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

Susanna-Assunta Sansone sansone at ebi.ac.uk
Wed Feb 24 02:44:30 PST 2010


Hi Natasha,

Eamonn is right, ref slow, but it is also true that we need to get the new
release out next month. Actually we have just submitted our first ISA
paper and we do refer to our use of BioPortal for accessing ontology
terms.

> Yes, we'll update the returned XML, but probably not immediately
Do you have any idea, when this can be done.

Thanks a lot in advance!!
Susanna


Eamonn Maguire wrote:
> Hi natasha,
>
> This is good! We probably won't release the new version of the
> configurator and creator with the new functionalities until this
> change in the service is made since it's simply too slow at the
> minute, although I have made it significantly faster by creating
> services which can make many asynchronous calls...still though, it's
> inefficient from our stand point and a possibly greater resource
> strain on the side of you guys.
>
> Let me know when you have this change in place, then we can get
> everything in place for release and have the branch queries in
> operation also! :)
>
> Thanks,
>
> Eamonn
>
> --
> Eamonn Maguire
> eamonnmag at gmail.com
> maguire at ebi.ac.uk
>
> On 24 Feb 2010, at 04:16, Natasha Noy <noy at stanford.edu> wrote:
>
>> 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/
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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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