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

Madani, Sina Sina.Madani at vumc.org
Thu Sep 7 10:06:33 PDT 2017


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.
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?

Thanks!
Sina

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Wednesday, September 06, 2017 3:52 PM
To: Madani, Sina
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Virtual Appliance ontology loading questions [WAS: search by id in a subtree]

Hello Sina,


On Sep 6, 2017, at 8:24 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

I was able to upload RxNorm and LOINC (downloaded from NCBO site) into our local instance without any error. However, it seems processing doesn’t start automatically.


I looked at the contents of the scheduler.log file you sent and saw two sections indicating that RxNorm and LOINC processing was initiated:

LOINC parsing:

I, [2017-09-05T07:56:58.495982 #3285]  INFO -- : Starting ontology process queue check
I, [2017-09-05T07:57:07.410794 #3285]  INFO -- : Logging parsing output to /srv/ncbo/repository/LOINC/1/parsing.log
I, [2017-09-05T07:57:07.418516 #3285]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/LOINC/submissions/1<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FLOINC%2Fsubmissions%2F1&data=02%7C01%7CSina.Madani%40vumc.org%7C54ca8d4842914805a6bd08d4f560b636%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636403243106615828&sdata=F7xCr0uwPUIhDIS9f5QWdj7XarsgUIG5vGguArST6Dk%3D&reserved=0>"]
I, [2017-09-05T07:57:07.860300 #3285]  INFO -- : ["Starting to process LOINC/submissions/1"]
I, [2017-09-05T07:57:08.862298 #3285]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse”]

RXNORM parsing:

I, [2017-09-05T09:56:48.083438 #4033]  INFO -- : Starting ontology process queue check
I, [2017-09-05T09:56:51.196790 #4033]  INFO -- : Logging parsing output to /srv/ncbo/repository/RXNORM/1/parsing.log
I, [2017-09-05T09:56:51.203966 #4033]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/RXNORM/submissions/1<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FRXNORM%2Fsubmissions%2F1&data=02%7C01%7CSina.Madani%40vumc.org%7C54ca8d4842914805a6bd08d4f560b636%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636403243106615828&sdata=fguNqeQDKplR1hpdtKBZXpqtZHIB3%2FkkhCcRACEiFfw%3D&reserved=0>"]
I, [2017-09-05T09:56:51.732885 #4033]  INFO -- : ["Starting to process RXNORM/submissions/1"]
I, [2017-09-05T09:56:52.791871 #4033]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse”]

Note that the ncbo_cron process checks the ontology parsing queue every 5 minutes, so there may be a small delay between when you create a new ontology submission and the time when parsing begins. The line that says “skipping OWLAPI parse” simply means that a UMLS TTL file was detected and it wasn’t necessary to feed this particular ontology file through the OWL API. The OWL API is 3rd party software that we use internally to parse all ontologies submitted to BioPortal, with the exception of the set of UMLS ontologies that we import twice per year from the National Library of Medicine.



The instruction for manual processing is not working either. http://localinstnace/admin page also doesn’t show the uploaded ontologies so that I can trigger “process” from the drop down selected action.


The contents of the Admin page are created from an ontology report that’s generated on a nightly basis, which is why you don’t see your new submissions there.

What happens when you issue a REST API call to retrieve the classes for LOINC or RxNorm? Are you seeing any data? Example query:

http://{ip_address_of_your_appliance}:8080/ontologies/LOINC/classes<http://%7bip_address_of_your_appliance%7d:8080/ontologies/LOINC/classes>



The UI under each ontology submission shows “uploaded”.


If you see that the REST endpoint is returning data, but the UI still only shows the Uploaded status, you may need to clear the caches. There are buttons to clear the caches on the Admin page (you can click all 4 to clear all of the various application caches). Note that only users with administrative privileges can access the Admin page that you refer to above. After clearing the caches, when you return to any ontology summary page, you should also refresh the browser page using the key combination to clear the cache memory (e.g., Apple + R on a Mac).

Kind regards,
Jennifer

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