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[bioontology-support] Query to get children.

Trish Whetzel whetzel at stanford.edu
Wed Aug 26 11:24:05 PDT 2009


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

 

 

 

 

 

 

 

 

 

 

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