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[bioontology-support] Question about Root Paths in BioPortal web services

Anthony Wenzel awenzel at dominiondigital.com
Mon Mar 7 07:23:35 PST 2011


Hi,

My team is working on a research project that is leveraging the BioPortal web services to gather terminology hierarchy information (specifically in the SNOMED-CT ontology). Thus far, we have found it generally very easy to use and understand, so thank you for that.

We are using the "rootpath" web service function to determine the path to root for a given term, using a call such as:
http://rest.bioontology.org/bioportal/virtual/rootpath/1353/126885006?email=example@example.org

That call returns 56 root paths, which is fine. Where I'm having difficulty is in understanding why some "root paths" don't seem to go all the way to the "root" of the hierarchy. For example, here are two root paths that are returned from that call (with term names):

*         Neoplasm of trunk(126637008) > Neoplasm of pelvis(126644004) > Neoplasm of urinary system(126879004) > Neoplasm of urinary tract proper(254913005)

*         Mass of body structure(300848003) > Mass of body region(300862005) > Mass of trunk(309524007) > Neoplasm of trunk(126637008) > Neoplasm of abdomen(128050000)

The first root path has 126637008 as it's root element, yet in SNOMED, that is not a hierarchy root element. In fact, in the second root path, that same element has 3 parent elements. Can you help me understand why the root paths don't seem to include elements all the way to one of the SNOMED root elements? Perhaps I'm misunderstanding the concept of a root path, in which case I would be grateful if you could provide some insight to this.

Thank you.
Anthony

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