Please send your letters to me at the address [hidden email] by January 15, 2016. If you know of others who might be able to help us out, then please forward this message directly to them. The more letters that we receive, the better!

Many thanks for your support and for your contributions to our user community,

Mark Musen

Principal Investigator, the Protégé project

Mark A. Musen, M.D., Ph.D. 
Professor of Medicine (Biomedical Informatics Research) 
Stanford Center for Biomedical Informatics Research 
Stanford University School of Medicine 
1265 Welch Road, Room X-215 
Stanford, CA 94305-5479 USA 
Phone: +1 (650) 725-3390 
Fax: +1 (650) 725-7944 

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