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[bioontology-support] [BioPortal] Feedback from Anna Duncan

Michael Dorf mdorf at stanford.edu
Tue Nov 17 13:23:01 PST 2020


Hi Anna,

Thank you so much for your report!  I was able to reproduce this behavior on my end, and, unfortunately, this looks to be a bug in our system.  When rendering the tree, BioPortal usually picks a single parent in the hierarchy and renders the term under that parent. In this case, the parent that’s picked is “Examination of Body System”:

[cid:48624C7F-DD9C-47C8-AB6F-D17B14D708A9]

However, when searching for “Children’s hearing test” within the ontology, a different branch in picked, with the parent “Hearing examination”, except that our term has already been rendered elsewhere in the tree, so it’s not shown under that branch. I’ve described this behavior in a Github issue that I created to track this behavior: https://github.com/ncbo/ontologies_linked_data/issues/113.

Unfortunately, we’re short on resources at this time, so it may be some time before we have a chance to address this. I’ll keep you posted once a fix is in place.

Thank you again!

----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Nov 16, 2020, at 5:58 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Anna Duncan

Email: anna.duncan at mcri.edu.au<mailto:anna.duncan at mcri.edu.au>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FSNOMEDCT%252F398171003

Feedback:

Error loading SNOMED CT classes tree:
Yesterday (about 22 hours ago), we noticed an error message when trying to load terms in SNOMED CT (cannot remember message), but if you refreshed a few times, it would load the details of the class eventually. However, I noticed that the tree wasn't loading properly, so you could read the information about the class, but couldn't see where in the tree it mapped to.
I checked this morning, and it is still the case. For instance, if you search 'children's hearing test' (http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=252957005), it should be a subclass of three other classes, the first of which is 'hearing examination' (http://purl.bioontology.org/ontology/SNOMEDCT/398171003) but you can't see 'children's hearing test', or other subclasses also listed there.
For instance, compare to the CSIRO shrimp version (at http://ontoserver.csiro.au/shrimp/?concept=252957005&version=http%3A%2F%2Fsnomed.info%2Fsct%2F32506021000036107%2Fversion%2F20201031&valueset=http%3A%2F%2Fsnomed.info%2Fsct%3Ffhir_vs&tour=true), which has ~20 subclasses.

Thanks in advance,
Anna

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