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HPO and Gene Ontology Licenses

From: Peter Ansell <ansell.peter@gmail.com>
Date: Wed, 8 Aug 2012 11:03:08 +1000
Message-ID: <CAGYFOCSWj6yqS6dNVxL=woQry+tQMVKktHe4Tp9dLrf-WF86jQ@mail.gmail.com>
To: Chris Mungall <cjmungall@lbl.gov>
Cc: Michel Dumontier <michel.dumontier@gmail.com>, HCLS <public-semweb-lifesci@w3.org>, bio2rdf <bio2rdf@googlegroups.com>, Peter Robinson <peter.robinson@charite.de>
On 8 August 2012 02:46, Chris Mungall <cjmungall@lbl.gov> wrote:
> Hi Michael
>
> I can't seem to connect to the triplestore.
>
> Have you considered adding associations between OMIM and phenotype ontology
> classes? These can be downloaded from
> http://www.human-phenotype-ontology.org/ as tab delimited files that can
> trivially be converted to an rdf model of choice (we will be providing OWL
> for this ourselves in the future, it will likely differ in modeling and URIs
> from bio2rdf).

The HPO files cannot be modified though given the following license condition:

"That neither the content of the HPO file(s) nor the logical
relationships embedded within the HPO file(s) be altered in any way."
[1]

in the same way that Gene Ontology files cannot be legally modifed
using a very similar license condition:

"That neither the content of the GO file(s) nor the logical
relationships embedded within the GO file(s) be altered in any way."
[2]

Therefore Bio2RDF should not be converting the HPO classes to RDF
ourselves, and I doubt that it is legal for anyone including Bio2RDF
to do so for Gene Ontology either.

I understand that ontology authors want to avoid confusion by avoiding
having multiple possibly inconsistent versions of an ontology
available from different locations under the same name.

However, as a consequence Bio2RDF and other Linked Data providers
really should not be republishing these and other ontologies that are
released under similar conditions, as we require the ability to change
the URIs and convert blank nodes to Bio2RDF URIs to make them
available as Linked Data for reuse and possibly modification by any
downstream user.

I went though doing a quick evaluation of the openness of bioportal
ontologies on The DataHub [3] recently and found very few that
actually provide any license statement on their websites, for those
that provide current websites. Since HPO and GO both clearly define
their licenses I switched them from Open Data to Not open data, as
they fail the Reuse condition in the Open Data Definition [4].  In
addition, any license incorporating an "academic-only" or
"non-commercial" clause fails the other clauses in the Open Data
Definition. It is not clear why bioportal [5] has loaded all of the
bioportal ontologies into The DataHub as if they are all "Open Data
with unknown conditions", by default, as bioportal does not seem to
internally verify the openness of any of the ontologies it provides
for download.

Peter

[1] http://www.human-phenotype-ontology.org/contao/index.php/legal-issues.html
[2] http://www.geneontology.org/GO.cite.shtml
[3] http://thedatahub.org/group/bioportal
[4] http://opendefinition.org/okd/
[5] http://thedatahub.org/user/bioportal
Received on Wednesday, 8 August 2012 01:03:36 GMT

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