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[bioontology-support] Contact from Linked AI

Paea LePendu plependu at stanford.edu
Fri Apr 23 16:56:38 PDT 2010


Hi Stefano.

Great to hear from you!  I hope all is well.

I am going to cc: the support list so the issue you list gets in the queue:

> http://bioportal.bioontology.org/search?q=PRO:000003035
>
> Unfortunately it seems that the REST interface remembers the previous search
> and does not really use the q= parameter, maybe something bioportal wants to
> correct?

I am glad that you've been able to use the BioPortal services to
enhance your plugins.  But, I am not sure what you mean by the
following:

> is not really suited to integrate extractor that also provide ids (the
> plugin was designed to use two steps, first extract the entities and then
> query a repository to get their ids).

Can you tell me a little more about that?

Paea


On Fri, Apr 23, 2010 at 7:47 AM, Stefano Bocconi
<stefano.bocconi at gmail.com> wrote:
> Hallo Paea,
>
> It was very nice meeting you too! I was aware of the Biolit plugin, and I
> had it installed on my machine, but I had forgotten it was linked to
> Bioportal services (indeed the name Microsoft was overwhelming other
> technologies). I also met and chatted with Lynn at a conference, when she
> told me that the Biolit project was finished for USCD although it is still
> an open source project.
>
> I am writing to you since I just finished integrating the bioportal services
> in our Word plugin. It works pretty well, although the design of our plugin
> is not really suited to integrate extractor that also provide ids (the
> plugin was designed to use two steps, first extract the entities and then
> query a repository to get their ids).
>
> One nice thing that I can do with the plugin is that I retrieve the id from
> bioportal, for example PRO:000003035 for p53, and I link this to info on
> line. For example, for Uniprot I am able from the identifier such as Q9TUB2
> to provide a link to http://www.uniprot.org/uniprot/Q9TUB2.
>
> For bioportal I use the search page http://bioportal.bioontology.org/search
> with a REST interface:
>
> http://bioportal.bioontology.org/search?q=PRO:000003035
>
>
> Unfortunately it seems that the REST interface remembers the previous search
> and does not really use the q= parameter, maybe something bioportal wants to
> correct?
>
> Thanks,
>
>   Stefano



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