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

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Mar 10 13:38:07 PST 2016


Hello Lorenz,


On Mar 9, 2016, at 2:15 AM, Lorenz B. <buehmann at informatik.uni-leipzig.de<mailto: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




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