DOI: 10.5281/zenodo.14859004
title: Immunopeptidomics publication analysis results

description: Immunopeptidomics publication analysis results



Results of immunopeptidomic analysis accompanying the publication "Expanding the definition of MHC Class I peptide binding promiscuity to support vaccine discovery across cancers with CARMEN".


 

Authors: Aleksander Palkowski, Michal Waleron, Ashwin Adrian Kallor, Emilia Daghir-Wojtkowiak, Javier Antonio Alfaro

 

Please refer to the README.md file for details.

License and Usage Notes—to be considered for commercial use

This dataset is a compilation of data from multiple sources. Some source data is shared under licenses that restrict commercial use or have other conditions. 

As a result, this compiled dataset is not licensed under a single open license.

You are responsible for reviewing and complying with the individual licenses of all source data before using aspects of the dataset that rely on them, especially for any commercial, redistributed, or derivative use.

A list of source datasets has been provided in the supplementary tables of the publication. 

The intention is to release the data as openly as possible according to the requirements of the European open data pilot. However, certain datasets and software licenses may be subject to additional restrictions such as commercial use. Hence we release the data as follows.

For Academic Non-Commercial Use:

This work is licensed under CC BY 4.0. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0.

For Commercial Use:

Our intent is to disseminate this work under the most open license practicable (e.g., Creative Commons Attribution 4.0 International License). Notwithstanding the foregoing, compliance with any applicable licenses, restrictions, or terms governing specific software or datasets, including but not limited to those applicable to individual columns or portions of the provided dataset, is exclusively the responsibility of the end-user.











 






Below is a listing of the type of licenses/acknowledgements/disclaimers to be considered when different aspects of the work are to be considered for commercial use.  



EMBL-EBI database—CC0 (no rights reserved) is preferred. However, it is possible to employ the EMBL-EBI Terms of Use in combination with more specific data licences.

GENCODE, BLAT, and KENT—for academic research, no license is required. For commercial purposes, a commercial license shall be purchased.

MASSIVE—for work released in public domain, the relevant one seems to be CC0 1.0 Universal (CC0 1.0).

COSMIC—no license required for academic use, however, a license required for commercial use—you can check  here which one you need based on your entity type and your purpose of use.

NMPD—license required for the latest frequency tables and updated manuscript tables, and figures. Open access license under CC BY-NC-ND license.

 NetMHCpan 4.1—license required for academic purposes (version 4.1 uses Creative Commons Attribution 4.0 International [CC BY 4.0] license). For commercial purposes, users are requested to contact the Software Package Manager at health-software@dtu.dk. 

GibbsCluster 2.0—license required: Creative Commons Attribution 4.0 International

LIFTOVER—custom license created by UCSC is required, which states that The Genome Browser source code in this directory and subdirectories are freely available for academic, nonprofit, and personal use. A license is required (needs to be purchased) for commercial download and installation of all software in this directory.

BLAT—BLAT is copyrighted by Jim Kent. License is granted for personal, academic, and non-profit purposes. However, commercial use is permitted only by explicit agreement with Jim Kent. See http://www.kentinformatics.com. This needs to be purchased for commercial purposes—full license text here from KentInformatics.

Cancer gene list from OncoKB—academic use is possible with the custom license, which must be registered for. Register for academic license: OncoKB™ is accessible for no fee for research use in an academic setting. This license type requires that you register your account using your institution/university email address. For commercial purposes, a license must be requested from OncoKB™. Here is a tool on their website to see what license you need for academic or commercial purposes.

SOPRANO—data published in an article in Nature—published under a Creative Commons Attribution 4.0 International License.

Open access publication in BRAUN PAPER 2020—open access articles in Nature Medicine are published under a CC BY-NC-ND (Creative Commons Attribution Non-Commercial No Derivatives 4.0 International licence) or CC BY (Creative Commons Attribution 4.0 International licence) licence.