Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: pyensembl
Upstream-Contact: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
Source: https://github.com/openvax/pyensembl
Files-Excluded:
 pyensembl.egg-info/SOURCES.txt
 pyensembl.egg-info/requires.txt

Files: *
Copyright: 2015-2025 Mount Sinai School of Medicine
License: Apache-2.0

Files: tests/data/gencode.ucsc.small.gtf
Copyright: 
 2025 EBI
License:
 General
 .
 EMBL’s European Bioinformatics Institute (EMBL-EBI) promotes open
 science through its mission to provide freely available Data Resources
 and Tools (which includes online services, databases and software)
 to the largest possible community. Where EMBL-EBI presents scientific
 data generated by others, EMBL-EBI imposes no additional restriction on
 the use of the contributed data than those provided by the data owner,
 unless otherwise specified in these Terms of Use.
 .
 EMBL-EBI expects attribution (e.g. in publications, services or products)
 for the use of any of its Data Resources and Tools in accordance with
 good scientific practice. The expected attribution will be indicated
 on the relevant web page of the resource.
 .
 Any feedback provided to EMBL-EBI on its Data Resources and Tools shall
 be considered as non-confidential.
 .
 All scientific data will be made available by a time and release
 mechanism consistent with the data type (e.g. human data where access
 needs to be reviewed by a Data Access Committee, pre-publication
 embargoed for a specific time period).
 .
 EMBL-EBI processes personal data according to its internal policy,
 which safeguards data for individuals. EMBL-EBI also reserves the right
 to collect data through cookies and registration. Personal data will
 be disclosed only in accordance with the applicable privacy notice for
 the relevant data resource or tool (see also Privacy section below).
 .
 EMBL-EBI may make information about the total usage of particular Data
 Resources and Tools, or data available, to the public and third party
 organisations who supply or fund the Data Resources and Tools without
 details of any individual’s use. Such information is in the form of
 aggregated statistics and does not identify any individual.
 .
 While EMBL-EBI will retain its commitment to Open Science, EMBL-EBI
 reserves the right to update these Terms of Use at any time. When
 alterations are inevitable, EMBL-EBI will attempt to give reasonable
 notice of any changes by placing a notice on its website, but users may
 wish to check each time they use the website. The date of the most recent
 revision will appear on this, the ‘EMBL-EBI Terms of Use’ page. If
 the user does not agree to these changes, please do not continue to use
 EMBL-EBI Data Resources and Tools. EMBL-EBI will also make available
 on request an archived copy of the previous Terms of Use for comparison.
 .
 EMBL-EBI shall not be liable to the user or third parties claiming
 rights through the user for any losses or damages.
 .
 For some Data Resources and Tools, additional specific terms and
 conditions and/or license agreements may apply, which in case of any
 conflict of inconsistency, will prevail over these Terms of Use.
 .
 Any questions or comments concerning these Terms of Use can be
 addressed to:
 .
  Head of EMBL-EBI Administration and Operations
  EMBL’s European Bioinformatics Institute (EMBL-EBI)
  Wellcome Genome Campus
  Hinxton CB10 1SD
 .
 Data Resources and Tools 
 .
 Users of EMBL-EBI Data Resources and Tools agree not to attempt to
 use any EMBL-EBI computers, files or networks apart from through the
 service interfaces provided.
 .
 EMBL-EBI will make all reasonable effort to maintain continuity of these
 Data Resources and Tools and provide adequate warning of any changes,
 discontinuities and possible discontinuance. However, EMBL-EBI accepts
 no responsibility for the consequences of any temporary or permanent
 discontinuity in service.
 .
 The user is exclusively responsible for their use of content accessible
 from Data Resources and Tools. Hosting and providing access to the
 content does not imply any endorsement by EMBL-EBI.
 .
 Any attempt to use EMBL-EBI Data Resources and Tools to a level that
 prevents, or is likely to prevent, EMBL-EBI providing services to others,
 will result in the user being blocked. EMBL-EBI will attempt to contact
 the user to discuss their needs and how (and if) these can be met from
 other sources.
 .
 If the user posts or sends offensive, unlawful, inappropriate or
 objectionable content anywhere on or to our websites or otherwise engages
 in any disruptive behaviour on any of our services, EMBL-EBI may use
 personal information from its security logs to stop such behaviour. Where
 EMBL-EBI reasonably believes that the user is or may be in breach of
 any applicable laws, EMBL-EBI may use personal information to inform
 relevant third parties about the content and the user’s behaviour.
 .
 Software that can be run from the EMBL-EBI web pages may be used by
 any individual for any purpose unless specific exceptions are stated
 on the web page or specified in these Terms of Use. Any software from
 EMBL-EBI made available for download through our web pages (either
 directly or from third party repositories) will have its own individual
 license agreement.
 .
 EMBL-EBI has implemented appropriate technical and organisational
 measures to ensure a level of security which we deem appropriate, taking
 into account the categories of data we collect and the way we process it.
 .
 EMBL-EBI does not accept responsibility for the consequences of any
 breach of the confidentiality or security of the EMBL-EBI site by
 third parties.
 .
 EMBL-EBI does not guarantee the accuracy of any provided data or Data
 Resources and Tools nor the suitability of these for any purpose. The
 Data, Resources and Tools are provided by EMBL-EBI ‘AS IS’ without
 warranties of any kind.
 .
 EMBL-EBI retains the right, at its sole discretion, without prior
 notice and without assuming any liability, (i) to rectify, delete,
 or restrict access to, content that it judges to be inappropriate,
 unlawful, infringing third party rights or inadequately protected,
 and (ii) to limit or revoke user access if it determines that access
 to EMBL-EBI’s Data Resources and Tools hinders its operations or
 breaches these Terms of Use and/or would be incompatible with relevant
 legal frameworks for example those related to privacy and intellectual
 property rights, export controls and sanctions.
 .
 The user is exclusively responsible for any material or content uploaded
 to EMBL-EBI’s Data Resources and Tools. The user responsible for the
 uploading of any content shall ensure: (i) that they have all required
 licences, authorisations, permissions and consents for open access
 dissemination, where the content is uploaded in an open access resource;
 (ii) that they have all required licences, authorisations, permissions
 and consents for dissemination, where the content is uploaded in a
 controlled access resource and have an appropriate mechanism in place
 to approve such controlled access, where under the specific terms of
 the resource,  it’s the user’s responsibility to grant such access,
 (iii) that the content does not infringe any third-party rights and
 (iv) that the content complies with all laws and regulations applicable
 to the user, including, without limitation, those related to privacy,
 intellectual property rights, export controls and sanctions.
 .
 Data 
 . 
 The Data Resources and Tools hosted by EMBL-EBI are generated in part
 from data contributed by the community who remain the data owners.
 .
 When the user contributes scientific data to a database through EMBL-EBI
 website or other submission tools this information will be released at
 a time and in a manner consistent with the scientific data and EMBL-EBI
 may store it permanently.
 .
 EMBL-EBI itself places no additional restrictions on the use or
 redistribution of the data available via its Data Resources and Tools
 other than those provided by the original data owners, unless otherwise
 specified in these Terms of Use.
 .
 The original data may be subject to rights claimed by third parties,
 including but not limited to, patent, copyright, other intellectual
 property rights, biodiversity-related access and benefit-sharing
 rights. For the specific case of the EGA database and human data
 consented for biomedical research, these rights may be formalised in
 Data Access Agreements. It is the responsibility of users of EMBL-EBI
 Data Resources and Tools to ensure that their exploitation of the data
 does not infringe any of the rights of such third parties.
 .
 Privacy
 .
 EMBL is an intergovernmental organisation, entrusted with a number of
 privileges and immunities necessary to fulfil its mission, including the
 inviolability of EMBL premises and archives. Within these limits, the
 user is granted certain rights in relation to its personal data. These
 are detailed in our Internal Policy on Data Protection.
 .
 More details of the personal data we collect from users when the website
 is browsed and how EMBL processes this personal data are detailed in
 our our Privacy notice.
 .
 EMBL-EBI’s websites use cookies to record information about user online
 preferences that allow EMBL-EBI to personalise users’ experience of
 the website. Users can control the use of cookies from the web browser,
 but if the user chooses not to accept cookies from EMBL-EBI’s websites,
 they will not be able to take full advantage of all of the website’s
 features. For information on how to manage cookies in different web
 browsers and a full list of EMBL-EBI and 3rd party cookies — see our
 cookies page.
Comment:
 This information is gathered from
 https://www.gencodegenes.org/human/releases.html 
 pointing to the EBI's data usage policies on
 https://www.ebi.ac.uk/about/terms-of-use/.
 

Files: tests/data/mouse.ensembl.81.partial.ENSMUSG00000017167.pep
       tests/data/mouse.ensembl.81.partial.ENSMUSG00000017167.fa
       tests/data/mouse.ensembl.81.partial.ncrna.ENSMUSG00000017167.fa
       tests/data/mouse.ensembl.81.partial.ENSMUSG00000017167.gtf
Copyright:
 2001-2025 EMBL-EBI, Hinxton, UK
License: Unrestricted
 Ensembl imposes no restrictions on access to, or use of, the data provided and the software used to analyse and present it. Ensembl data generated by members of the project are available without restriction.
 .
 From https://www.ensembl.org/info/about/legal/disclaimer.html.

Files: tests/data/refseq.ucsc.small.gtf
Copyright:
 1996-2025 NCBI
License:
 .
 Molecular Data Usage
 .
 Databases of molecular data on the NCBI Web site include such examples
 as nucleotide sequences (GenBank), protein sequences, macromolecular
 structures, molecular variation, gene expression, and mapping data. They
 are designed to provide and encourage access within the scientific
 community to sources of current and comprehensive information. Therefore,
 NCBI itself places no restrictions on the use or distribution of
 the data contained therein. Nor do we accept data when the submitter
 has requested restrictions on reuse or redistribution. However, some
 submitters of the original data (or the country of origin of such data)
 may claim patent, copyright, or other intellectual property rights in
 all or a portion of the data (that has been submitted). NCBI is not in
 a position to assess the validity of such claims and since there is
 no transfer of rights from submitters to NCBI, NCBI has no rights to
 transfer to a third party. Therefore, NCBI cannot provide comment or
 unrestricted permission concerning the use, copying, or distribution
 of the information contained in the molecular databases.
 .
 From https://www.ncbi.nlm.nih.gov/home/about/policies/

Files: debian/*
Copyright: 2021,2025 Steffen Moeller <moeller@debian.org>
           2022 Étienne Mollier <emollier@debian.org>
           2023 Lance Lin <lq27267@gmail.com>
License: Apache-2.0

License: Apache-2.0
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 .
     http://www.apache.org/licenses/LICENSE-2.0
 .
 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
 .
 On Debian systems this license is available at
 '/usr/share/common-licenses/Apache-2.0'
