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[bioontology-support] get tree of a given class via REST interface

Lorenz B. buehmann at informatik.uni-leipzig.de
Tue Mar 15 00:47:14 PDT 2016


Hello Jennifer,

ah, great. Now I understand. This is exactly what I was looking for. 
Thank you very much.


Kind regards,
Lorenz

> Hello Lorenz,
>
> The /ontologies/:ontology/classes/:cls/tree call returns the tree 
> structure for the given :cls object.  In other words, you’ll get a 
> path to the root from the :cls object you designate (as well as 
> sibling classes in the structure).
>
> In your examples below, you used the “Physical object” (ID: 
> http://purl.bioontology.org/ontology/SNOMEDCT/260787004 
> <http://purl.bioontology.org/ontology/SNOMEDCT/260787004>) and 
> “Clinical finding” (ID: 
> http://purl.bioontology.org/ontology/SNOMEDCT/404684003) classes. 
>  Both of these classes are top-level classes in the SNOMEDCT 
> hierarchy.  So, there isn’t any tree structure to return here, other 
> than the sibling classes at the root of the ontology, i.e. for 
> Physical object the structure is:
>
> |-- Body structure
> |-- Clinical finding
> |-- Environment or geographical location
> |-- Event
> |-- Observable entity
> |-- Organism
> |-- Pharmaceutical / biologic product
> |-- Physical force
> |-- Physical object
> |-- etc…
>
> If your example had used a class further down the hierarchy such as 
> “Industrial transport vehicle” (ID: 
> http://purl.bioontology.org/ontology/SNOMEDCT/705447007), e.g.:
>
> http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F705447007/tree 
> <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/705447007/tree>
>
> … the results contain the tree structure for this class, i.e., the 
> path to root and sibling classes:
>
> |-- Physical object
>     |-- Floor mat
>     |-- Device
>     |-- Instrument of aggression
>     |-- Vehicle
>         |-- Nontraffic vehicle
>         |-- Mobile medical facility
>         |-- *Industrial transport vehicle*
> **|-- Transport vehicle
>         |-- Pedestrian conveyance
>     |-- Printed material
>     |-- etc…
> |-- etc…
>
> Best,
> Jennifer
>
>
>
>> On Mar 11, 2016, at 3:56 AM, Lorenz buehmann 
>> <buehmann at informatik.uni-leipzig.de 
>> <mailto:buehmann at informatik.uni-leipzig.de>> wrote:
>>
>> Hello Jennifer,
>>
>> thank you, that's quite helpful. I will try the inclusion of 
>> properties via REST parameters.
>>
>> But can you clarify the meaning of
>>
>> /ontologies/:ontology/classes/:cls/tree
>>
>> For me it seems like it returns the root classes of the ontology, but 
>> then I'm wondering why :cls is sued as parameter.
>>
>>
>> Kind regards,
>> Lorenz
>>
>> On 10.03.2016 22:38, Jennifer Leigh Vendetti wrote:
>>> Hello Lorenz,
>>>
>>>
>>>> On Mar 9, 2016, at 2:15 AM, Lorenz B. 
>>>> <buehmann at informatik.uni-leipzig.de> wrote:
>>>>
>>>> Hello,
>>>>
>>>> I'm wondering whether it's possible to get children of a given 
>>>> class via the REST interface.
>>>
>>>
>>> Yes, you can either get direct children, or all children.
>>>
>>>
>>> *Direct Children*
>>>
>>> Uses this format:
>>>
>>> /ontologies/:ontology/classes/:cls/children
>>>
>>> Using your class as an example:
>>>
>>> http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F260787004/children 
>>> <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/260787004/children>
>>>
>>> *
>>> *
>>> *All Children*
>>>
>>> Uses this format:
>>>
>>> /ontologies/:ontology/classes/:cls/descendants
>>>
>>> Using your class as an example:
>>>
>>> http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F260787004/descendants 
>>> <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/260787004/descendants>
>>>
>>>
>>>
>>>
>>>> I know that there is one request
>>>>
>>>> /ontologies/:ontology/classes/:cls/tree
>>>>
>>>> but it looks like it always returns the root classes only, and not 
>>>> the subclasses of the given class. see for example both links below:
>>>>
>>>> "http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F260787004/tree" 
>>>> <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F260787004/tree>
>>>>
>>>> http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F404684003/tree
>>>>
>>>> For me this looks like a bug because otherwise there would be no 
>>>> need to have this for each class, but only for the ontology itself. 
>>>> Moreover, the
>>>> "children" property is always an empty array here.
>>>>
>>>> Indeed I could use as REST request
>>>>
>>>> /ontologies/:ontology/classes/:cls/children
>>>>
>>>> but this does not return information like "hasChildren" which is 
>>>> quite useful when building the class tree, like it's done in the 
>>>> public BioPortal UI.
>>>
>>>
>>>
>>> If you want to get information about whether a class has children, 
>>> or the child count, you can use the “include” parameter, e.g.:
>>>
>>> http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F260787004?include=hasChildren,childrenCount 
>>> <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/260787004?include=hasChildren,childrenCount>
>>>
>>> Hope that helps.
>>>
>>> Best,
>>> Jennifer
>>>
>>>
>>>
>>>
>>
>
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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