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Re: HPO and Gene Ontology Licenses

From: Peter Ansell <ansell.peter@gmail.com>
Date: Thu, 9 Aug 2012 10:28:29 +1000
Message-ID: <CAGYFOCQOdxiy9MwDK8_NEBM8T1R43cECVmKm-PXxhab+ugY7sg@mail.gmail.com>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Cc: "Robinson, Peter" <peter.robinson@charite.de>, Chris Mungall <cjmungall@lbl.gov>, Michel Dumontier <michel.dumontier@gmail.com>, HCLS <public-semweb-lifesci@w3.org>, bio2rdf <bio2rdf@googlegroups.com>
On 9 August 2012 00:00, Alan Ruttenberg <alanruttenberg@gmail.com> wrote:
> We have discussed that the OBO Foundry policy is to use CC0 or CC-BY
> and it has been put to the GO that we would like to migrate to that
> license. I don't know the status of that discussion.

Was there a discussion of the merits of CC-BY-SA as a possible license?

> That said, I would be strongly discouraging of (but unable to prevent)
> any "no-blank-node" rendering of GO ontologies, and in particular
> would note that such a transformation would render any OWL we publish
> unsyntactic.

I have always been intrigued as to why OWL was designed to make it
syntactically incorrect to give URIs to restrictions etc. What was the
background behind this choice?

> Further, the OBO ID Policy has been, for the most part, been put in
> place and we do not use hash URIs and are moving to having all OBO
> URIs resolving to page per view. See for example
> http://purl.obolibrary.org/obo/IAO_0000032

That is a great step! Along with blank nodes and annotating resources
with known links in the Linked Data sphere, resolvable URIs are the
main goals of Bio2RDF.

> So the Foundry is already in the process of making all of the OBO
> available as linked ontology data. I would suggest other groups join
> this effort rather than setting out to duplicate and add confusion by
> having a parallel set of identifiers for the same set of entities.

I think you and I have always had a difference of opinion about the
relative benefits and difficulties of a non-unique URI Linked Data
sphere. It is great to have a freely accepted single effort on a
single goal, but disjoint communities need to be Free/Open to explore
other value-added options in my opinion. Where we know another URI for
an item Bio2RDF always attempts to refer back to it in some
semantically useful way.

> In fact, there have been a number of OBO participants who prefer the
> the current GO license precisely because it prevents this kind of
> duplicative, confusing practice, a practice that is discouraged even
> by the W3C standards these groups are chartered to work with.

It may be useful while communities are active to synchronise efforts,
but as soon as a community becomes inactive the locked down artifacts
it produced are unable to be revived. In addition, if the community
legitimately has a fundamental disagreement, then there may only be
one possible winner if the data is not Open, which may not be the best
thing in evolutionary terms. Even inside of an organisation as active
as OBO, the community around a particular ontology might become
inactive and discourage people from either contributing suggestions,
or worse, ignore suggestions by not responding, leading eventually to
a completely new effort--with the huge startup costs attached to that
process--*if* the ontology cannot be forked.

I would prefer that there was another method used by GO to encourage
the use of a single definitive source, without requiring it. For
example, one alternative may be to using trademarks to prevent
redistribution under the same or similar names, but not preventing
forking if it becomes necessary due to inactivity or other legitimate
reasons that are not known at the current time.

It would also be nice to have people submit their license terms to
BioPortal, in particular, (if possible in a similar way to when OBO
has a standard across the board of either CC0 or CC-BY/CC-BY-SA) so
people don't have to go fishing to find them. It would also be nice if
people avoided describing things as Open when their intentions are
incompatible with the generally accepted principles of Open'ness in
terms of Open Source [1] and Open Data [2]. Trademarking is designed
to prevent this duplicity/confusion--which noone desires--without
impeding on either copyright or Open/copyleft principles.

Cheers,

Peter

[1] http://opensource.org/docs/osd
[2] http://opendefinition.org/okd/
Received on Thursday, 9 August 2012 00:28:57 GMT

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