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[bioontology-support] XSD for hierarchy services...

Natasha Noy noy at stanford.edu
Tue Feb 23 20:16:48 PST 2010


Hi Eamonn,

Yes, we'll update the returned XML, but probably not immediately  
(since it is not a one-line change -- we need to put the reference to  
the XSD only in specific types of responses, etc.).

As for your second request -- yes, this has come up before. And it  
seems that on our side, now is a good time to get this added. We'll  
try to get the beans in the hierarchy services to have all the key  
information that the beans from other services contain: fullID, label,  
synonyms, definition. So, hopefully soon you won't have to call all  
those multiple services. Watch this space :)

Natasha


On Feb 21, 2010, at 1:56 AM, Eamonn Maguire wrote:

> Hi Natasha et al :),
>
> Cool, but the XML served from the bioportal web services will need  
> to be changed for addition of the xml name space: xmlns="http://bioontology.org/bioportal/classBeanSchema# 
> "
>
> Also, do you know if it will be possible and quick to add the full  
> id and label to the result of the hierarchy queries? :) At the  
> minute I have to do a separate query for each term in an ontology  
> tree (to provide the browsing functionality) and it's quite slow  
> (and very inefficient) even though I have written code to do  
> multiple downloads in parallel so as to quicken things up a bit!
>
> Thanks,
>
> I'll post the other XSDs for the other services soon too, this week  
> is very busy for me but I should send them next week :)
>
> Thanks and have a nice Sunday! :)
>
> Eamonn
>
> On 21 February 2010 06:20, Natasha Noy <noy at stanford.edu> wrote:
> Eamonn,
>
> Thanks a lot! I've added it to the wiki page (http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#XML_Schema_Definitions_for_the_REST_services 
> )
>
> If you have any updates, we'll be happy to post them and we'll try  
> to maintain and update it as well if the format of the service  
> results changes.
>
> Thanks a lot again!
>
> Natasha
>
>
> On Feb 18, 2010, at 12:28 PM, Eamonn Maguire wrote:
>
> Hi all,
>
> So I've been working on the schema and other bioportal xml  
> processing stuff a bit today and I've attached an XSD which I think  
> works pretty well for the services described below at least...
>
> root concepts for an ontology: http://rest.bioontology.org/bioportal/concepts/40832/root
> term information: http://rest.bioontology.org/bioportal/concepts/40832/snap:IndependentContinuant
> children/parents of a node: http://rest.bioontology.org/bioportal/concepts/parents/40832/snap:Continuant?level=1
>
> and anything with the following xml structure:
>
> <success xmlns="http://bioontology.org/bioportal/classBeanSchema#">
>  <accessedResource>/bioportal/concepts/40832/root</accessedResource>
>  <accessDate>2010-02-18 11:33:38.731 PST</accessDate>
>  <data>
>    <classBean/>
>    <list/>
>  </data>
> </success>
>
> I have code which inserts the name space into the xml file returned  
> from the webservice as well, but it would obviously be good if you  
> guys could do this automatically.
>
> I will create XSD for the other services as soon as I can, but this  
> was my priority today. I will probably generalise this schema more  
> if I find that some results don't process properly, but i've put it  
> through a lot of files and it has worked well so far!
>
> <xsd_schema_classBean.xsd>
>
>
>
>
>
> Eamonn Maguire
> Software Engineer - NET Project
> http://www.ebi.ac.uk/~maguire
> http://ebiinterfaces.wordpress.com/
>
>
>
>
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>
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>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
> -- 
> Eamonn Maguire
>
> maguire at ebi.ac.uk
> eamonnmag at gmail.com
>
> http://www.ebi.ac.uk/~maguire




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