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[bioontology-support] Query to get children.

Michael Dorf mdorf at stanford.edu
Thu Aug 20 11:42:54 PDT 2009


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_0000
352

 

or 

 

http://rest.bioontology.org/bioportal/concepts/40394/efo:EFO_0001456?email
=example 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
=example 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_0000
352 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&
searchBranch=> &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_000035
2, will get the child term of clinical history or
http://rest.bioontology.org/bioportal/concepts/children/39885/efo:EFO_0000
352 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

 

 

 

 

 

 

 

 

 

 

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