Hi Egon,

On 26 January 2014 10:45, Egon Willighagen <egon.willighagen at gmail.com>wrote:

> Nina, others,
>
> how can I get links out in OpenTox/AMBIT for structures, preferably
> Linked Data style?
>
> What I am thinking of is the SD file WikiPathways, which we had a
> first go on last week. But I want to have links to the matching
> WikiPathways pages. Some metabolites have multiple pathways in which
> they are involved, some many, such as ATP...
>
> So, OpenTox already is Link*able* Data itself (each compound has a
> URI) that is even dereferencable (the URI returns RDF), but how can we
> get it to make links out, OpenTox being a node in a Linked Data
> network... Is this functionality already existing (if not, let's make
> this a proposal)?
>
> At a SD file level, I was thinking of providing these links with
> predicates as property fields:
>
> > <http://www.w3.org/2000/01/rdf-schema#seeAlso>
> http://www.wikipathways.org/index.php/Pathway:WP1034
>
> Or if there are multiple:
>
> > <http://www.w3.org/2000/01/rdf-schema#seeAlso>
> http://www.wikipathways.org/index.php/Pathway:WP1034
> http://www.wikipathways.org/index.php/Pathway:WP245
> http://www.wikipathways.org/index.php/Pathway:WP1
>
> So, it nothing exists, my proposal is to make a few URIs "special"
> features in OpenTox, in that they define a Linked Data network, and in
> that are expected to be handled slightly different... at least, not
> like a label/name or a LogP value...
>
> In particular, I want to see them as clickable links.
>
> 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.



> How
> should the OpenTox API do this?
>

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",
"sameAs":"http://www.opentox.org/api/dblinks#ChEMBL",
"sameAs":"http://www.opentox.org/api/dblinks#ChemSpider",
"sameAs":"http://www.opentox.org/api/dblinks#CMS",
"sameAs":"http://www.opentox.org/api/dblinks#ToxbankWiki",

Is this what you have in mind?  Inventing a type for WikiPathways would be
straightforward.

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
>