The Gypsy Database:Privacy policy

THE GYPSY DATABASE (GyDB) OF MOBILE GENETIC ELEMENTS

The GyDB is owned and operated by Biotech Vana S.L. (Biotechvana), Lab 16D, Parc Cientific, University of Valencia, Polígono de la Coma S/N, 46980, Valencia, Spain.

SCOPE

The GyDB is a Computer Supported Cooperative Work in Genetics and Microbiology that furthers the scientific objective of excellence in research, services and education by making available worldwide, an open access with a focus on the diversity, evolution, and impact of viruses and mobile genetic elements in their host evolution.

The GyDB uses non-redundant full-length genomes as reference models to create non-redundant databases and analyze phylogenetically the different protein domains encoded by all mobile genetic elements classified to create phylogeny-based Hidden Markov Models (HMM) Profiles.

SUPPORT BOARD

• Carlos Llorens
• Lucia Bernad
• Ricardo Futami
• Alfonso Muñoz-Pomer
• Laura Dominguez

TERMS AND CONDITIONS

1. All contents at GyDB are distributed under the terms of the CREATIVE COMMONS ATTRIBUTION LICENSE, which allows unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (see however the Section below, "Subscribing").
2. The GyDB consists of an open access database supported by Wiki software to let any author interested in the topic contribute to the project. Navigation of the open access is free. Simply visiting it you do not publicly expose your identity unless you choose to provide this information when subscribing to the project, or login the Wiki, which is accessible only for registered users. This is in order to support and guarantee the maintenance and scientific accuracy of the database (for more information, see the Section below, "Subscribing").
3. Any members of the scientific community (including students and educators) can be GyDB editors and contribute material related with the topic. The GyDB can also be used as a repository of contents and supplementary material attached to your research publication in scientific journals (see also the Section below, "Subscribing").
4. A priori, the material submitted to the GyDB project should concern non-redundant sequences with their full-length genome publicly available in the Genbank, the Repbase, or any other database supporting a system of classification of viruses and mobile genetic elements. Should you characterize a new mobile genetic element you may submit it, as it is customary to any of these databases, give it a classification, name or ID and notice us the accession assigned.
5. The GyDB sets a temporary session cookie (PHPSESSID) whenever you visit the site (a cookie is a small data file that web sites commonly write to a site visitor's hard drive when the site is visited). The cookie and the information concerning your session will be automatically eliminated shortly after you close your browser. It is not stored long-term on your computer. Alternatively, you can deny the cookie, but keep in mind that doing so you prevent the use of our cookie-dependent features.
6. Use of the GyDB for any illegal purpose, or that in any manner could exceed authorized access or infringe damage, disable, overload, or harm the operation of any part or site of this project, is strictly prohibited.
7. By subscribing, accessing or using the GyDB in any way, including login to the wiki, using servers, or solely browsing the open access, you agree to and are bound by the terms of use described throughout this document.

SUBSCRIBING

1. The Wiki at GyDB is a research networking supported by a board of curators and accessible only by registered users.
2. The Wiki has identical database design and architecture to that of the open access. Registered users can modify or create contents in the wiki, contribute databases, multiple alignments, phylogenies, servers, and tools that they decide if they should be and when should be uploaded in the open access. Registered users can also start new lines in the topic (for instance, new sites classifying viroids and virusoids) and can also establish working groups on which we anticipate accepting senior researchers to revise or coordinate the different working groups. Registered users have also availability of technical support, private workspace, and full-access to the GyDB collection of multiple alignments, HMM profiles and consensus sequences. Users can also start automatic services such newsletters, alerts related to a particular topic in the field, and others.
3. URLs, databases, tools and contents contributed as supplementary material related to standard research publications can be a priori only edited by the original authors and these links are permanent. However, depending on the terms involving the content (in the context of the original publication, for example, a multiple alignment related to a paper), an author decides should he give permission to other authors to edit the content.
4. Registration is under subscription. Subscribers can be research departments of both academic and industrial centers, and other database projects interested in the topic (individual researchers can also subscribe by their own).
5. Biotechvana levies a processing charge of 500 euros (or the equivalent in other currencies) for every subscriber, just to cover the costs incurred by the technical support and open access maintenance. When subscribing you are contributing to guarantee the continuity of this project. For institutions including more than one department, it is possible to agree to a collective low-priced subscription covering all departments (for more information in these cases, please contact us).
6. The subscription is annual and comprises a number of users per subscriber. Personal information of registered users is used only for administrative purposes and will not be released to other databases for any type of illegitimate use. However, registered users contributing material are authors which take responsability for their entries, their names are properly cited where correspond to in the open access, even if the entries have been replaced or updated by other authors.
7. Biotechvana reserves its right to remove, at any time, any content from the open access involving inmoral, pseudo-scientific and/or off-topic references.

COPYRIGHT

The copyright on the material contained within the GyDB project belongs to Biotechvana, or its editors and other software licensors. The trademarks appearing on the GyDB are protected by the laws of Spain or the European Union and international trademark laws. Subscribing authors who contribute material to the GyDB retain copyright to their work but accept and agree to be bound by the terms of the CREATIVE COMMONS ATTRIBUTION LICENSE, which allows unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The GyDB project is compatible to, and may also be used as a repository related to the standard publication in other journals. Upon that, authors are required to ensure:

1. No material submitted to the GyDB project infringes existing copyrights, or the rights of a third party.
2. No material submitted contains any content unlawful, or libelous, or which would constitute a breach of contract, or confidence, or commitment given to secrecy.

The GyDB incorporates images of biological organisms we think are helpful in facilitating improved perspective concerning biodiversity and relationships among mobile genetic elements and hosts. We make this material available for informative purposes only, and do not redistribute these images.We are glad to authorize you to retrieve the images of which we are owners but note that limitations of copyright are imposed on images provided by other authors (transmission or reproduction of protected items beyond that allowed by fair use as defined in the copyright laws requires the permission of the copyright owners). Should you are interested in any image courtesy of other authors, you should contact the copyright owner.

INTERACTIVE POLICY

We make every effort to review this policy and its legacy in light of the commentary we receive; please check the latest version. If you have any additional question explicitly concerning privacy, please contact us.

DISCLAIMERS

Links to other web sites are provided by the GyDB in good faith and for informational purposes, only. Biotechvana disclaims any responsibility for the materials contained in any web site linked to the GyDB project.

Access to the open access is available free of charge for ordinary use in the course of research, and no kind of agreement or contract is created between open access users and the GyDB providers beyond the CREATIVE COMMONS ATTRIBUTION LICENSE.

Biotechvana does not give any kind of warranty nor assume any kind of liability or responsibility for the accuracy or correctness of contents, material provided, services, incidences or results reported or involving servers at GyDB project (despite of our efforts and those of other contributors to improve the accuracy of this project, its completeness, quality or others).

Biotechvana makes efforts to keep the GyDB project available twenty-four hours a day and seven days a week, but does not guarantee that the service will be uninterrupted or error-free, or that the service will be free of viruses or other harmful components.

Certain parts of GyDB may contain advertising. Biotechvana is not responsible for the content of any advertising material or any errors or inaccuracy in any advertising or sponsorship, which is the responsibility of the advertiser.

MEDICAL QUESTIONS

The GyDB is a research project and does not provide specific medical advice. Personal questions for diagnosis must be addressed to qualified professionals.

ACKNOWLEDGMENTS

In the Iteration II (in preparation) of this project we are grateful to:

• Pavel Neumann, Institute of Plant Molecular Biology, Czech Republic, for useful revision of Ogre LTR retrotransposon.
• Teo Chee How, Unit of Genetic and Molecular Biology. University of Malaya, Malaysia for useful revision and update of Monkey LTR retrotransposon.
• Eric W. Ganko, Department of Bioinformatics, Biology Dept. UNC-Chapel-Hill, for useful corrections and information about C. elegans-like Mag and Cer2-3 LTR retroelements.
• Claudia Copeland, Department of Bioinformatics, University of Leipzig, for useful information about the Boudicca LTR retrotransposon.
• The GyDB project is partly supported by financial grant 17092008 from ENISA (Empresa Nacional de Innovacion S.A), and by grant IMIDTD/2008/103 from IMPIVA.
• All contributors in the iteration I.

In the iteration I of this project we are grateful to:

• University of Valencia for support and permission to use the URL http://gydb.uv.es with research and education purposes, and by providing funding for publication charges.
• Alfredo Martinez, Department of Plant Pathology, University of Georgia, for contributing an image of Fusarium sp.
• Wikipedia, the free encyclopedia from where we have picked up the image of Takifugu rubripes, Copyright of the user Chris 73, and free available under the dual terms of the Wikipedia Commons image and the Creative Commons licenses.
• Jean-Jacques Eckert and Patrick Bertrand of Recif France, for contributing an image of Tripneustes gratilla.
• Joaquin Panadero, our friend and Biotechvana partner of the Centro Nacional de Biotecnologia (CNB), for his collaboration in this project and contributing the images of Mandrill sp., Primates sp., Saccharomyces cerevisiae, Mus musculus, Mandrillus sphinx, Saccaromyces exiguus, and Cricetelus, griseus.
• Pierre J.G.M. de Wit of Laboratory of Phytopathology, Wageningen University (http://www.php.wur.nl/uk), for contributing an image of Cladosporium fulvum by way of Alejandro Perez of the Universidad de Malaga.
• Alberto Urbaneja of "Instituto Valenciano de Investigaciones Agrarias" (IVIA), for contributing an image of Ceratitis capitata.
• Valmir Duarte of Faculdade de Agronomía, UFRGS, Porto Alegre, for contributing an image of Colletotrichum gloeosporioides.
• Duncan van Vliet of the Web site "http://www.onderwaterwereld.net", for contributing an image of Ciona intestinalis.
• Hugh D. Wilson of TAMU herbarium, Texas A&M University, for contributing an image of Zea diploperennis.
• "Aquaria Central" for contributing an image of Stizostedion vitreum.
• Marcel Lecomte, for contributing an image of Pyrenophora graminea, by way of the Web site "http://Skynet.be".
• Tom Volk of the University of Wisconsin-La Crosse, for contributing an image of Tricholoma magnivelare, the american matsutake mushroom.
• Michael Schleicher of the Ludwig-Maximilians-Universitaet, for contributing an image of Dictyostelium discoideum, host of the Gypsy-like Skipper retrotransposon.
• The Web site "http://www.knoch1.de", for making online available a comprehensive database of images of plant organisms from which we have picked up the images of Arabidopsis thaliana and Nicotiana tomentosiformis for educational and research purposes, following the on-line permission of the copyright owner.
• Chris Glenn of JC Raulston Arboretum, for contributing an image of Phascolarctos cinereus with permission of the copyright owner, Bryce Lane, Department of Horticultural Science, NC State University.
• David Pearce of the Web site "http://primates.com", for contributing an image of Hylobates syndactylus.
• Jaap van Tuyl of Wageningen University and Research Center, for contributing an image of Lilium henryi by way of the Lilium information page.
• Alan Hill of Hopwood Hall College, for contributing an image of Pan paniscus by way of the "http://ZipCodeZoo.com" Web site project.
• Marc Hauser of the Cognitive Evolution Laboratory of Harvard University, for contributing an image of Cercopithecus aethiops tantalus.
• Juan Bibiloni of "Jardín Botánico Mundani" in Mallorca, for contributing an image of Sorghum bicolor.
• David Stand of BayScience Foundation, for contributing an image of Macaca mulatta by way of the "http://ZipCodeZoo.com" Web site project.
• J. Michael Miller of the Science National Center for Zoonotic, Vector-borne, and Enteric Diseases, of Coordinating Center for Infectious Diseases (CCID), Atlanta, for contributing an image of Schistosoma japonicum.
• Richard J Howard of DuPont Experimental Station, for contributing an image of Magnaporthe grisea reprinted, with permission, from the Annual Review of Microbiology, Volume 50 © 1996 by Annual Reviews (http://www.annualreviews.org).
• Tim.J. Goodwin of the University of Otago, for useful information and comments concerning the DIRS1 lineage of retrotransposons.
• Ralf J. Sommer of the Max Planck Institute for Developmental Biology, for contributing an image of Caenorhabditis elegans.
• Alex Wild, author of the insect photography Web site "http://myrmecos.net", for contributing an image of Tribolium castaneum.
• Rita Bernhardt, Lehrstuhl für Biochemie, Universität des Saarlandes, for contributing an image of Schizosaccharomyces pombe.
• John H. Wahlert et al. of Baruch College, City University of New York, for contributing an image of Clonorchis sinensis.
• Cal Vornberger, nature photographer, for contributing an image of Meleagris gallopavo by way of the Animal Diversity Web of the University of Michigan Museum of Zoology.
• Ralph Cavaliere of Gettysburg College for contributing an image of Aspergillus nidulans.
• Enrique Donat and Cristina Campos for contributing the images of Pinus sp., Ovis sp., and Gallus gallus.
• Margarita Lopez of SESBE (Sociedad Española de Biología Evolutiva) for contributing two images of Capra pyrenaica copyright of Jorge Aguilar Bosch.
• Rachel Epstein, Washington University, for all English revisions.
• Maria Consuelo Palacios for her collaboration in this project.
• Javi Ortiz, Isaac Fernandez and Bernardo Celda for technical support at the Servicio Central de Soporte a la Investigacion Experimental (SCSIE) of the University of Valencia.
• Miguel Vicente Ripollés, Ausias March Institute of Valencia, for coordinate the collaboration of Virtudes Planelles, Fran Frechina, Jordi Cervera, Pablo Sabater, and Emilio Javaloyas. Our thanks to all them, also.
• Peter Balint-Kurti from the United States Agricultural Research Service, for useful information of the Monkey LTR retrotransposon.
• Howard Laten of Loyola University of Chicago, for useful information of the Diaspora LTR retrotransposon.
• Andreas Trepte of Max-Planck-Institute, for contributing an image of Drosophila melanogaster.
• Thomas Kaufman of Flybase, for contributing the images of Drosophila virilis and Drosophila ananassae.
• Sarah LaRose of the Virtual Museum of Canada, for contributing an image of Alternaria alternata copyright of George Barron.
• CEEI of Valencia for supporting us at the start of this project.
• We have been awarded the NOVA 2006 by IMPIVA and Conselleria d`Empresa, Universitat I Cìencia of Valencia.
• The GyDB project have been partly supported by European Union funding grants IMCBTA/2005/45, IMIDTD/2006/158 and IMIDTD/2007/33 from IMPIVA and by grant BFU2005-00503 from Ministerio de Educación y Ciencia to Andres Moya.

Last revised: February 6, 2009