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[bioontology-support] [BioPortal] Feedback from Ashleigh Lewis

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jul 19 16:29:41 PDT 2018


Hello Ashleigh,

Thank you for providing additional detail.


On Jul 19, 2018, at 1:47 PM, Ashleigh Lewis <lewisa2 at uw.edu<mailto:lewisa2 at uw.edu>> wrote:

Hi Jennifer,

Thank you for your email and checking on those ontologies. I did do some initial troubleshooting with our servers prior to contacting you as well as testing on another version of the REDCap software to determine it was not isolated to a certain software version at which I would have contacted the REDCap Developers. I believe this is still a Bioportal malfunction specific to the MDDB (Master Drug Data Base Clinical Drugs) ontology. When I look at the class here:
https://bioportal.bioontology.org/ontologies/MDDB?p=classes&conceptid=bp_fake_root

This does not show the drug codes and names it once did. This should be a pharmaceutical lookup list but when you type in for example Cetirizine HCl Tab 10 MG which used to show up with code 09133 no longer shows up. You can get it to search the table which now contains different codes such as “body system”.

I think I thought originally it was an issue not pulling any of the table list because I was searching for pharmaceuticals but it does filter but only when you type in the new list items it has so working properly just what I believe is not the correct look up table.

I noticed that the most recent submission was uploaded on 7/6/2018 so I am wondering if this ontology has now changed and no longer actually is a Master Drug Data Base Clinical Drugs or if there was some error in the most recent upload.


OK - I think this is the root of the issue. MDDB is one of a group of ontologies made available by the National Library of Medicine as part of their UMLS distribution [1]. Twice per year we do bulk imports of their new releases. It looks like MDDB was included in the UMLS 2017AA release, but has been removed from the two subsequent releases (2017AB and 2018AA). I think we missed the fact that MDDB was removed from the UMLS distribution and our import process created two new submissions in BioPortal for 2017AA and 2018AA that were mostly void of content. I deleted those last two submissions, and reverted the system to serve content from the 2017AA release. I verified that the example class you listed above is accessible via our REST endpoint:


[cid:7C21CAF0-B666-4918-9A4A-638533982B13 at stanford.edu]

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/



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