Chado

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Chado

http://gmod.org/wiki/Chado
tools to add/extract data from Chado

This package contains several tools that can be used to extract data from Chado database or prepare data before upload. It is a subset above the Chado database schema and libraries.

Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny.



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License

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Debian

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20 March 2013

Notes

License: Artistic-2.0

The Artistic License 2.0

Copyright (c) 2000-2006, The Perl Foundation.

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

Preamble

This license establishes the terms under which a given free software Package may be copied, modified, distributed, and/or redistributed. The intent is that the Copyright Holder maintains some artistic control over the development of that Package while still keeping the Package available as open source and free software.

You are always permitted to make arrangements wholly outside of this license directly with the Copyright Holder of a given Package. If the terms of this license do not permit the full use that you propose to make of the Package, you should contact the Copyright Holder and seek a different licensing arrangement.

Definitions

"Copyright Holder" means the individual(s) or organization(s) named in the copyright notice for the entire Package.

"Contributor" means any party that has contributed code or other material to the Package, in accordance with the Copyright Holder's procedures.

"You" and "your" means any person who would like to copy, distribute, or modify the Package.

"Package" means the collection of files distributed by the Copyright Holder, and derivatives of that collection and/or of those files. A given Package may consist of either the Standard Version, or a Modified Version.

"Distribute" means providing a copy of the Package or making it accessible to anyone else, or in the case of a company or organization, to others outside of your company or organization.

"Distributor Fee" means any fee that you charge for Distributing this Package or providing support for this Package to another party. It does not mean licensing fees.

"Standard Version" refers to the Package if it has not been modified, or has been modified only in ways explicitly requested by the Copyright Holder.

"Modified Version" means the Package, if it has been changed, and such changes were not explicitly requested by the Copyright Holder.

"Original License" means this Artistic License as Distributed with the Standard Version of the Package, in its current version or as it may be modified by The Perl Foundation in the future.

"Source" form means the source code, documentation source, and configuration files for the Package.

"Compiled" form means the compiled bytecode, object code, binary, or any other form resulting from mechanical transformation or translation of the Source form.

. Permission for Use and Modification Without Distribution

(1) You are permitted to use the Standard Version and create and use Modified Versions for any purpose without restriction, provided that you do not Distribute the Modified Version.

. Permissions for Redistribution of the Standard Version

(2) You may Distribute verbatim copies of the Source form of the Standard Version of this Package in any medium without restriction, either gratis or for a Distributor Fee, provided that you duplicate all of the original copyright notices and associated disclaimers. At your discretion, such verbatim copies may or may not include a Compiled form of the Package.

(3) You may apply any bug fixes, portability changes, and other modifications made available from the Copyright Holder. The resulting Package will still be considered the Standard Version, and as such will be subject to the Original License.

. Distribution of Modified Versions of the Package as Source

(4) You may Distribute your Modified Version as Source (either gratis or for a Distributor Fee, and with or without a Compiled form of the Modified Version) provided that you clearly document how it differs from the Standard Version, including, but not limited to, documenting any non-standard features, executables, or modules, and provided that you do at least ONE of the following:

(a) make the Modified Version available to the Copyright Holder of the Standard Version, under the Original License, so that the Copyright Holder may include your modifications in the Standard Version.

(b) ensure that installation of your Modified Version does not prevent the user installing or running the Standard Version. In addition, the Modified Version must bear a name that is different from the name of the Standard Version.

(c) allow anyone who receives a copy of the Modified Version to make the Source form of the Modified Version available to others under . (i) the Original License or

(ii) a license that permits the licensee to freely copy, modify and redistribute the Modified Version using the same licensing terms that apply to the copy that the licensee received, and requires that the Source form of the Modified Version, and of any works derived from it, be made freely available in that license fees are prohibited but Distributor Fees are allowed.

. Distribution of Compiled Forms of the Standard Version or Modified Versions without the Source

(5) You may Distribute Compiled forms of the Standard Version without the Source, provided that you include complete instructions on how to get the Source of the Standard Version. Such instructions must be valid at the time of your distribution. If these instructions, at any time while you are carrying out such distribution, become invalid, you must provide new instructions on demand or cease further distribution. If you provide valid instructions or cease distribution within thirty days after you become aware that the instructions are invalid, then you do not forfeit any of your rights under this license.

(6) You may Distribute a Modified Version in Compiled form without the Source, provided that you comply with Section 4 with respect to the Source of the Modified Version.

. Aggregating or Linking the Package

(7) You may aggregate the Package (either the Standard Version or Modified Version) with other packages and Distribute the resulting aggregation provided that you do not charge a licensing fee for the Package. Distributor Fees are permitted, and licensing fees for other components in the aggregation are permitted. The terms of this license apply to the use and Distribution of the Standard or Modified Versions as included in the aggregation.

(8) You are permitted to link Modified and Standard Versions with other works, to embed the Package in a larger work of your own, or to build stand-alone binary or bytecode versions of applications that include the Package, and Distribute the result without restriction, provided the result does not expose a direct interface to the Package.

. Items That are Not Considered Part of a Modified Version

(9) Works (including, but not limited to, modules and scripts) that merely extend or make use of the Package, do not, by themselves, cause the Package to be a Modified Version. In addition, such works are not considered parts of the Package itself, and are not subject to the terms of this license.

. General Provisions

(10) Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

(11) If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

(12) This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

(13) This license includes the non-exclusive, worldwide, free- of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

(14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF

ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Verified by

Debian

Verified on

20 March 2013

Notes

License: BSD-3

BSD-3 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright

notice, this list of conditions and the following disclaimer.

  • Redistributions in binary form must reproduce the above

copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Indiana University, Bloomington nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

POSSIBILITY OF SUCH DAMAGE.

License

Other

Verified by

Debian

Verified on

20 March 2013

Notes

License: Artistic-2.0 or Artistic or GPL-1+

Artistic-2.0:

 The Artistic License 2.0
 Copyright (c) 2000-2006, The Perl Foundation.
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.
 Preamble
 This license establishes the terms under which a given free
 software Package may be copied, modified, distributed, and/or
 redistributed. The intent is that the Copyright Holder maintains
 some artistic control over the development of that Package while
 still keeping the Package available as open source and free
 software.
 You are always permitted to make arrangements wholly outside of
 this license directly with the Copyright Holder of a given
 Package.  If the terms of this license do not permit the full use
 that you propose to make of the Package, you should contact the
 Copyright Holder and seek a different licensing arrangement.
 Definitions
 "Copyright Holder" means the individual(s) or organization(s)
 named in the copyright notice for the entire Package.
 "Contributor" means any party that has contributed code or other
 material to the Package, in accordance with the Copyright
 Holder's     procedures.
 "You" and "your" means any person who would like to copy,
 distribute, or modify the Package.
 "Package" means the collection of files distributed by the
 Copyright Holder, and derivatives of that collection and/or of
 those files. A given Package may consist of either the Standard
 Version, or a Modified Version.
 "Distribute" means providing a copy of the Package or making it
 accessible to anyone else, or in the case of a company or
 organization, to others outside of your company or organization.
 "Distributor Fee" means any fee that you charge for Distributing
 this Package or providing support for this Package to another
 party.  It does not mean licensing fees.
 "Standard Version" refers to the Package if it has not been
 modified, or has been modified only in ways explicitly requested
 by the Copyright Holder.
 "Modified Version" means the Package, if it has been changed, and
 such changes were not explicitly requested by the Copyright
 Holder.
 "Original License" means this Artistic License as Distributed
 with     the Standard Version of the Package, in its current
 version or as     it may be modified by The Perl Foundation in
 the future.
 "Source" form means the source code, documentation source, and
 configuration files for the Package.
 "Compiled" form means the compiled bytecode, object code, binary,
 or any other form resulting from mechanical transformation or
 translation of the Source form.
 . Permission for Use and Modification Without Distribution
 (1)  You are permitted to use the Standard Version and create and
 use Modified Versions for any purpose without restriction,
 provided that you do not Distribute the Modified Version.
 . Permissions for Redistribution of the Standard Version
 (2)  You may Distribute verbatim copies of the Source form of the
 Standard Version of this Package in any medium without
 restriction, either gratis or for a Distributor Fee, provided
 that you duplicate all of the original copyright notices and
 associated disclaimers.  At your discretion, such verbatim copies
 may or may not include a Compiled form of the Package.
 (3)  You may apply any bug fixes, portability changes, and other
 modifications made available from the Copyright Holder.  The
 resulting Package will still be considered the Standard Version,
 and as such will be subject to the Original License.
 . Distribution of Modified Versions of the Package as Source
 (4)  You may Distribute your Modified Version as Source (either
 gratis or for a Distributor Fee, and with or without a Compiled
 form of the Modified Version) provided that you clearly document
 how it differs from the Standard Version, including, but not
 limited to, documenting any non-standard features, executables,
 or modules, and provided that you do at least ONE of the
 following:
 (a)  make the Modified Version available to the Copyright Holder
 of the Standard Version, under the Original License, so that the
 Copyright Holder may include your modifications in the Standard
 Version.
 (b)  ensure that installation of your Modified Version does not
 prevent the user installing or running the Standard Version. In
 addition, the Modified Version must bear a name that is different
 from the name of the Standard Version.
 (c)  allow anyone who receives a copy of the Modified Version to
 make the Source form of the Modified Version available to others
 under .                       (i)  the Original License or
 (ii)  a license that permits the licensee to freely copy,
 modify and redistribute the Modified Version using the same
 licensing terms that apply to the copy that the licensee
 received, and requires that the Source form of the Modified
 Version, and of any works derived from it, be made freely
 available in that license fees are prohibited but Distributor
 Fees are allowed.
 . Distribution of Compiled Forms of the Standard Version  or
 Modified Versions without the Source
 (5)  You may Distribute Compiled forms of the Standard Version
 without the Source, provided that you include complete
 instructions on how to get the Source of the Standard Version.
 Such instructions must be valid at the time of your distribution.
 If these instructions, at any time while you are carrying out
 such distribution, become invalid, you must provide new
 instructions on demand or cease further distribution. If you
 provide valid instructions or cease distribution within thirty
 days after you become aware that the instructions are invalid,
 then you do not forfeit any of your rights under this license.
 (6)  You may Distribute a Modified Version in Compiled form
 without the Source, provided that you comply with Section 4 with
 respect to the Source of the Modified Version.
 . Aggregating or Linking the Package
 (7)  You may aggregate the Package (either the Standard Version
 or Modified Version) with other packages and Distribute the
 resulting aggregation provided that you do not charge a licensing
 fee for the Package.  Distributor Fees are permitted, and
 licensing fees for other components in the aggregation are
 permitted. The terms of this license apply to the use and
 Distribution of the Standard or Modified Versions as included in
 the aggregation.
 (8) You are permitted to link Modified and Standard Versions with
 other works, to embed the Package in a larger work of your own,
 or to build stand-alone binary or bytecode versions of
 applications that include the Package, and Distribute the result
 without restriction, provided the result does not expose a direct
 interface to the Package.
 . Items That are Not Considered Part of a Modified Version
 (9) Works (including, but not limited to, modules and scripts)
 that merely extend or make use of the Package, do not, by
 themselves, cause the Package to be a Modified Version.  In
 addition, such works are not considered parts of the Package
 itself, and are not subject to the terms of this license.
 . General Provisions
 (10)  Any use, modification, and distribution of the Standard or
 Modified Versions is governed by this Artistic License. By using,
 modifying or distributing the Package, you accept this license.
 Do not use, modify, or distribute the Package, if you do not
 accept this license.
 (11)  If your Modified Version has been derived from a Modified
 Version made by someone other than you, you are nevertheless
 required to ensure that your Modified Version complies with the
 requirements of this license.
 (12)  This license does not grant you the right to use any
 trademark, service mark, tradename, or logo of the Copyright
 Holder.
 (13)  This license includes the non-exclusive, worldwide, free-
 of-charge patent license to make, have made, use, offer to sell,
 sell, import and otherwise transfer the Package with respect to
 any patent claims licensable by the Copyright Holder that are
 necessarily infringed by the Package. If you institute patent
 litigation (including a cross-claim or counterclaim) against any
 party alleging that the Package constitutes direct or
 contributory patent infringement, then this Artistic License to
 you shall terminate on the date that such litigation is filed.
 (14)  Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE
 COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS" AND WITHOUT ANY EXPRESS
 OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE
 DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS
 REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE
 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
 DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF
 ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Artistic:

 This program is free software; you can redistribute it and/or
 modify it under the terms of the Artistic License, which comes
 with Perl.
 On Debian systems, the complete text of the Artistic License can
 be found in `/usr/share/common-licenses/Artistic'.

GPL-1+:

 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License as
 published by the Free Software Foundation; either version 1, or
 (at your option) any later version.
 On Debian systems, the complete text of version 1 of the GNU
 General Public License can be found in `/usr/share/common-
licenses/GPL-1'.




Leaders and contributors

Resources and communication

AudienceResource typeURI
Python (Ref)https://pypi.org/project/chado
Debian (Ref) (R)https://tracker.debian.org/pkg/libchado-perl
Downloadhttp://gmod.org/wiki/Chado_-_Getting_Started


Software prerequisites




Entry






















"Python (Ref)" is not in the list (General, Help, Bug Tracking, Support, Developer) of allowed values for the "Resource audience" property.


"Debian (Ref) (R)" is not in the list (General, Help, Bug Tracking, Support, Developer) of allowed values for the "Resource audience" property.








Date 2013-03-20
Source Debian import
Source link http://packages.debian.org/sid/libchado-perl

[[Category:]]



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The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.