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[bioontology-support] New rest API

Phillips, Lori C. LCPHILLIPS at PARTNERS.ORG
Wed Dec 11 06:49:35 PST 2013


Hi,
I use bioportal to extract terms for a given ontology.  I need to know term names, ids and relationships such as parent ids.
I plan to use something analogous to this: http://data.bioontology.org/ontologies/RXNORM/classes and page through the data.
I am looking at the new interface...  I can handle format changes.. but have a few questions about the data being returned.


1.       IDs

In the past we had <id> and <fullId>.

Looks like the new interface uses the old fullId as the new <id>
I can parse out the info I need
                <id>http://purl.bioontology.org/ontology/RXNORM/706898</id<http://purl.bioontology.org/ontology/RXNORM/706898%3c/id>>  would become id = 706898.
But I need to  know if all the ontologies follow this format.


2.       For each term I need to know its parent.

In the past I extracted this info from the <relation><entry> lists.

Now it looks like I have to follow a link to get this info?  I've tried that and I seem to end up with an orphanClass.



Page 1 of RXNORM gives me Fentanyl as the first term.

Which has :

<parents href=http://data.bioontology.org/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F706898/parents



When I go to this page I get:

"@id": "http://bioportal.bioontology.org/ontologies/umls/OrphanClass"<http://bioportal.bioontology.org/ontologies/umls/OrphanClass>,




Thanks,
Lori Phillips




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