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

Anna Duncan (MCRI) anna.duncan at mcri.edu.au
Tue Nov 17 15:23:29 PST 2020


Hi Michael,

Thanks so much for your quick reply, much appreciated.

A quick FYI (that might help to track the issue down):

-        Our team have been looking up terms extensively over the last few weeks and only really noticed this issue in the last 48 hours (Monday our time)

-        I don’t recall it occurring last Wednesday (our time, and the last time I used the system), especially not the error messages when trying to load

-        My colleague used the system on Friday and, when looking up photograph<http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F257444003&jump_to_nav=true>, remembers not being able to see it in the tree, much like the children’s hearing test below, but did not receive any error messages like Monday

-        If something was changed in the coding that renders the tree mid-late last week your time, I’d say that is where the culprit is

-        Good luck!

Cheers,
Anna

Dr Anna Duncan PhD
Project Coordinator
Melbourne Children’s LifeCourse Research

Murdoch Children's Research Institute
The Royal Children's Hospital, 50 Flemington Road
Parkville, Victoria 3052 Australia

T   +61 3 9936 6231 (66231)
E   anna.duncan at mcri.edu.au<mailto:anna.duncan at mcri.edu.au>
W  mcri.edu.au<https://www.mcri.edu.au/>
     lifecourse.melbournechildrens.com<https://lifecourse.melbournechildrens.com/>

Work days:   Monday, Tuesday, Wednesday, Friday



From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: Wednesday, 18 November 2020 8:23 AM
To: support at bioontology.org
Cc: Anna Duncan (MCRI) <anna.duncan at mcri.edu.au>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Anna Duncan

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<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<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<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<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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