Which Bioinformatics Databases Are Available Under The Panton Principles?

Question

[Egon Willighagen]

The Panton Principles describe the notion that facts are not copyrightable, and suggests to formalize the public domain idea, by using formal waivers like CC0 or PDDL. This Open nature is particularly important for remixing of facts, something scientists do all the time.

Do bioinformatics databases exist that use the CC0 of PDDL license, and when did they start using that license (if known)?

[Blunders]

@Egon Willighagen: Facts are not copyrightable, but a collection of facts is, and more over by default the creation of a item that falls under the jurisdiction of copyright law gives it copyright protect; though that does not in itself provide a solid grounds for defending the copyrights related to said collection.

[Blunders]

@Egon Willighagen: Facts are not copyrightable, but a collection of facts are, and more over by default the creation of a item that falls under the jurisdiction of copyright law gives it copyright protect; though that does not in itself provide a solid grounds for defending the copyrights related to said collection.

[Egon Willighagen]

Indeed, and this is why CC0 and PDDL waivers exists.

Answer 1

[Neilfws]

I don't think that the vast majority of biological data providers have given very much thought to licensing at all, except to add a clause along the lines of "free for non-commercial use."

A quick survey by Google search:

• bioinformatics+database+panton+principles - nothing relevant
• bioinformatics+database+cc0 - nothing relevant
• bioinformatics+database+creative+commons - a few mentions, such as ChEMBL (which is BY-SA 3.0)

It's worth remembering that the debate around licensing is very recent, compared with the age of many "legacy" databases (legacy in the sense that they were designed as long ago as the 1970s, in the case of the PDB). Not to say that this "excuses" providers from being aware of licensing. However, it does seem to be one of those issues about which some people care very passionately, but of which a much larger group (i.e. most people) are completely unaware.

[Neilfws]

In that case the answer is "none that I know of."

[Egon Willighagen]

Well, yes, I know there is a lot that is not available under those terms... but that's not the point of my question ;)

Answer 2

[Cameron Neylon]

The obvious place to go would be NCBI, which as a US government operation is by default in the public domain. If you look at the copyright statement (bottom left at http://ncbi.nlm.nih.gov) and scroll down a litle you will find:

[?] Molecular Database Availability

Databases of molecular data on the NCBI Web site include such examples as nucleotide sequences (GenBank), protein sequences, macromolecular structures, molecular variation, gene expression, and mapping data. They are designed to provide and encourage access within the scientific community to sources of current and comprehensive information. Therefore, NCBI itself places no restrictions on the use or distribution of the data contained therein. Nor do we accept data when the submitter has requested restrictions on reuse or redistribution. However, some submitters of the original data (or the country of origin of such data) may claim patent, copyright, or other intellectual property rights in all or a portion of the data (that has been submitted). NCBI is not in a position to assess the validity of such claims and since there is no transfer or rights from submitters to NCBI, NCBI has no rights to transfer to a third party. Therefore, NCBI cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in the molecular databases.[?]

Now in practice NCBI has refused data with restrictions imposed on it. The HapMap project was an example of this where they tried to impose a restriction that no-one could patent results. So in a sense it is technically Panton Compliant, and I believe in practice as well. But this isn't as explicit and clear as we were really looking for when we drafted the principles. Nor is it prominent.

One thing we should do is list Panton Compliant data sources on the website. I'm not sure that pointing at CKAN per se is in and of itself particularly helpful.

[Blunders]

@Cameron Neylon: "The obvious place to go would be NCBI, which as a US government operation is by default in the public domain" this is a misleading statement, since the information in question was not produced by the US Federal Government employees, which is a requirement for that statement to be true, among other factors. NCBI has no rights other than to publicly host the data, beyond that, it is your responsibility to secure any and all rights of use to the data.

Answer 3

[User 59]

The Panton Principles FAQ "Where can I see examples of Open Data?" points to a single PDDL resource, for crystallography "CrystalEye" but also also mentions CKAN (Comprehensive Knowledge Archive Network) but neither the bioinformatics section nor the biology section seem to have anything under PDDL. Lots are CC-SA however.

[Egon Willighagen]

Indeed... in the Chemistry Section there are a few CCO resources, and was therefore wondering about uptake in the biosciences...