[Bioc-devel] [EXTERNAL] Deeptarget package

Mon Jul 8 23:23:20 CEST 2024

Dear Dr. Kristian,

We consulted with experts at our NIH/NCI here and per their suggestion, we have added the following paragraph to the description and document of Workflow Demonstration as below:
“The user of this package is required to agree to the terms and conditions of DepMap portal (https://depmap.org/portal/).  Some of these terms and conditions are problematic for U.S. Federal Government employees, and they should consult their technology transfer office/legal office before agreeing to such terms and conditions”

Best,

Trinh

From: Kristian Ullrich <ullrich using evolbio.mpg.de>
Date: Tuesday, June 25, 2024 at 1:45 AM
To: Nguyen, Trinh (NIH/NCI) [C] <tinh.nguyen using nih.gov>
Cc: Laurent Gatto <laurent.gatto using uclouvain.be>, Kern, Lori <Lori.Shepherd using RoswellPark.org>, bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [EXTERNAL] [Bioc-devel] 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
ullrich using evolbio.mpg.de<mailto:ullrich using 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)

--
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On 12. Jun 2024, at 15:53, Nguyen, Trinh (NIH/NCI) [C] <tinh.nguyen using nih.gov<mailto:tinh.nguyen using 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.gatto using 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.gatto using uclouvain.be> to chime in to address your concern.

Thanks,

Trinh

From: Kristian Ullrich <ullrich using evolbio.mpg.de<mailto:ullrich using evolbio.mpg.de>>
Date: Wednesday, June 12, 2024 at 2:42 AM
To: Nguyen, Trinh (NIH/NCI) [C] <tinh.nguyen using nih.gov<mailto:tinh.nguyen using nih.gov>>
Cc: Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>, bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using 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
ullrich using evolbio.mpg.de<mailto:ullrich using 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 using r-project.org<mailto:bioc-devel using r-project.org>> wrote:

Thank You!

Trinh

From: Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Date: Tuesday, June 11, 2024 at 12:19 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>, Nguyen, Trinh (NIH/NCI) [C] <tinh.nguyen using nih.gov<mailto:tinh.nguyen using 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/.  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-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Nguyen, Trinh (NIH/NCI) [C] via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Sent: Tuesday, June 11, 2024 12:10 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using 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

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