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[bioontology-support] Virtual Appliance ontology loading questions [WAS: search by id in a subtree]

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Sep 7 11:35:14 PDT 2017


Hello Sina,


On Sep 7, 2017, at 10:06 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Thank you very much Jennifer for the explanation.
It turned out the Audio module of the Virtual machine was causing the instance to pause and go into hibernation. After I disabled that module the appliance started parsing ontologies immediately.
I tested loading and parsing LOINC and RxNorm so far and everything seems fine. However, both terminology names are showing as “unknown” under submission section. I only filled out the mandatory fields though.


If you want the UI to display a version number, you can go to any ontology summary page, click the “Edit submission information” link, enter a value in the “VERSION” field, and click the Save submission button.



Also, I guess the current UMLS2RDF does not include obsolete concepts so there is no function in the API to query for the status of a given concepts. Is that right? Do you have any suggestion/workaround for us?


I’m not sure I’m following your question. Could you give me an example of a concept you know to be obsolete that isn’t being displayed in BioPortal?

Also, if you issue a REST call against the classes endpoint using the “include=all” parameter, the API will show whether or not a concept is obsolete, as well as a list of all properties with their values. Here’s an example of a REST call to retrieve the “Surveys” class from LOINC:

http://data.bioontology.org/ontologies/LOINC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FMTHU000004?include=all<http://data.bioontology.org/ontologies/LOINC/classes/http://purl.bioontology.org/ontology/LNC/MTHU000004?include=all>

… and a screen shot of the result:


[cid:DE7C4F51-302F-4AB6-9353-D9198C23CF0F at stanford.edu]

Is the information you’re looking for contained in this result?

Kind regards,
Jennifer

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