I agree that it is important to only redistribute data in a way that is consistent with whatever terms are encountered when accessing the data.
Some options I've seen include (1) using an API that allows authentication (the httr2 'auth' vignette provides workflows; I took the time recently to figure out how to authenticate against Globus for access to restricted data, https://mtmorgan.github.io/software/2024/06/20/globus-oauth.html); (2) point the user to the data source and provide functions / etc to incorporate data that has been downloaded by the user into your work flow (e.g., 'use `browseURL(…)` to access and download the data, then use `import_my_data()` to continue with the workflow'; (3) require that the user acknowledges the license of the data before retrieving it (e.g., AlphaMissenseR asks the user to accept licensing using `readline()`) (4) contact the data owner and ask for a written exception to access restrictions (I believe this was the case for the msigdb package); (5) rely on 'advertised' data methods that are less encumbered by licensing requirements (I believe KEGGREST takes this approach?); (6) find a different data resource providing unrestricted access to similar data. It is equally important to communicate licensing restrictions to the user. This often seems challenging. For instance KEGGREST mentions restrictions to academic use in the Description field (good) but the sole purpose of the package is to provide this data resource so its 'Artistic-2.0' license is appropriate for the code, but somehow not for the package as a whole; R can be configured to exclude certain types of packages from discovery / installation via `available.packages(filter =…)` based on the License field of the DESCRIPTION file. A cursory look suggests msigdb does not mention in a prominent location that data redistribution has been allowed by the data owner. It also seems appropriate to acknowledge the data source in the Authors@R: field of the DESCRIPTION file, with roles documented on the help page `?person` (e.g., 'dtc' data contributor or 'cph' copyright holder). It would be interesting / challenging to identify packages that do an excellent job of this. Generally, I believe we should be advocating for open data resources, maybe using https://docs.nih-cfde.org/en/latest/the-fair-cookbook/content/recipes/Compliance/fairshake/ or other resources for assessing openness. Martin From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Kristian Ullrich <ullr...@evolbio.mpg.de> Date: Tuesday, June 25, 2024 at 1:45 AM To: Nguyen, Trinh (NIH/NCI) [C] <tinh.ngu...@nih.gov> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] [EXTERNAL] Deeptarget package Dear Nguyen, Thank you for your response. I am just a bit puzzled, and no other developer has answered so far. E.g. in the description of the depmap package it says: "This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0))." Anyhow if you visit the original source database it comes with the Terms and conditions that one need to agree and it says specifically: "Governing Law The terms and conditions herein shall be construed, governed, interpreted, and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A. Furthermore, by accessing, downloading, or using the Database, You consent to the personal jurisdiction of, and venue in, the state and federal courts within Massachusetts with respect to Your download or use of the Database." So if it comes to law, it does not matter, that you just use a subset of the original data or that you just get it from another source, since the statement is kind of very clear. I do not see any kind of agreement in the depmap package nor a "warning" statement, like "by using this package you agree on the following terms …" So how to deal correctly (legally and code-wise) in this situation? Best regards -- Kristian Ullrich, Ph.D. Max Planck Institute For Evolutionary Biology Scientific IT group Department of Evolutionary Genetics August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullr...@evolbio.mpg.de “Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so gut wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen Hummer; Moritz Krämer) -- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. > On 12. Jun 2024, at 15:53, Nguyen, Trinh (NIH/NCI) [C] <tinh.ngu...@nih.gov> > wrote: > > Dear Kristian, > > This is very important question. Thanks for checking in. The manuscript is > under review, and I believe that we already agreed and followed to Depmap’s > policies. The input data we used in this package here contains only a subset > of the data we used in the manuscript, and it is for demonstration how the > package works. In addition to this, Deeptarget does have a function to pull > out the data from Depmap and it is called Depmap2DeepTarget. I think this is > where your concern is coming from. This function we incorporated the Depmap > package from @Laurent Gatto <mailto:laurent.ga...@uclouvain.be> which allows > users to download data from depmap.org <http://depmap.org/>. Therefore, I > would love to leave this for @Laurent Gatto > <mailto:laurent.ga...@uclouvain.be> to chime in to address your concern. > > Thanks, > > Trinh > > From: Kristian Ullrich <ullr...@evolbio.mpg.de> > Date: Wednesday, June 12, 2024 at 2:42 AM > To: Nguyen, Trinh (NIH/NCI) [C] <tinh.ngu...@nih.gov> > Cc: Kern, Lori <lori.sheph...@roswellpark.org>, bioc-devel@r-project.org > <bioc-devel@r-project.org> > Subject: [EXTERNAL] Re: [Bioc-devel] Deeptarget package > > Dear Nguyen, > > I have a question related to the data that you use and I just bring it up > here since I would also like to ask the bioconductor developers, how this can > be handled properly. > > The depmap.org <http://depmap.org/> portal has a clear "Terms and Condition" > statement that you need to agree on if one uses any of the data that is > provided by the portal. (See below) So one need to click a "I agree" button > to stick to their policies. > > How have you managed that a user of your package first send this agreement to > the depmap.org <http://depmap.org/> portal once the user uses data from the > portal? > > Thank you in anticipation > > Best regards > > Kristian > > Here is their policy: > > " > Terms and Conditions > > By using this site, you agree to our terms and conditions below. > > Overview of Terms > > These Terms of Use reflect the Broad Institute’s commitment to Open Science > through its mission to provide freely available online services, databases > and software relating to data contributed from life science experiments to > the largest possible community. They impose no additional constraints on the > use of the contributed data than those provided by the original data owners. > The data made available on this website were generated for research purposes > and are not intended for clinical 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. It is the > responsibility of users of Broad Institute services to ensure that their > exploitation of the data does not infringe any of the rights of such third > parties. > The information and materials ("Data") made available on this web site > including the database of genomic profiles, mutations, genetic and > pharmacologic screening data (referred to collectively herein as the > "Database") are made available to you (and your employing entity, where the > download or use is within the scope of your employment by such entity- > collectively "You"). > Any questions or comments concerning these Terms of Use can be addressed to: > Cancer Dependency Map, Broad Institute, 415 Main Street, Cambridge, MA 02142, > USA > By accessing and viewing this Database, You agree to the following terms and > conditions: > Attribution > > You agree to acknowledge the Broad Institute (e.g., in publications, services > or products) for any of its online services, databases or software in > accordance with good scientific practice. You agree to use the acknowledgment > wording provided for the relevant Data (provided by the original data owners) > as indicated on the appropriate web page. > Confidentiality > > In the case of cell lines in the Database, many of which are established and > have been in the public domain for years, You agree to preserve, at all > times, the confidentiality of Data pertaining to identifiable Data Subjects. > In particular, You shall undertake not to use, or attempt to use the Data to > deliberately compromise or otherwise infringe the confidentiality of > information on Data Subjects and their right to privacy. > Updating the Terms of Use > > While we will retain our commitment to Open Science, we reserve the right to > update these Terms of Use at any time. When alterations are inevitable, we > will attempt to give reasonable notice of any changes by placing a notice on > our website, but you may wish to check each time you use the website. The > date of the most recent revision will appear on this, the ‘DepMap.org > <http://depmap.org/> Terms of Use’ page. If you do not agree to these > changes, please do not continue to use our online services. We will also make > available an archived copy of the previous Terms of Use for comparison. > Indemnification and Disclaimer of Warranties > > You are using this Database at Your own risk, and You hereby agree to hold > Broad and its contributors and their trustees, directors, officers, > employees, and affiliated investigators harmless for any third party claims > which may arise from Your download or use of the Database or any portion > thereof. The Database is a research database and is provided "as is". Broad > does not represent that the Database is free of errors or bugs or suitable > for any particular tasks. > ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED > WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, > NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS ARE DISCLAIMED. IN > NO EVENT SHALL BROAD OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, > INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 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 > DATABASE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. > Governing Law > > The terms and conditions herein shall be construed, governed, interpreted, > and applied in accordance with the internal laws of the Commonwealth of > Massachusetts, U.S.A. Furthermore, by accessing, downloading, or using the > Database, You consent to the personal jurisdiction of, and venue in, the > state and federal courts within Massachusetts with respect to Your download > or use of the Database. > Privacy > > See our privacy policy here <https://depmap.org/portal/privacy/>. > " > -- > Kristian Ullrich, Ph.D. > Max Planck Institute > For Evolutionary Biology > > Scientific IT group > Department of Evolutionary Genetics > August Thienemann Str. 2 > 24306 Plön > Germany > +49 4522 763 313 > ullr...@evolbio.mpg.de <mailto:ullr...@evolbio.mpg.de> > > “Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so > gut wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen > Hummer; Moritz Krämer) > > -- > CONFIDENTIALITY NOTICE: > The contents of this email message and any attachments are intended solely > for the addressee(s) and may contain confidential and/or privileged > information and may be legally protected from disclosure. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > copying, or storage of this message or its attachments is strictly prohibited. > > > On 11. Jun 2024, at 20:04, Nguyen, Trinh (NIH/NCI) [C] via Bioc-devel > <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>> wrote: > > Thank You! > > Trinh > > From: Kern, Lori <lori.sheph...@roswellpark.org > <mailto:lori.sheph...@roswellpark.org>> > Date: Tuesday, June 11, 2024 at 12:19 PM > To: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> > <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>>, Nguyen, Trinh > (NIH/NCI) [C] <tinh.ngu...@nih.gov <mailto:tinh.ngu...@nih.gov>> > Subject: [EXTERNAL] Re: Deeptarget package > Two things: > > > 1. The package was accepted on Friday. Currently our software builds are > only building twice a week Tue and Fri. You can see the schedule of all the > different builds at https://bioconductor.org/checkResults/ > <https://bioconductor.org/checkResults/>. Eventually devel Bioc will go back > to daily builds but there are some configurations we are currently working > on. Once the package builds/checks cleanly on the daily builder it will then > be available (likely later today) > > > 1. Your package will only be available in Bioc devel 3.19 until the fall > release as newly accepted package are placed until devel until a full release > announcement. > > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org > <mailto:bioc-devel-boun...@r-project.org>> on behalf of Nguyen, Trinh > (NIH/NCI) [C] via Bioc-devel <bioc-devel@r-project.org > <mailto:bioc-devel@r-project.org>> > Sent: Tuesday, June 11, 2024 12:10 PM > To: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> > <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>> > Subject: [Bioc-devel] Deeptarget package > > Dear Bioconductor team, > > Deeptarget package has been accepted. However, when I installed it has error > of �package �DeepTarget� is not available for Bioconductor version '3.18'� > > Could you please give me some guidance? > > Thanks, > > Trinh > > > [[alternative HTML version deleted]] > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > CAUTION: This email originated from outside of the organization. Do not click > links or open attachments unless you recognize the sender and are confident > the content is safe. > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > CAUTION: This email originated from outside of the organization. Do not click > links or open attachments unless you recognize the sender and are confident > the content is safe. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
