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
Wed Aug 26 12:04:49 PDT 2009


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_000035
> 2
>
>
>
> or
>
>
>
> http://rest.bioontology.org/bioportal/concepts/40394/efo:EFO_0001456?email=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?email=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_000035
> 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=39885&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_0000352,
> will get the child term of clinical history or
> http://rest.bioontology.org/bioportal/concepts/children/39885/efo:EFO_000035
> 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_0000352
>
>
>
> 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