Historical Record of Discussion on Transition to Subscriptions

2009-10-16 21:12:58.0

Dr. Abdullah Makhzoum, This is very useful database for Arabidopsis genome information and it will be damaged to reduce its activities. Basically, it must be improved with new features like genome regulators or differential gene expression.

Hongxia Zhang

2009-10-16 21:43:17.0

We think taht TAIR is the most important public database for our Arabidopsis researchers all over the world. We benefited a lot from the information TAIR provides and are greatly indebted to the contributions that TAIR make to the whole plant molecular biology, in general and Arabidopsis studies, in particular. In my opinion, the funds from NSF program to TAIR should be augmented but not reduced, because it is so important for all researchers and TAIR has been developing very rapidly during past years. If more supports are given to TAIR, it will play increasingly essential role in plant and crop sciences and potentially return the favor to the whole society.

2009-10-17 18:39:28.0

TAIR is providing plenty of information here and it is not wise to reduce its funds. NSF should continue to fund TAIR to preserve and improve its activities.

2009-10-17 19:29:13.0

I don't think it's a wise manner to cut the support of TAIR.

2009-10-18 00:00:53.0

TAIR is very important database for plant research!!! the funds from NSF should NOT be cutted!! I think TAIR deserves more supports not only from NSF but also from other funding agency!! I am fully convinced that TAIR will and should play more important role in biology science!!!

2009-10-19 01:12:43.0

TAIR is useful for the community and there are no other resources that can replace it.

2009-10-19 01:20:15.0

TAIR is very important and essential data source not only for Arabidopsis researchers but also for other plant scientists especially for crop scientists all over the world. I think compared with other database related to plant TAIR is the best organized database. If NSF reduce the funding for TAIR, the basic research associated with plant growth and development will be drastically impaired. In the genome and proteomic era, TAIR should be granted more by NSF rather than less.

Eva Huala

2009-10-19 09:12:24.0

Thanks for the great comments so far! I would love to hear something about what kind of research problem you're working on and how you're using TAIR data for your work. Are you applying TAIR data to research on another plant? If you're an educator or student, please comment on what role TAIR data plays in your teaching or learning.

2009-10-19 12:26:28.0

Despite emergence of new model plants, Arabidopsis still effectively serves as a tool for plant biology study. TAIRS has fulfilled this purpose and long been an extremely useful database for the Arabidopsis community world-wide. This decrease of funding for the organization, I believe, will affect not only Arabidopsis research but also the study of plant biology as a whole.

Ernest Retzel

2009-10-19 12:35:00.0

I was stunned to hear that NSF is considering pressing TAIR into an alternative funding model. While grant periods are familiar to all of us, the criticality of TAIR to the plant community has and will continue to warrant the support at a national level at the highest level possible. Whatever the dataset (sequence, map, expression, metabolite, etc), TAIR has set the highest standards in annotation, biocuration and availability. In my own current work, we are exploring Arabidopsis meiosis, and rely heavily on the detailed annotations within TAIR to indicate whether were have discovered new genes and/or new exons being expressed as part of the meiotic process. The accuracy of the known genes and predicted models are critical to us. Only a researcher who has ?skin in the game? will provide us with the gold standard annotations that are available to us in TAIR. For all the desire of agencies to find sustainable models other than direct grants to database groups, it is clear that no privately funded database has, to my knowledge, been successful in maintaining itself. It is hard to imagine that such a private funding model would allow for the continued growth of the database. TAIR is an integral part of the community. Actually, it is beyond integral ? it is the fulcrum on which so much of the plant community depends to leverage the relatively small amounts of money available, particularly in crop science. I foresee no positive consequences from a decision to force TAIR to become the collector of little fees from users and to enforce policies imposed on it. It will build a divide between well-funded laboratories and the more moderately funded (or those unfunded at all ? beginning investigators, or those who work on orphan species). If some sliding scale is made for all contingencies, TAIR will have to have an accounting and ?awards? staff to track who pays for what, and when, rather than what new tools can be built for researchers. For all the outreach activities that have been constructed around TAIR and its connected resources (e.g., ABRC), there is likely to be a crashing gate that closes between the hopeful teachers and students and the researchers who have worked hard to provide these resources. And, while the mandate of the agencies to keep us focused on utilizing and contributing to significant resources such as TAIR, there will now be every excuse to build small, non-standard, un-connected databases external to TAIR. As we move toward a research publishing model in our academic work that is focused on open access and free availability of research publications in the face of stiff opposition from the for-profit journals, it seems that we are taking a retrograde step to be asking our most successful public model organism database to begin a path of closed access and user fees. I will repeat: I am unaware of any long-term successful fee-for-service database. We cannot afford to allow TAIR to even falter for a moment. It is too critical to the plant community. TAIR has become the model of a cost-effective, well-run, forward thinking community database. In this case, the community extends far beyond Arabidopsis to every model and crop plant being explored. There is no crop species database that does not have significant numbers of instances saying ?Similar to Arabidopsis ?? If there needs to be some solution other than the normal competitive granting competition, I would say that it is to tithe every Plant Biology Program, and turn that money over to TAIR to maintain its free availability. There is not a genomics project that doesn?t, at some point, rely on the data, biocuration and professionalism of TAIR.

2009-10-19 14:17:58.0

I think TAIR is a tremendous resource! Perhaps though some of its funding should come from advertisements and donations. Losing NSF funding shouldn't be the end. --Marcelo Grad Student OSU

2009-10-19 14:20:44.0

TAIR has been a great resource to all Arabidopsis researchers in past several years. Without TAIR Arabidopsis research would not have progressed so quickly. TAIR is not only beneficial to the Arabidopsis community but also to researchers working on other model plants. Researcher working on other model plants routinely use TAIR as a resource for comparative analysis. An updated and evolving TAIR database is absolutely essential for plant science to move forward.

2009-10-19 15:48:45.0

TAIR is very helpful source for plant researchers all over the world. It is also the base of plant science resarch.

2009-10-19 19:55:45.0

Without TAIR plant scientist don't have the ability to have the overview on a comprehensible, smartly designed website where you can look up gene information at any time. I really hope TAIR can continue with its leading position as a plant genetics database in the future.

2009-10-19 20:10:35.0

TAIR is so important to the scientific world and I hope the US goverment can help its maintenance and development.

2009-10-20 02:35:47.0

Yes, We need TAIR!

2009-10-20 03:53:22.0

TAIR is very important for plant biology research!!

Arjun Krishnan

2009-10-20 05:47:00.0

TAIR is *the* resource for plant scientists like me involved in both experimental and computational work. Searching/viewing existing data has been so easy, and data presentation and integration/linking-out with external databases is remarkable. For my computational needs, data is up-to-date, very well organized and documented, and formatted for easy use. It is extremely easy to find the file you want within TAIR. The other *the most* important positive about TAIR is its curator-team. They are very involved in this work, are very quick to respond to a question, do not mind going back-and-forth on an issue, and are most willing to cater to very personalized requests (ftp://ftp.arabidopsis.org/home/tair/User_Requests /). Rarely does a day go by when I don't use TAIR. It is a clear model for web resource for other plants. I strongly support continued funding for TAIR to keep up its great work.

2009-10-20 07:22:12.0

No plant biology without TAIR!

2009-10-20 07:44:52.0

I don't see how a subscription service will be a successful long term model for TAIR and the plant community. TAIR will be limited to those arabidopsis researchers who use it on a regular basis, while crop scientists and teachers + students may not be able to justify a fee (even though TAIR is important to there work). A move away from grant funding seems to me to be a negative for transferring the knowledge gained in arabidopsis to other species. It will be interesting to hear other views from the community but I see only negative in a subscription approach.

2009-10-20 15:41:00.0

There are so many databases are available for various plants, crops but nothing is even close to TAIR. We all plant scientists are not only dependent on TAIR's computational resources but also dependent on experimental material. In my opinion, TAIR should be funded in a permanent manner so that all the data, and experimental material can be maintained by its permanent staff members. If my request can help, I request all the concerned authorities for financial support to TAIR as it is important, essential, carry accurate and reliable information, and very unique as there is no other TAIR in the world so please support.

2009-10-20 18:00:12.0

TAIR is critical to plant biology research. Please support this resource.

2009-10-21 05:21:04.0

Dont tear TAIR down!!!!!!

2009-10-21 05:27:54.0

Still much needs to be done using model plants. TAIR is very useful and imp. tool for model plant arabidopsis. So, pl. cont to fund TAIR..!! Thanks

2009-10-21 08:53:43.0

TAIR is an essential resource for the entire plant research community. For every year that TAIR has been in existence, it has consistently set the bar for plant genome annotation and data curation while ensuring that these data are readily and freely available to the global plant research community. My work in genome evolution and dynamics spans all available plant genomes, and no other plant genome comes close to the depth and quality of information available as those for arabidopsis. I frequently refer to arabidopsis gene models and annotations to better inform orthologies in other plant genomes, and often come across annotation mistakes in these other plant genomes. I believe that TAIR's mission of continuing to provide the entire research community with the highest quality plant genome information is essential, and this resource needs to be funded directly as a publicly available resource. I strongly believe that alternative funding models such as pay-for-access will ultimately be the demise of TAIR. Since most users of TAIR are academic researchers, such a funding model change does not reduce the public's cost of supporting TAIR. Instead, this shifts the costs from a direct grant to TAIR to dispersed costs in many other grants. This presents two significant ways our limited time and funding resources are wasted. First, this increases the number of bureaucratic steps taken by many individual researchers to ensure their grants have additional funding for access to TAIR, and the additional time needed by TAIR to process and charge for access to its data. Second, this presents a signifiant impediment to researchers without a grant who need to use TAIR's data for the first stages of their grant writing process. In addition, TAIR's ability to provide continual improvement to its data depends upon an inherent collaboration with the research community at large. Individual researchers provide TAIR with their data in order to improve and refine TAIR's data, which in turn feedback to the community. If these researchers do not have free access to TAIR, the flow of data from the community into this shared resource will significantly ebb. Over time, this too will cause the death of TAIR. Of the many science-driven online resources available, TAIR is one of the best. NSF's tag-line, "Where Discoveries Begin", could not be a more appropriate description of TAIR. NSF must continue its support for TAIR. Eric Lyons, Postdoc Department of Plant and Microbial Biology, UC Berkeley http://syntney.cnr.berkeley.edu/CoGe

2009-10-21 09:02:48.0

TAIR is one of the best databases in plant science research. Without TAIR it is very difficult to contribute something to society in the form of food/medicine/fuel etc?It is time for us to think of improving the exciting database with robots computer applications to help all the researchers throughout the world including developing countries. It is unfortunate TAIR funding is shrinking! I strongly support funding TAIR to continue its tremendous work. Thanks TAIR keepup! Sanjay, MSU

2009-10-21 09:28:05.0

I work both computationally and in the lab and make heavy use of TAIR for both. With the escalating power and reducing costs of high throughput methods, resources like TAIR will become even more important in the future, not less so; to reduce its funding would be bonkers. There is it seems a growing interest in data storage and sharing methods, and perhaps TAIR may attract more funding by participating as a benchmark to the wider audience? There is talk of having journals enforce data sharing as a requisite to publication, perhaps TAIR might play a role in that and gain its finding that way?

2009-10-21 12:00:39.0

I am a project manager at UC Berkeley overseeing NSF-funded research in comparative genomics within the genus Arabidopsis. TAIR has been an essential part of my work, as I rely heavily on this site to keep me up to date on the most recent annotations in thaliana. I consider TAIR one of the best databases for plant research, and it must be continued to be funded. Margaret Woodhouse, UCB

Erin Osborne

2009-10-21 13:03:53.0

I am shocked to hear of this unfortunate situation. Though I work in the field of yeast biology, I use TAIR on a regular basis and find its easy to navigate pages and succinct information very useful. For me, it is an efficient way to keep up to date on the histone modification enzymes in the Arabidopsis model system. In short, Arabidopsis is a gorgeous model system, and as such it impacts many fields outside of the plant world.

2009-10-21 13:11:21.0

TAIR is the most cruicial resource for plant research. I am a graduate student at UC Berkeley. I am using TAIR routinely and for many aspects of my thesis project.

Shai Lawit

2009-10-21 13:33:50.0

I am a PI at Pioneer Hi-Bred a DuPont Business. I perform discovery research using Arabidopsis as a model system. TAIR is a critical resource to my research program and, I am sure, to many others in my company and other plant biotech companies. TAIR has been critical tool in every project and stage of my scientific development; from grad student to post-doc to PI. The TAIR resource is invaluable not only to those of us using Arabidopsis, but as a annotation and comparative tool to anyone in plant biology. I highly support sponsorship for TAIR from any and all source.

2009-10-21 13:57:32.0

TAIR is an invaluable resource for any Arabidopsis and plant researcher or student!

Stacey Harmer

2009-10-21 14:17:37.0

TAIR is essential to the research being carried out in my lab. Given the large investment NSF has made in genome-enabled research (both in Arabidopsis and in other species) I am puzzled as to why the need for a long-term, stable archive of such genome data is not immediately obvious. Although a subscription-based model for funding may initially seem appealing to NSF, this would curtail the ability of smaller plant labs and non-plant labs to use the wonderful tools and data available at TAIR. It would also discourage data sharing between TAIR and other databases. As one of the explicit goals of the NSF-funded cyberinitiative iPlant is to improve data access, it would be ironic if NSF were to reduce funding to TAIR and in the process raise barriers between datasets. I strongly believe that NSF should provide stable, long-term funding for TAIR. TAIR is so central to NSF's other investments in plant biology that it would be illogical to do otherwise.

2009-10-21 14:24:35.0

TAIR is very important for plant research. We have constantly order seeds from TAIR and the service was fast. It did helped our research a lot.

2009-10-21 14:25:38.0

TAIR is a critical tool for my research work. From gene finding to gene models and T-DNA mutant searches, TAIR has become a big part of the day to day work in any plant molecular biology lab. It is user friendly, regularly updated and well maintained. A great tool to work with! Decreasing funding for TAIR are very sad news to all plant field research. It would be good to know whether there is some way plant scientists could organize and send their views to NSF.

Brad Day

2009-10-21 14:39:43.0

TAIR has enabled me, as a new investigator, to pursue avenues of research and experimentation that would otherwise be cost prohibitive or too timely in which to invest. The availability of, and access to, a broad range of resources has streamlined the basis for hypothesis-driven research, and more importantly, positioned TAIR as a foundation for so many in the community. As a central forum, TAIR's mission has always been the dissemination of information and resources to the community. Without resources like TAIR, I fear the pace of plant science research would take a step back, slowing the advance of new ideas and technology.

Daphne Autran

2009-10-21 14:47:53.0

Every day we are using the ressources, tools, informations available at TAIR. This is a tool exceedingly interesting to speed up research in Arabidopsis and for comparative projects with crop species. To maintain and expand the TAIR project is critical for the future of both basic and applied research in plants.

2009-10-21 14:52:14.0

TAIR is an amazing resource and is crucial for plant biology research. I have used TAIR for many years and would be very frustrated without it. It not only successfully provides user-friendly information, tools and resources but it also serves as a model for how genome-based data should be available for any organism. One of the best features of TAIR is that anyone can access it from anywhere; if TAIR were to become subscription based it would negatively impact how TAIR is utilized. Ideally TAIR would have funding to not only keep operating as is but to also continue to grow and develop new tools, etc. (as it has done in the past).

Abraham Koo

2009-10-21 15:53:31.0

My research starts with TAIR. It served as invaluable tool for my research in the past and will no doubt be in the future. While there are other similar databases, TAIR is the launch pad that I use to navigate other resources because it has everything. TAIR has served a vital role to the majority of Arabidopsis community. It is one of the most successful and high impact resulting investment by NSF that had direct influence on my research. Funding for TAIR should be continued if not increased.

2009-10-21 17:26:09.0

I am a graduate student at Duke University and I use TAIR everyday. The investment in TAIR pays off in increased productivity.

2009-10-21 17:50:07.0

Without Tair, the research on the model plant Arabidopsis will not be so quick. The whole research on plant science has benefited from it. If the platform was reduced, the database and material resources will be not as good as now and the plant sicence research will be retarded.

2009-10-21 17:53:47.0

TAIR is an invaluable resource for the entire Arabidopsis community, and it is a model for cooperative effort and dissemination of knowledge and strains. I use seed from enhancer trap lines from TAIR to introduce plant development to large numbers of undergraduate students in our introductory lab course. I know from experience that asking individual investigators for materials can spotty at best (most never reply to an inquiry). TAIR is a model of models and I hope that sources of support can be identified to allow this critical resource to continue.

2009-10-21 18:55:13.0

I thought we had progressed beyond the Reagan era where public services had to be privatized because the market is more efficient. But beyond the ad homenim, although I only use the seed stock resources, they change everything about what kind of educational experiences I can offer undergraduates. The ease of use and reasonable charges mean I can have students working with the materials they read about in text books and get them to do some real science. Most won't become scientists but they will become something far more important: educated citizens.

2009-10-21 19:05:42.0

I am an undergraduate from China. I and my lab collegues are using TAIR almost everyday in our research. It is an invaluable resource indeed. The funding for it should be guaranteed and it will sure pay off.

2009-10-21 19:29:55.0

TAIR is invaluable to the Arabidopsis community. I use the TAIR website for my research on a daily basis and TAIR is a vital asset for Arabidopsis research. Funding to TAIR needs to be increased, not cut!

2009-10-21 20:37:50.0

TAIR is very important for plant biology communities, the funding to TAIR should not be decreased.

Pierre Hilson

2009-10-21 21:26:07.0

In the past years, NSF has been a staunch advocate of public and free access to scientific results. The fact that in certain programs NSF funding requires the release of materials and data to resource centers such as TAIR has been a remarkable asset and an invaluable boost to research progress in the Arabidopsis community and beyond. In fact, NSF?s visionary position has been an example for other funding bodies, including at the European level, that now have similar policies. Of course, this excellent policy can only be enacted if top notch resource centers such as TAIR are sufficiently supported. Life sciences increasingly requires the integration of data from transcript, metabolite and protein profiles with information about phenotypic variation and allelic diversity. These efforts would be significantly hampered without the immediate and seamless access to the information provided by TAIR. TAIR is a partner of choice in disseminating the results of our efforts. While there are indeed multiple on line sources for data and information about Arabidopsis, TAIR has grown over the years to be the unrivaled and necessary reference to all of them. It is the cement that keeps the international information structure together. While NSF is investing significantly in forging the next generation of tools for integrative plant biology via iPlant, it would be nonsensical to abruptly end TAIR?s funding. Why build a roof and sap the foundation at the same time?

2009-10-21 21:52:36.0

NSF should just see these comments and come to the their senses. We, at small research institutions, are maintaining small research labs, only because of this rich resources available to us with a minimum cost.

2009-10-21 21:56:56.0

While my principal research efforts are on crop plants, I occasionally have students who pursue projects in Arabidopsis. I often find myself jealous at the ease with which they can obtain mutants or genome information from TAIR. This is clearly a resource that is critical to the future of plant biology research and rather than seeing such a resource shrink from lack of funding, I would like to see it enlarged to encompass other model species, like Brachypodium.

Josh Mylne

2009-10-21 22:11:21.0

As the central repository for data on Arabidopsis I consider the TAIR site essential for my research in Arabidopsis. The Arabidopsis data and biological resources are of great use to work I also do in sunflower. We recently annotated an EST pilot project in a non-model plant using the annotations of Arabidopsis genes we downloaded from TAIR. TAIR is essential to a wide range of biological research ranging from development of new crops to increasing our understanding of fundamental biological and evolutionary processes in plants and other organisms.

2009-10-21 23:24:04.0

catherine Bergounioux Oct 29, 2009 . I used TAIR every days. TAIR is the tool required by all the scientific community to search and to spread information.

Richard Cooke

2009-10-21 23:48:23.0

We have been using TAIR (and its predecessors) since the beginning of Arabidopsis genomics. We teach TAIR, we cite TAIR as a unique example of what can be done when all available information on a model organism is collected and presented in an integrated form, and we use TAIR almost every day, both for bioinformatic analyses or in the framework of our wet-lab biology. Invaluable.

2009-10-22 00:14:57.0

The Arabidopsis research community is able to share information and resources through the efforts of TAIR in a way that that is the envy of other research communities. The TAIR encourages a sharing culture that allows the advancement of scientific knowledge by all users, no matter where they are in the world. The access to data and resources is crucial to understanding biological processes not only in Arabidopsis, but also non-model plants. The work of teh TAIR is vital to the Plant Science Community and deserves financial support to keep it functioning as well as it does.

2009-10-22 00:17:25.0

TAIR is the resource most widely used by the Arabidopsis Research community. Killing TAIR just means killing plant research.

2009-10-22 00:21:42.0

TAIR is simply indispensible for the plant community. Most users should be willing to pay a subscription fee.

2009-10-22 00:34:12.0

TAIR is the perfect website for researchers that work on Arabidopsis as it gathers all the available data on this model organism. As a PHD student, I use it on a daily basis and it is a very useful and time saving device. I'll make sure to acknowledge it in my future works.

2009-10-22 00:44:50.0

TAIR is a fundamental tool to explore the wealth of gene/protein/metabolite information available and makes efficient research work possible. That way ideas develop, knowledge is gained, benefit arises and costs are saved. If there is a need for plant research in the future to ensure sufficient and sustainable crop production bioinformatic means like TAIR are indispensable for the scientific community. Steffen Rietz, Germany

2009-10-22 00:51:07.0

user TSAGRIS EFTHIMIA MINA UNIVERSITY OF CRETE TAIR IS A VERY USEFUL DATABASE FOR ALL PLANT SCIENTISTS IN RESEARCH AND EDUCATION. IT SHOULD BE FUNDED BY INTERNATIONAL ORGANIZATIONS THROUGH GRANTS, BY (NOT TOO HIGH) FEE FROM ACADEMIC INSTITUTIONS, BY GRANT APPLICATIONS (COOPERATION BETWEEN NATIONAL AUTHORITIES) AND BY GRANTS FROM THE INDUSTRY

Marc Knight

2009-10-22 00:53:30.0

In my opinion, it is unimaginable that TAIR finds itself in a position to reduce its activities, in the face of its immense success and contribution to moving forwards plant science research. This comes, ironically, at a time when food security is a major global issue, which is not going to go away, and will get worse. I would urge those controlling funding of TAIR to consider its contribution to date, and extrapolate the vital role it will play in the future. In a field of reseach so important to a basic human need: food, it seems incredible that the tools and resources available to practictioners in this area should become reduced and more meagre as the challenge is increasing exponentially!

Miguel Botella

2009-10-22 01:06:56.0

I cannot believe the mail I have received indicating that TAIR funding in a problem. This database is not only essential for the Arabidopsis community but for all people working on plant science. EVERYONE goes to TAIR to ask for fundamental questions, even if you are working in crop species. I use TAIR everyday, and have requested so many resources that is unimaginable that TAIR is getting into funding troubles. If there is anything else I could do, in addition to write this letter I am willing to do it. I also agree that if needed a subscription fee for keeping the database not only running but improving you can count on me. However I think that this must be funded generously by public grants. I also think that TAIR must be acknowledge in the Ms that uses TAIR resources and then those people responsible for the grants would be aware how important is for the plant community.

2009-10-22 01:07:34.0

I can not do plant science without TAIR database. It's vital to have TAIR running at full capacity and more, to help TAIR improving. Elena

Jose Feijo

2009-10-22 01:48:05.0

TAIR became a fundamental tool for virtually every plant biologist doing any sort of genetic analysis, and a useful resource for the whole community. The level of service has been great, and the amount of publications out relying heavily on the reliability and updated annotation of TAIR is enormous. NSF has a (very good) tradition of keeping up with centers that provide such kind of services for the community for decades, as long as they continue to prove useful, and it's hard to understand how a resource like this which is a pillar for a whole community, does not qualify as such. I ignore the numbers involved, or if NSF plans for an alternative, but I strongly plea that whatever is the case a service like the one TAIR has been providing may continue to be available for the plant biology community, there is just too many things which dependent on their services.

2009-10-22 01:49:56.0

Without TAIR, the work that I do would not be possible. Systems biology - which is currently a field receiving priority funding from NSF, BBSCR and numerous other funding bodies - requires the bioinformatics tools that TAIR provides.

2009-10-22 02:07:43.0

TAIR is the most central node among plant databases, and many take their information from it. Such a database, and further development of it, is instrumental for progress in plant biology. This is needed for crop and energy plant development to cover the demands for increased food and renewable energy production in a climate becoming more hostile to production in many agricultural areas.

2009-10-22 02:12:42.0

TAIR has been the best resource I have used for researching data on candidates derived from proteomics. It is the best starting point for obtaining information regarding a wide range of general characteristics for a gene. The loss of funding over time will have a severe impact on the hability of the database to update itself which is imperative for a resource of this magnitude to continue being the best for the plant biologist community. So many aspects of research depend solely on this service that its loss could deal a decisive blow in plant research accross the world.

Michel Schneider

2009-10-22 02:19:04.0

The annotation of Arabidopsis thaliana proteins in the UniProt Knowledge Base (UniProtKB) draws heavily on information derived from TAIR. TAIR is the only resource which maintains and curates a complete set of all predicted Arabidopsis genes. The high quality annotation of protein coding sequences performed by TAIR is an absolute prerequisite for accurate functional annotation at UniProtKB. We maintain active and fruitful collaborations with TAIR and the responsiveness of TAIR curators is of major benefit to our own annotation efforts. Free access to TAIR is essential to our annotation process and the proposed closure of TAIR will have extremely negative consequences for our own plant protein annotation program. Michel Schneider, UniProtKB/Swiss-Prot program leader, Switzerland

Miriam Gifford

2009-10-22 02:28:49.0

TAIR is critical for plant biology across the world-wide community. One of our strengths as a community is our openness and willingness to share data and resources. TAIR is a critical facilitator of this. And as new bioinformatic resources are developed and vast amounts of novel and important data is generated (e.g. from proteome-interaction mapping and next-gen sequencing of thousands of Arabidopsis ecotypes) we need this a central node to be a funded service to curate, collate and distribute this information and to develop new tools with which to apply the data in our research. As food security becomes an even bigger priority to address, the need for TAIR is paramount.

2009-10-22 02:37:15.0

I just cannot think of any scientific research at the advance molecular level without the TAIR's critical presence. It is most definitely indispensable world-wide.

2009-10-22 02:41:09.0

TAIR is the first place to look for so many tools esential for the modern plant biologist. I access the various bioinformatics tools available here most weeks. My research colleagues working with Arabidopsis and other model plant species are similarly regular users. Should this resource be cut, how would the plant research community continue its work? A decision to end its funding could only be made by those who have no appreciation of the value of biological sciences research to our global environment and society. Dr Mags Pullen, University of Durham, UK

2009-10-22 02:48:16.0

It is astonishing that anyone would even consider cutting funding to TAIR. It is the best database of its kind in plant science and as such is essential to plant science research. If anything it needs more finding to improve the site and informartion available (gene/protein interactions information would be good) as it currently lags behind similar databases from other fields including the S. cerevisiae yeastgenome.org. With food security increasingly becoming a problem, reducing funding for a resource so essential for plant science would be a shockingly irresponsible decision.

2009-10-22 03:29:26.0

My research - no matter what plant species - has always centered around the TAIR databases. TAIR is so essential for my work i find it hard to image how large the detrimental impact of cutting funding would be. I am convinced the plant community as a whole requires and depends on TAIR. Henrik Buschmann UK / Germany

2009-10-22 03:44:13.0

I'm a post-doc and I have NEVER worked on a project that DID NOT use TAIR. If the information in TAIR had not been freely available, most of my time and effort of the course of years would have been spent obtaining the information that otherwise was accessed in a question of minutes via TAIR, for even things as simple as primer or marker design (which requires access to well annotated genome sequence and polymorphism information), just to pick a small example. TAIR's role in facilitating research and making funding use most efficient (by avoiding the same things having to be generated over and over again by each lab in the relevant but never to be shared subsets) CAN NOT be underestimated. It is unimaginable what a ridiculous waste of everyone's time and money it would be to have to generate this kind of data on an individual lab basis for each project, and in fact would impossibile for many, and render many projects unviable. Furthermore, subscriptions would penalise small labs and occasional users, and even more so non-plant labs (and hence valuable collaborations and cross-disciplinary work), unless they were really very cheap - like the cost of personal membership to a society like SEB or the Genetics society, rather than a level comparable to the exorbitant cost of, let's say a journal subscription. To finish: this is an essential plant science resource. It is imperative that it has every support to remain accessible to the research community.

2009-10-22 03:57:20.0

The information provided and shared via TAIR is essential for fast and efficient progress in plant biology, which is absolutely necessary to cope with the demands for food and feed of a growing world population. Everyone, including members of governments, who is responsible for funding of research can be aware of this fact. It is a shame that such an important knowledge database will be limited in future by funding, but I have no doubt that funding will be reduced.

2009-10-22 04:02:49.0

I use TAIR on a daily basis and is invaluable to my research, not just as a data repository but also as an integrated set of tools tailored to fundamental plant biology. The curating and data integration availiable through TAIR far surpasses any other database for any species and has removed many of the obstructions to science be it secrecy of just knowing where to find a certain type of data. TAIR is a fantastic example of what open science can achieve with data contributions from all over the world on all aspects of plant science. If anything TAIR needs more funding to allow it to add much of the data becoming availiable from modelling, -omics experiments, epigenetics and maybe even related species to aid in evo/devo work. Integration with data from crop species would also aid in crossover work. Ending or reducing TAIR funding would put many reserachers in the dark and significantly reduce the efficiency of plant science. Given the isuues surrounding food security and climate change it seems very short sighted to cut funding for a keystone of fundamental plant science. A small fee for access would probably be within budget for most users but I feel the scope of TAIR goes beyond what could be achived through subscription. I also feel uncomfortable with the idea of TAIR becoming subject to market forces and all of the issues that it would entail.

2009-10-22 04:03:39.0

TAIR is an indispensable resource which needs to be mainitained to its current high standards

Franziska Turck

2009-10-22 04:33:26.0

The TAIR site is the "homepage" of many scientists working with Arabidopsis and one of the reasons why this model organism had such a success story. Now an enormous amount of data coming from next generation sequencing approaches will have to be integrated and presented to the community - impossible to cut funding now when the team behind TAIR should actually be empowered to meet the new challenges. If NSF is too poor, ask for more participation from European or Asian funding bodies. We all profit enormously from TAIR.

Michael Nodine

2009-10-22 05:11:05.0

TAIR is a central depository that provides high quality annotations for the premier plant model system Arabidopsis thaliana. I use this resource on a daily basis to design wet-lab experiments and to download genomic data. If TAIR funding is significantly decreased, then this will have a negative impact on basic plant research and ultimately impede our ability to make research advances in agriculture and medicine.

2009-10-22 05:41:07.0

TAIR is instrumental and absolutely crucial for Plant Biology. The quality of plant research in general will decrease significantly without a resource like TAIR

2009-10-22 05:59:41.0

Amanda

2009-10-22 06:00:19.0

Amanda Benson Oct 22,2009

2009-10-22 06:07:44.0

TAIR is an essential teaching tool for for undergraduate education in Plant Biology. I have used the ecotype lines to design several undergraduate labs. And I would urge NSF to increase their commitment to TAIR.

Greg Lampard

2009-10-22 06:09:22.0

As a professor at a primarily undergradute university, the continued funding of TAIR is extremely important both for my research and for my undergradute education programs. TAIR has an extremely well organized collection of biological data and I feel that limited funding would significantly diminish the impact that it has on all plant biologists.

Claire Grierson

2009-10-22 07:09:10.0

I am deeply concerned to hear about the forthcoming decreases in TAIR funding. TAIR is a fantastic resource that supports a huge proportion of, if not all, international plant science. Whilst it is clear that increasing amounts of future research will involve plant species other than Arabidopsis, it would be a serious mistake to think that this will reduce the importance of TAIR. If anything the coming acceleration in the genome analysis of other species will increase the importance of TAIR as an integrated and accessible source of existing data on Arabidopsis - data that can be used to greatly inform studies in other species. Plant science has never been more important (see yesterday's report from the Royal Society, UK, and the mid-October report from the Food and Agriculture Organisation of the United Nations). TAIR and the Arabidopsis stock centres have underpinned the phenomenal success of plant science over the last twenty years. A sensible move to the future would retain these as a strong core whilst building new resources on other species around them. To allow TAIR to fall out of date would be a criminal waste of an invaluable and hard-earnt resource.

Helen Tai

2009-10-22 07:15:45.0

I am a potato genomics researcher, who has used TAIR regularly. TAIR has made important contributions to my research program and to many other crop genomics efforts. The need for TAIR will grow as more plant genomes become sequenced. Governments and funding agencies need to recognize that TAIR is not just a tool for scientists but that it plays an integral part in developing agriculture and forestry innovations that contribute to the economy, environment and human health. Maintaining funding for resources like TAIR can often be faced with challenges, even with the track record of success that TAIR has had. Public funding is not always the most steady stream of resources as changes in government policy that sometimes occur almost overnight can impact long-term projects like TAIR. TAIR has a large user base that reaches researchers around the world and may be an attractive site for advertising. Unless a successful campaign can be mounted to convince public funding agencies to maintain funding for TAIR, alternatives such as generating advertising revenue may have to be considered. The most important aspects of TAIR to maintain are its free access and its freedom to operate. The power of TAIR is in its wide variety of resources, ease of use and the large number of users. User fees will compromise access for smaller labs that are not directly working on Arabidopsis thaliana and will not be able to justify paying TAIR fees. TAIR has enabled small labs to make large impacts on plant science to the benefit of the whole community.

2009-10-22 07:50:24.0

TAIR is instrumental for my reseach in Plant Biology. I hope the EU system can help (join Nasc and Tair)

2009-10-22 08:29:53.0

TAIR is a critical resource for plant researchers in Canada and the US and abroad and it would be a disaster if this resource lost its funding. Funding MUST be maintained at all costs. Every single person in my lab uses this resource every single day (multiple times), to check out gene info, for cloning and primer design, for bioinformatics, to learn about mutant phenotypes, to order seeds, to find contact information, etc. The only other resources that we use to the same extent are PubMed and Google. I firmly believe that this resource should remain open-access but if I need to contribute to its upkeep I certainly will because my research and the research of everyone else in the Plant Biology teaching and research communities would suffer greatly without it. All sources of funding should be considered: public, government, advertising revenue, donations, subscriptions, merging with NASC, anything to keep it open-access.

Magdalen Lindeberg

2009-10-22 08:33:31.0

Many millions of dollars have been spent on Arabidopsis research and for a relatively small sum, TAIR leverages the massive amounts of data into a widely and easily accessible form. For example, I maintain a genome resources database for Pseudomonas syringae, a model bacterial pathogen of Arabidopsis, and as part of modeling host pathogen interactions I rely extensively on hyperlinks to TAIR. Were these hyperlinks to be available only to registered users, the usability of my interacting database would be substantially diminished. I have also put substantial effort into the design of lessons on plant-pathogen interactions for middle school and high school students, in accordance with NSF priorities. Databases such as TAIR are invaluable as teaching tools but clearly public schools (as well as many undergraduate institutions) will not have the financial resources to pay for access.

2009-10-22 08:37:23.0

TAIR is the first place I look for new/definitive information on Arabidopsis. It has been invauable to my research. It provides a fantastic resource for thousands of labs worldwide. This includes those working on other plants and, I daresay, non-plant organisms. The cost benefit ratio is tiny; that is to say the help it gives to the whole community far outweighs what is required to maintain it. NSF should fund it, as should other national and international fundng agencies. Sam Zeeman 22 October 2009

2009-10-22 09:01:37.0

As a PhD student I would be lost without TAIR. It is an essential resource for my day to day work in the lab and an instant, easy to use reference for all things Arabidopsis. I wouldn't know what to do without it and my research would certainly be a lot slower and more difficult.

2009-10-22 10:10:52.0

I've been using TAIR since its inception while I was a graduate student, now it is an integral part of every project in my own lab. It is used daily by my lab personnel and myself, and is the first place to look for information on pretty much anything related to doing molecular genetics in Arabidopsis. It is an incredible resource to the community and I use it in my courses (Molecular & Cell Biology Laboratory, Genetics) as an example of a one-stop resource database. I don't know what I would do without it - probably spend a lot time "re-inventing the wheel". TAIR should be publicly funded, as many researchers with smaller, less well-funded labs would do be able to afford a subscription, or perhaps even have access to well-stocked libraries or access to other databases to look up the information without TAIR. T Western, McGill University, Canada

David Meinke

2009-10-22 11:54:10.0

I am one of the individuals who submitted a letter to the TAIR advisory board in strong support of TAIR before a final decision on renewed NSF funding was made. I attach that letter here: I am writing to express my concern about the future of TAIR. I have learned that TAIR funding will expire August 31 and that a renewal proposal is currently under consideration at NSF. I have also heard that questions are being raised about the need for NSF to provide long-term support for TAIR, with talk of moving instead to a model of self-support through paid subscriptions. I find this both alarming and disheartening. I have devoted my entire scientific career to promoting the use of Arabidopsis as a model system. I have also served NSF in multiple capacities over the years. I was a member of the original review team that urged NSF to support the TAIR project, I served as an early member of the TAIR executive committee, and I worked for a year as the program director for the NSF Plant Genome Program. I use TAIR on a regular basis for both teaching and research, and I have the greatest respect and admiration for the curators and database experts who provide TAIR as a service free of charge to members of the Arabidopsis community and beyond. What a cruel irony that questions about NSF support for TAIR should be raised at this point in time, when NSF has just received a significant infusion of new funds to support a wide range of programs and when the value of Arabidopsis for research and education in modern biology is finally being realized. Years ago, NSF made a commitment to increase support for basic research in plant biology. The benefits can be found in just about every major discipline of biology. In addition to funding individual research projects, that commitment brought certain responsibilities with respect to maintaining both a central database and a biological resource center to ensure that investments in basic research were not wasted. I am very concerned that a move by NSF to abandon its commitment to support either of these critical facilities for the long term would have a chilling effect on current and future research efforts in plant biology and on the training of new scientists at all levels. I realize that NSF is constantly faced with making difficult decisions about funding priorities. But I am convinced that abandoning support for TAIR, despite an outstanding track record and incredible community-wide utilization and appreciation, would send a clear message to the scientific community that NSF has moved away from its commitment to play a unique role in supporting basic research in plant biology. And that, in my opinion, would be a big mistake. I cannot image a system that would require a subscription fee to access the TAIR database. Here are just a few problems that come to mind: 1. How can I encourage public school teachers to make use of TAIR when they have difficulty paying for just about anything these days? 2. How can we encourage people to continue working on Arabidopsis, the premier model system for research in plant biology, when the premier funding agency for scientific research (NSF) is unwilling to support the database that makes the results of that work accessible and understandable to the broad scientific and education communities? 3. Why should I provide data to TAIR that will be available to just a limited subset of people in the scientific community? 4. How do I encourage people not familiar with Arabidopsis to make use of large amounts of information on Arabidopsis when they need to pay up front in order to learn how valuable that information might be to their own research? 5. NSF would still end up paying for at least part of TAIR because some of those fees would be put on NSF research grants. The difference is that NSF support for TAIR under the subscription plan would be more difficult to predict. And the negative press that a subscription plan would generate for NSF should not be underestimated. 6. How can TAIR continue to support its excellent staff through a transition period to an uncertain source of funding in the future? We cannot afford to lose the combined expertise of TAIR staff members all at once. 7. How do you prevent people from sharing their subscription access numbers to other people who do not pay the subscription fee? The logistics of this could be difficult to say the least. 8. How can you predict future revenue generated by subscription fees to a level of accuracy that allows for rational planning of future projects and enhancements? 9. How do we keep TAIR as the primary focal point for information on Arabidopsis, which simplifies information management, with a subscription fee that encourages people to look for bits and pieces of Arabidopsis information (often not curated) elsewhere for free? I urge NSF to maintain its longstanding commitment to support and facilitate research with Arabidopsis by approving the next round of funding for TAIR without moving to a m

David Meinke

2009-10-22 12:08:02.0

Here is the final sentence of my letter above, which was cut short. "I urge NSF to maintain its longstanding commitment to support and facilitate research with Arabidopsis by approving the next round of funding for TAIR without moving to a model of self-support through subscription fees." David Meinke; Oklahoma State University.

Gabriel Leon

2009-10-22 13:26:39.0

I´ve been working in plant biology since I was an undergrad student. Since the begining, TAIR was the most important resource for my research. Now, as PI of my own lab, I am deeply concerned about the strong cut in TAIR´s funding. I can not even imagine our day-to-day research activities without TAIR! Certainly it will negatively impact plant research worldwide.

David Ehrhardt

2009-10-22 14:47:18.0

I think that David Meinke just about said it all. Arabidopsis is my primary research organism and my program would suffer greatly if TAIR was not maintained. I consider databases like TAIR to be essential infrastructure for basic research and science education. If the US government values basic research and science education then it needs to fund the infrastructure that supports these activities. Because such basic infrastructure benefits not just a few research projects, but the life sciences in general, it is an appropriate and indeed ideal subject for government support.

2009-10-22 14:54:33.0

TAIR is absolutely essential for our work on Arabidopsis and other plant species. Reducing or aborting its services will strongly impact all areas of plant science.