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Re: HPO and Gene Ontology Licenses

From: Alison Callahan <alison.callahan@gmail.com>
Date: Wed, 8 Aug 2012 09:52:44 -0400
Message-ID: <CAPYDNm0xE=PLEUp+=X8GmJc8nc1eDoPHY_bSN9o+KoWgyKV8kg@mail.gmail.com>
To: peter.robinson@charite.de
Cc: bio2rdf@googlegroups.com, Peter Ansell <ansell.peter@gmail.com>, Chris Mungall <cjmungall@lbl.gov>, Michel Dumontier <michel.dumontier@gmail.com>, HCLS <public-semweb-lifesci@w3.org>
Hi Peter,

We have made a preliminary RDFization guide for Bio2RDF, available here:
http://github.com/bio2rdf/bio2rdf-scripts/wiki/RDFization-Guide-v1.0

This guide will give you a general idea of how we generate Bio2RDF URIs
when converting datasets to Bio2RDF linked data.

If you have any questions, please feel free to email the Bio2RDF mailing
list at bio2rdf@googlegroups.com.

Cheers,

Alison

On Wed, Aug 8, 2012 at 2:07 AM, Robinson, Peter
<peter.robinson@charite.de>wrote:

> Hi Peter,
>
> please do make some suggestions and or send me a link to some
> documentation.
>
> cheers 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 07:36
> An: Robinson, Peter
> Cc: Chris Mungall; Michel Dumontier; HCLS; bio2rdf
> Betreff: Re: HPO and Gene Ontology Licenses
>
> 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
>
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Received on Wednesday, 8 August 2012 22:25:02 GMT

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