Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Query to get children.

maguire at ebi.ac.uk maguire at ebi.ac.uk
Thu Aug 27 11:48:02 PDT 2009


I'll prepare a document detailing the usecase tomorrow! :o)

thanks,

Eamonn

> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> *        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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> *          maguire at ebi.ac.uk
>>>>
>>>> :           http://www.ebi.ac.uk/~maguire
>>>>
>>>> :     http://www.ebi.ac.uk/net-project
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>
>





More information about the bioontology-support mailing list