Rephetio: Repurposing drugs on a hetnet [rephetio]

Uncovering disease-disease relationships through the incomplete interactome

Incomplete Interactome licensing

Our protein interaction catalog includes data from the supplementary material of the Incomplete Interactome publication [1]. Specifically, we incorporate a subset of DataS1_interactome.tsv.

The License to Publish agreement for Science, which authors must sign, states that:

In consideration of publication by AAAS in one of its Science journals of the work currently titled [title] and all associated supplemental materials, data, audio and/or video files (the "Work") and authored by [author] ("Author"), the sole and exclusive, irrevocable right is hereby granted to AAAS to publish, reproduce, distribute, transmit, display, store, translate, create derivative works from and otherwise use the Work in any form, manner, format, or medium, whether now known or hereafter developed, throughout the world and in any language, for the entire duration of any such right and any renewal or extension thereof and to permit/sublicense others to do any or all of the foregoing as well.

I bolded the relevant phrases that lead me to believe that we require the permission of the AAAS rather than the dataset authors. Science's reprints and permissions page suggested using the Copyright Clearance Center's Rightslink service. I made an account, but my request was not supported by Rightslink. Therefore, I emailed the AAAS Permissions Department with my special request. This is our first request to a publisher regarding supplementary data. The email is below.

Dear AAAS Permissions Department,

I am a graduate student at UCSF, and I have been using supplementary data from Menche et. al 2015 for my research. My project aims to predict new uses for existing drugs by integrating many different types of biomedical information. Recently, the issue of database copyright and licensing came up, and we are now trying to ensure that we have sufficient permissions for each of the 28 databases we're integrating.

Currently, several resources I have created may be non-compliant with your terms.

My GitHub repository (dhimmel/ppi) contains:

My GitHub repository (dhimmel/integrate) for integrating many resources into a single network contains:

  • a subset of the protein interactions from the supplement stored as network nodes and edges.

@leobrueggeman assisted with parts of the analysis. His GitHub repository (LABrueggs/incomplete-interactome) contains:

  • datasets of disease names derived from the supplement

The public availability of the aforementioned resources is important so others can reproduce and build off of our work. Thus, we request permission for our aforementioned redistribution and derivative works of the publication's supplemental data. Ideally, we could be granted permission to release the supplemental data under a Creative Commons license without a No Derivatives restriction. Applying a CC license would lessen the burden on downstream users.

Thanks for your consideration. Our research is academic in nature, and we suspect it falls under the intended use of supplemental materials but perhaps not your terms and conditions.

Finally, we're performing our project using an open science platform called Thinklab. I've posted a copy of this email on Thinklab and will update the discussion with our progress. Alternatively, feel free to respond via Thinklab rather than email. By detailing each step of our research process publicly, we're hoping to create a valuable resource and explore a more holistic and collaborative medium of publication.

Daniel Himmelstein
Graduate Student
University of California, San Francisco

Emilie David — Assistant Director, Copyright, Licensing and Special Projects at AAAS — responded to our request. She indicated that AAAS does not generally allow Science content to be republished under Creative Commons licenses. However for Supporting Online Materials, authors are able to authorize use.

I looked deeper into the License to Publish and found the relevant section:

Author also retains the non-exclusive right to use the Work in the following ways without further permission but only after publication of the Work by AAAS and subject to the requirement that credit be given to its first publication in the appropriate issue of the applicable Science journal:

9) Author may use or authorize use of Supporting Online Material associated with the Work for any purpose and in any format.

Thus, we will proceed by requesting permission from the authors.

Author permission

Yesterday, I emailed the authors, and first author, Jörg Menche, promptly responded.

He indicated that they published the supporting data with the hope that others would find it useful. As far as they're concerned, we are free to use it anyway we like.

He also mentioned that they compiled their interactions from a variety of resources (as discussed here). Jörg was unsure whether this placed any restrictions on the downstream use of their dataset.

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Status: Completed
Referenced by
Cite this as
Daniel Himmelstein (2015) Incomplete Interactome licensing. Thinklab. doi:10.15363/thinklab.d111

Creative Commons License