On 26 January 2014 11:16, Egon Willighagen <egon.willighagen at gmail.com>wrote:

> On Sun, Jan 26, 2014 at 10:03 AM, Nina Jeliazkova
> <jeliazkova.nina at gmail.com> wrote:
> > On 26 January 2014 10:45, Egon Willighagen <egon.willighagen at gmail.com>
> > wrote:
> >> Does that make sense? Does something like this already exist?
> >
> > Yes :)
> >
> > Well, at least in AMBIT - was invented several months ago to handle
> links to
> > ToxBank wiki, ChEBI and COSMOS database (SEURAT cluster) as well as
> public
> > databases.
>
> What kind of links are these? That is not entire clear from me from
> the below examples...
>

owl:sameAs

Have a look at the N3

http://apps.ideaconsult.net:8080/ambit2/query/compound/search/allnlinks?search=http://apps.ideaconsult.net:8080/ambit2/compound/1&media=text/n3&page=0&pagesize=1


or JSON
http://apps.ideaconsult.net:8080/ambit2/query/compound/search/allnlinks?search=http://apps.ideaconsult.net:8080/ambit2/compound/1&media=application/json&page=0&pagesize=1



> > These are usual features, with sameAs values looking like these
> >
> > "sameAs":"http://www.opentox.org/api/dblinks#ChEBI",
> > "sameAs":"http://www.opentox.org/api/dblinks#Pubchem",
>
> How is this used? Can I see this in action somewhere?
>

It's currently used in Toxbank data warehouse dashboard and COSMOS client
accessing Toxbank DW . Both are under development and not open to the
public at the moment  :(



> It looks like these are sameAs relations for features, not
> compounds... also, in my immediate WikiPathways use case, it is not
> sameAs-like, but partOf-like... technically that should not matter,
> though...
>

Yes - this is a relation for features - and I would argue this is the
correct semantic for such links - the link is a feature which has the
meaning of let's say PubChem ID .  And the compound is assigned that
feature (i.e. the link to PubChem ID).

Nina


>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
>