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Re: HPO and Gene Ontology Licenses

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Wed, 8 Aug 2012 12:12:02 -0400
Message-ID: <CALcEXf46AanZY10mJC3DqswN0UBeu7WWTc6rO1qN0KVXeB4FZQ@mail.gmail.com>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Cc: Peter Ansell <ansell.peter@gmail.com>, "Robinson, Peter" <peter.robinson@charite.de>, Chris Mungall <cjmungall@lbl.gov>, HCLS <public-semweb-lifesci@w3.org>, bio2rdf <bio2rdf@googlegroups.com>
Hi Alan,


On Wed, Aug 8, 2012 at 10:00 AM, 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.
>
>
We certainly welcome the adoption of standard licenses for OBO ontologies.



> 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.
>

Not sure what you mean by "unsyntactic". The objective here would be to
provide an RDF and SPARQL friendly version of OBO ontologies. It would
reduce the ontological commitment to RDF, so in this sense, it would be a
semantic loss, but makes it easier to retrieve relations between entities.
 We could always provided links to OWL versions, if they are available.


>
> 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
>
>
does the OBO Foundry automatically check conformance?  Is there a report
page for each ontology?




> 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 know about berkeley's download page -

http://www.berkeleybop.org/ontologies/

is this what you are referring to?



> 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.
>
> For more information about OBO efforts in this area, please see
> http://code.google.com/p/oboformat/  and
> http://code.google.com/p/owltools/
>
> -Alan
>
>
I don't see RDF or SPARQL endpoints being provided at either of those links.


m.


> On Wed, Aug 8, 2012 at 1:36 AM, Peter Ansell <ansell.peter@gmail.com>
> wrote:
> > Hi Peter,
> >
> > I understand completely. The usage policy is very liberal in terms of
> > distribution and we are glad for that!
> >
> > Would it be possible for us (Michel and I) to make suggestions with
> > the goal of publishing a version that matches the no-blank-node policy
> > that Bio2RDF attempts to follow and uses URIs structures that can
> > resolve using http://bio2rdf.org/. We don't want to make material
> > changes to any of the terms but we would like to make the resulting
> > RDF graph browsable as Linked Data, as far as possible. To enable that
> > we need to directly resolve URIs for items to their definitions, by
> > replacing fragment/hash identifiers with
> > http://bio2rdf.org/ns:identifier equivalents, for example.
> >
> > Thanks,
> >
> > Peter Ansell
> >
> > On 8 August 2012 15:20, Robinson, Peter <peter.robinson@charite.de>
> wrote:
> >> Hi Peter,
> >>
> >> given that the HPO is being used by medical groups for real patient
> data, we think it is potentially dangerous to allow external groups to
> change the data and present it elsewhere, given some of the notorious
> difficulties in actually understanding what some medical terms mean (even
> for us MDs).  This was the reason for the license statement, which other
> than that is quite liberal. However, we would be happy to work with you to
> find a solution, which could forsee us providing RDF on our website which
> you could import.
> >>
> >> BW Peter
> >>
> >>
> >>
> >>
> >>
> >> PD Dr. med. Peter N. Robinson, MSc.
> >> Institut für Medizinische Genetik und Humangenetik
> >> Charité - Universitätsmedizin Berlin
> >> Augustenburger Platz 1
> >> 13353 Berlin
> >> Germany
> >> +4930 450566006
> >> Mobile: 0160 93769872
> >> peter.robinson@charite.de
> >> http://compbio.charite.de
> >> http://www.human-phenotype-ontology.org
> >> Introduction to Bio-Ontologies:
> http://www.crcpress.com/product/isbn/9781439836651
> >> ________________________________________
> >> Von: Peter Ansell [ansell.peter@gmail.com]
> >> Gesendet: Mittwoch, 8. August 2012 03:03
> >> An: Chris Mungall
> >> Cc: Michel Dumontier; HCLS; bio2rdf; Robinson, Peter
> >> Betreff: HPO and Gene Ontology Licenses
> >>
> >> 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
> >
>



-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
Received on Wednesday, 8 August 2012 16:12:52 GMT

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