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[bioontology-support] Query to get children.

Trish Whetzel whetzel at stanford.edu
Thu Aug 27 11:41:02 PDT 2009


Misha, do you mean UI from BioPortal or UI from the ISAcreator tool?

Eamonn, can you provide these additional details?

Thanks,
Trish

>-----Original Message-----
>From: Michael Dorf [mailto:mdorf at stanford.edu]
>Sent: Thursday, August 27, 2009 10:26 AM
>To: 'Trish Whetzel'; maguire at ebi.ac.uk
>Cc: support at bioontology.org; 'Natasha Noy'
>Subject: RE: Query to get children.
>
>Hi Trish,
>
>It would help to get a better picture of what type of UI workflow this
>additional feature would require.  What would one need to do (type in,
>select from a dropdown etc.) to have the search narrowed to a specific
>branch.  I presume the user would need to know the exact name of the
>concept that will serve as the top of the tree. Would the user just type
>it into a textbox? Will the search include sibling concepts and their
>sub-trees? What happens if the user-entered concept doesn't exist?
>Would
>we expect a full-concept including the namespace or a short one?
>
>In short, I do need more detailed requirements to produce an estimate.
>A
>couple of use-cases with success and exception scenarios would be ideal.
>
>Thanks!
>
>Misha
>
>
>
>-----Original Message-----
>From: Trish Whetzel [mailto:whetzel at stanford.edu]
>Sent: Wednesday, August 26, 2009 12:18 PM
>To: maguire at ebi.ac.uk
>Cc: 'Michael Dorf'; support at bioontology.org
>Subject: RE: Query to get children.
>
>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_0
>0
>>0035
>>> 2
>>>
>>>
>>>
>>> or
>>>
>>>
>>>
>>>
>>http://rest.bioontology.org/bioportal/concepts/40394/efo:EFO_0001456?em
>a
>>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?em
>a
>>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_0
>0
>>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=3988
>5
>>>
>><http://rest.bioontology.org/bioportal/search/protocol/?ontologyids=398
>8
>>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_000
>0
>>352,
>>> will get the child term of clinical history or
>>>
>>http://rest.bioontology.org/bioportal/concepts/children/39885/efo:EFO_0
>0
>>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_00003
>5
>>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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> *    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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>>>
>>>
>>>
>>>
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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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>>>
>>>
>>> --
>>>
>>> *          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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