Policy

This page lays out the principles under which Lipidbook operates. In particular it defines how the data are licensed and how we deal with personal information stored in the database.

If you have any questions, concerns, or comments regarding this policy please contact one of the individuals listed in the Contacts section.

Preamble — striving for Open Knowledge

Scientific progress benefits from data that anyone can access, use, modify, and redistribute without encumberance, as spelt out in the Open Knowledge Definition.

Scientists tend to subscribe to this point of view as part of their common work ethos. However, to avoid any ambiguity, we are expressing clearly the legal status for each data set. (If you wonder if this is necessary you can read the Open Data Commons FAQ.)

Definition of terms

parameter files, parameters, data
In the following, parameter files or parameters means any user-deposited files that are published through this web site. Typically, these files contain topologies, force field parameter values, and coordinates. Uploaded files are stored without modifications in the Lipidbook database.
meta data
Meta data are user-supplied data other than files; this includes abstracts and comments.
package
A collection of parameter files for one molecule type in a specific force field and software file format is termed a package. A package is the unit in which parameters are deposited. A package also contains meta data.
curator
The curator of a package is the registered user who deposits the parameter files. Curators have exclusive write and editing access to their submitted files. Note that a curator does not have to be the author of the parameter files.
linked file, parameter URL
A linked file is a cached copy of a parameter file that is stored in the WebCite® archive. The link to the cached file and the original link and the date of archival are stored in the Lipidbook database but not the actual file, as described under Archival of links instead of files through WebCite.

Licensing of data

Parameter files

On deposition of parameter files, the curator must choose a licence for the data. If the curator does not have the authority to publish the data then they cannot upload the package.

A curator has the authority to publish the parameter files either because they own the copyright, or because they have obtained permission from the copyright holder, or because the data's licence grants this permission, or because they can claim a case of fair use, or for other reasons not listed here.

If the parameters were derived by the curator or if the curator is an author on the primary citation then they own the copyright on their work unless they explicitly transferred copyright. A copyright holder can freely choose a licence or decide to place the uploaded files into the public domain. Specifying a licence such as the Creative Commons Attribution-Share Alike Licence described below does not in any way compromise the copyright; the copyright holder is free to licence the same files to other parties under completely different terms.

If the parameter files are placed in the public domain (using, for instance, the PDDL as described below) then the rights holder relinquishes all rights (including copyright) irrevocably and the data become as free and open as legally possible.

Parameter files can only be downloaded from the site if

  1. the package has a licence associated with it
  2. the package contains a primary reference for any licence that requires a citation.

Lipidbook database and site

The Lipidbook database is made available under the Open Database Licence: http://opendatacommons.org/licenses/odbl/1.0/. Any rights in individual contents of the database are licensed as indicated by the individual package licences. All meta data (abstracts, comments, ...) are published under the Creative Commons Attribution-Share Alike Licence.

Lipidbook's static content (i.e. the text apart from user-supplied content as defined above and logos) is published under the Creative Commons Attribution Licence. It means you can use text and styles as long as you link back to lipidbook.bioch.ox.ac.uk.

Available Licenses

On deposition, the curator can either choose a licence that conforms to the Open Knowledge Definition or assert fair use for the use of the data. Fair use is not a licence but indicates cases when the curator cannot obtain proper clearance from the copyright holder but is confident that the parameters (or links to the parameter files) can be published on Lipidbook anyway.

Public Domain Open Knowledge
The Open Data Commons Public Domain Dedication and License (PDDL) places your data into the public domain and ensures that it becomes open knowledge. Once you do this, no-one (including you) can license this work again. As a matter of academic courtesy it is expected that the work will be attributed to you but this is not a legal requirement.
cc-by-sa Open Knowledge
The Creative Commons Attribution-Share Alike (cc-by-sa) Licence allows anyone to use, modify, and distribute your work, provided they attribute it to you (e.g. by citing you) and if they distribute it they must do so under the same or a compatible licence.
(c)
If the licencing status is not clear but if you are confident that deposition of the data falls under fair use or fair dealing (in particular see 6.i Research and private study) then you can deposit them; however, the copyright holders can have the data removed at any time by contacting the operators or they can licence the data under one of the other licences. When depositing under fair use then you must make sure that there is some reference to the original author(s).
A typical example of fair use is the case when parameters have been taken from a printed publication and translated into a machine-readable file.

Attribution and citations

Cite the authors of the parameters that you are using! The appropriate citation can be found in the file citations.txt that is included in each package. Also check the description and the abstract of the package for further relevant citations.

Any parameter set that has been released under a Attribution-Share Alike Licence or under fair use requires attribution to the original author (not the curator!). If you do not cite the original author then you cannot use these data in your work.

We also ask you to acknowledge Lipidbook in any publication in which you use parameters obtained through our site, citing

J. Domański, P. Stansfeld, M.S.P. Sansom, and O. Beckstein. Lipidbook: A Public Repository for Force Field Parameters Used in Membrane Simulations. J. Membrane Biol. 236 (2010), 255—258. doi:10.1007/s00232-010-9296-8. URL:http://lipidbook.bioch.ox.ac.uk

preprint (pdf)

Thank you.

Names and e-mail addresses

Names and e-mail addresses are required for depositing data. This is the only way that one can link a curator to a real person. In order to ensure that data is not deposited in someone else's name we have to ensure that the address is valid.

The full name of the curator is shown for each package owned by this person. The e-mail address is not shown. (In the future we might implement a private mail feature through which short notes can be sent to a curator or a e-mail notification system when comments are posted on a package. By default we will not send e-mail from Lipidbook and have the user opt-in into any kinds of communications.) The operators will contact a curator if there are questions about the licensing of the parameters or other exceptional circumstances.

Names and e-mail addresses of persons who granted permission to include and licence a package on lipidbook are stored in the database but are not publicly visible.

We will not pass on your personal data to any other parties or use them for any other purpose than set out here.