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[bioontology-support] Query to get children.

Trish Whetzel whetzel at stanford.edu
Wed Aug 26 12:18:13 PDT 2009


Got it.

Misha, are there more details that are needed to get a time estimate to
implement this?

Trish

>-----Original Message-----
>From: maguire at ebi.ac.uk [mailto:maguire at ebi.ac.uk]
>Sent: Wednesday, August 26, 2009 12:05 PM
>To: Trish Whetzel
>Cc: 'Eamonn Maguire'; 'Michael Dorf'; support at bioontology.org
>Subject: RE: Query to get children.
>
>hi trish,
>
>the second case is the correct one :o)
>
>thanks,
>Eamonn
>
>> To clarify the request a bit further, would the parameter
>'searchBranch'
>> be
>> predefined terms in various ontologies? For example, the set of terms
>that
>> can be used to annotate various object models such as FuGE, MAGE-ML,
>etc.
>>
>> OR
>>
>> Would 'searchBranch' be a user-defined term and would be used to limit
>the
>> search space to only those terms that are children terms of the term
>> specified in 'searchBranch'?
>>
>>
>>
>> Trish
>>
>>
>>
>>
>>
>> From: Eamonn Maguire [mailto:maguire at ebi.ac.uk]
>> Sent: Friday, August 21, 2009 10:11 AM
>> To: Michael Dorf
>> Cc: 'Trish Whetzel'; support at bioontology.org
>> Subject: Re: Query to get children.
>>
>>
>>
>> Hi Michael,
>>
>>
>>
>> This is very useful.
>>
>>
>>
>> Coming back to the original feature request of adding an extra
>parameter
>> to
>> the search query to specify a branch to search under, how long do you
>> think
>> it will take before this feature is implemented? By the way, I'm happy
>to
>> contribute with the effort of doing it since any implementation I do
>now
>> will simply be replaced by whatever is created by you guys when the
>actual
>> ability to query under a branch is realised.
>>
>>
>>
>> Any code i write now will essentially take the result of the hierarchy
>> function and then filter for terms containing the string searched for
>by
>> the
>> user.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Eamonn
>>
>>
>>
>> On 20 Aug 2009, at 19:42, Michael Dorf wrote:
>>
>>
>>
>>
>>
>> Hi Eamonn,
>>
>>
>>
>> This is the correct URL to use:
>>
>>
>>
>> http://rest.bioontology.org/obs_hibernate/ontologies
>>
>>
>>
>> The complete list of OBS services is available here:
>>
>>
>>
>> http://rest.bioontology.org/test_obs.html
>>
>>
>>
>> The Hierarchy Services subsection of this page is the one you are
>> referencing from BioPortal. For example, the service
>>
>>
>>
>> http://rest.bioontology.org/obs_hibernate/parents/MSH/C0025202
>>
>>
>>
>> is also available as
>>
>>
>>
>> http://rest.bioontology.org/bioportal/concepts/parents/MSH/C0025202
>>
><http://rest.bioontology.org/bioportal/concepts/parents/MSH/C0025202%20>
>> in
>> a slightly different (more BioPortal-centric) XML format.
>>
>>
>>
>>
>>
>> Hope this helps.
>>
>>
>>
>> Misha
>>
>>
>>
>>
>>
>>
>>
>> From: Eamonn Maguire [mailto:maguire at ebi.ac.uk]
>> Sent: Thursday, August 20, 2009 9:39 AM
>> To: Trish Whetzel
>> Cc: Michael Dorf; support at bioontology.org
>> Subject: Re: Query to get children.
>>
>>
>>
>> I can't access it no.
>>
>>
>>
>> Eamonn
>>
>> On 20 Aug 2009, at 17:35, Trish Whetzel wrote:
>>
>>
>>
>>
>>
>>
>> The hierarchy services are currently geared towards certain versions
>of an
>> ontology, so 39885 is the version that has been processed to generate
>data
>> for the ontology hierarchy services. This version also includes the
>'efo:'
>> prefix for the term while the version 40394 does not.
>>
>>
>>
>> There is a service to call to get the list of ontologies that are used
>in
>> the ontology hierarchy service, however I have been having difficulty
>> accessing this from outside Stanford and trying to sort out the
>reason.
>> The
>> URL is: http://ncbo <http://ncbo/>
>> -obs-prod1:8080/obs_hibernate/ontologies.
>> Are you able to access this?
>>
>>
>>
>> Trish
>>
>>
>>
>>
>>
>> On Aug 20, 2009, at 9:13 AM, Eamonn Maguire wrote:
>>
>>
>>
>>
>>
>>
>> Hi trish et al :o)
>>
>>
>>
>> now, this is closer to what i need :o) i didn't realise this service
>was
>> available! if anything there is too much metadata associated with this
>> query
>> though. We'd only really metadata similar to that returned in
>bioportals
>> search function. For a large hierarchy, this file could be massive
>> particularly in an ontology with a hierarchy containing large numbers
>of
>> axioms. You'd essentially be returning a subset of the OWL file in a
>> differing XML format.
>>
>>
>>
>> however i see that the version of EFO you are making me query with is
>old.
>> Whenever i attempt to query with the latest version i get the same
>error
>> that i got yesterday when i reported the problems with the children
>query
>> returning a 'No child in hierarchy found' message.
>>
>>
>>
>>
>http://rest.bioontology.org/bioportal/concepts/children/40394/efo:EFO_00
>0035
>> 2
>>
>>
>>
>> or
>>
>>
>>
>>
>http://rest.bioontology.org/bioportal/concepts/40394/efo:EFO_0001456?ema
>il=e
>> xample at example.org
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Eamonn
>>
>>
>>
>>
>>
>> On 20 Aug 2009, at 16:49, Trish Whetzel wrote:
>>
>>
>>
>>
>>
>>
>> Hi Eamonn,
>>
>>
>>
>> The last I talked to the developers on the design of the bean from the
>> hierarchy services the information I received is that the hierarchy
>> service
>> needs to be used with the concept service, e.g.
>>
>http://rest.bioontology.org/bioportal/concepts/39885/efo:EFO_0000352?ema
>il=e
>> xample at example.org, to generate the additional term information.
>>
>>
>>
>> Misha, can you add more on this design decision and whether the
>preferred
>> term field can be added to the bean from the ontology hierarchy
>service?
>>
>>
>>
>> Thanks,
>>
>> Trish
>>
>>
>>
>>
>>
>> On Aug 20, 2009, at 3:58 AM, Eamonn Maguire wrote:
>>
>>
>>
>>
>>
>>
>> Thanks trish,
>>
>>
>>
>> So now my next question relates to the metadata. In the result from
>>
>http://rest.bioontology.org/bioportal/concepts/children/39885/efo:EFO_00
>0035
>> 2 we have a result which looks like this:
>>
>>
>>
>> <classBean>
>>
>>     <ontologyVersionId>39885</ontologyVersionId>
>>
>>     <id>efo:EFO_0000493</id>
>>
>>     <relations>
>>
>>         <entry>
>>
>>             <string>Level</string>
>>
>>             <int>1</int>
>>
>>         </entry>
>>
>>     </relations>
>>
>> </classBean>
>>
>>
>>
>> now, this doesn't give me much in terms of anything i can use straight
>> away.
>> can i request the addition of the concept name and concept short name
>like
>> you have in the main search result to avoid making many additional
>queries
>> to find out what EFO_0000493 actually is.
>>
>>
>>
>> For those of you in this email who don't know the use-case we want to
>> implement, i'll give you a quick overview.
>>
>>
>>
>> inside isacreator we offer people the choice of querying either a
>> recommended ontology (provided through a configuration tool) or to
>search
>> the whole ontology. the latter case is already fulfilled by BioPortal
>> obviously :o) in the case of querying a recommended ontology(ies) you
>also
>> have what we would need if we just wanted to query for terms matching
>> 'protocol' for example in OBI or EFO through supplying ontology ids.
>> However, what if i wanted to restrict the search space as well as the
>> ontology, meaning restricting the search to a certain part of one or
>more
>> ontologies. e.g., in EFO
>http://bioportal.bioontology.org/visualize/40394
>> when a search is made, only the terms under 'process (EFO_0001433)'
>should
>> be searched for.
>>
>>
>>
>> I have already requested via trish an extra parameter in BioPortals
>search
>> query to allow one to provide an ontology term id or unique name
>> (dependent
>> on the ontology being used) to restrict the search space to a
>particular
>> part of the ontology.
>>
>>
>>
>> the query would look like this:
>>
>>
>>
>>
>http://rest.bioontology.org/bioportal/search/protocol/?ontologyids=39885
>>
><http://rest.bioontology.org/bioportal/search/protocol/?ontologyids=3988
>5&se
>> archBranch=> &searchBranch=EFO_0001433
>>
>>
>>
>> not only would such a search be greatly advantageous to us, but it
>could
>> also speed up searches made by others on bioportal since the search
>space
>> is
>> restricted!
>>
>>
>>
>> i hope this is clear,
>>
>>
>>
>> thanks for all your great efforts thus far!!
>>
>>
>>
>> Eamonn
>>
>>
>>
>>
>>
>> On 19 Aug 2009, at 17:26, Trish Whetzel wrote:
>>
>>
>>
>>
>>
>>
>> There was a change in the identifiers for EFO a few versions back. The
>> change is that there was an extra 'efo' in the fully qualified term
>name.
>>
>>
>>
>> The term id in version 39885 is:
>> http://bioportal.bioontology.org/visualize/39885/efo:EFO_0000001
>>
>> The term id in version 40394 is:
>> http://bioportal.bioontology.org/visualize/40394/EFO_0000001
>>
>>
>>
>> So using
>>
>http://rest.bioontology.org/bioportal/virtual/children/1136/efo:EFO_0000
>352,
>> will get the child term of clinical history or
>>
>http://rest.bioontology.org/bioportal/concepts/children/39885/efo:EFO_00
>0035
>> 2 will work.
>>
>>
>>
>> Trish
>>
>>
>>
>>
>>
>>
>>
>> On Aug 19, 2009, at 6:16 AM, Eamonn Maguire wrote:
>>
>>
>>
>>
>>
>>
>> Hi Trish,
>>
>>
>>
>> Just a quick question.
>>
>>
>>
>> I'm having trouble getting the "Get parents/children of a given
>concept in
>> a
>> specific ontology version" query to work properly. For instance, I
>thought
>> that making the following queries should work, but they return a
>message
>> saying that no children exist in the hierarchy when they clearly do.
>>
>>
>http://rest.bioontology.org/bioportal/concepts/children/40394/EFO_000035
>2
>>
>>
>>
>> i get the same message using the virual ontology equivalent of this
>method
>>
>>
>http://rest.bioontology.org/bioportal/virtual/children/1136/EFO_0000352
>>
>>
>>
>> any ideas?
>>
>>
>>
>> thanks,
>>
>> Eamonn
>>
>> --
>>
>> *    maguire at ebi.ac.uk
>>
>> :     http://www.ebi.ac.uk/~maguire
>>
>> :     http://www.ebi.ac.uk/net-project
>>
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>> --
>>
>> *    maguire at ebi.ac.uk
>>
>> :     http://www.ebi.ac.uk/~maguire
>>
>> :     http://www.ebi.ac.uk/net-project
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>> --
>>
>> *        maguire at ebi.ac.uk
>>
>> :         http://www.ebi.ac.uk/~maguire
>>
>> :     http://www.ebi.ac.uk/net-project
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>> --
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>> *            maguire at ebi.ac.uk
>>
>> :             http://www.ebi.ac.uk/~maguire
>>
>> :     http://www.ebi.ac.uk/net-project
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>> --
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>> *          maguire at ebi.ac.uk
>>
>> :           http://www.ebi.ac.uk/~maguire
>>
>> :     http://www.ebi.ac.uk/net-project
>>
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