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[bioontology-support] RXNORM (how to generate RDF from UMLS)

Emonet vincent.emonet at lirmm.fr
Wed Nov 25 08:23:44 PST 2015


Hi David,

For more details on how to generate UMLS turtle files:
It is simplified to go to the essential needed to generate the RDF files 
you want
Note that I am using linux and the 2015AB release for this tutorial

Michael, maybe it can be interesting to add it to 
http://www.bioontology.org/wiki/index.php/Importing_UMLS_To_Virtual_Appliance 

It should save a lot of time to users that need those imports

There are 3 steps:

 1. *Install UMLS using mmsys*

  * Download everything from
    https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html
  * Unzip mmsys.zip
  * Put the following files in the now unzipped mmsys directory :
      o 2015AB-1-meta.nlm
      o 2015AB-2-meta.nlm
      o 2015AB-otherks.nlm
      o mmsys.zip (why not?)
      o 2015AB.CHK

  * ./run_linux.sh (or run.bat or run_mac.sh)
  * "Install UMLS"

  * Source: path to mmsys directory and Destination: path of a directory
    where the subset file will be generated
  * Semantic Network -> Choose Database Load Scripts: Mysql 5.6 (to
    generate the mysql load script for the semantic network subset, aka
    STY in bioportal)

  * Select "New configuration.."
  * Select Default Subset: select the default subset you want (it is not
    really important, you can specificaly choose each thesaurus in the
    next step)

  * Go to the "Output Options" tab > Write Database Load Scripts
      o Select database > MySQL 5.6

  * Go to the "Source List" and select the sources (aka ontologies in
    bioportal) you want
      o hold ctrl to select many
      o careful there is an option to define if you want the selected
        source excluded or included in the subset
  * Then click on "Done" in the top command on the window
  * And wait for UMLS to install

Note: mmsys will generate RRF files. You can use the mmsys software to 
browse it, but we will just use it to populate a SQL database


 2. *Load subset in MySQL*

  * Go to mysql
      o  > create database umls2015ab;
  * Configure database character encoding to UTF-8
      o  > ALTER DATABASE umls2015ab CHARACTER SET utf8 COLLATE
        utf8_unicode_ci;

  * Go to the 2015AB directory (where UMLS has been installed) in the
    META directory

  * Open the populate_mysql_db.sh script and change the first lines with
    your MySQL credentials:

(note: for MYSQL_HOME it adds "/bin/mysql" to find the mysql bin)

MYSQL_HOME=/usr
user=<username>
password=<password>
db_name=umls2015ab

  * Then run ./populate_mysql_db.sh


 3. *Generate RDF from MySQL*

  * Clone https://github.com/ncbo/umls2rdf
  * Rename conf_sample.py as conf.py and configure the access to your
    database (example when database in local)

#Folder to dump the RDF files.
OUTPUT_FOLDER = "output"

#DB Config
DB_HOST = "localhost"
DB_NAME = "umls2015ab"
DB_USER = "root"
DB_PASS = "<password>"

UMLS_VERSION = "2015ab"

UMLS_BASE_URI = "http://purl.bioontology.org/ontology/"

  * Define the ontology you want to generate in umls.conf
      o Example for LNC-RU-RU: "LNC-RU-RU,LNC-RU-RU.ttl,load_on_codes"
      o If you want to get the name used for you ontology in the
        database you can get them by going to mySQL, select the umls
        database and get it from the following query: "select distinct
        SAB from MRCONSO;"

  * Run ./umls2rdf.py
  * Get the ttl files in the output directory



And it is done.

Have a good day,

Vincent Emonet


On 24/11/2015 21:11, Michael Dorf wrote:
> Hi David,
>
> I'm not sure what you mean by "batch querying", but I believe the 
> answer is NO. The rest services available in the virtual machine are 
> the same that we have documented on the NCBO site:
>
> http://data.bioontology.org/documentation
>
> We have a short doc that details the process of own import of UMLS 
> ontologies, but I know it's not super detailed. Perhaps it can help:
>
> http://www.bioontology.org/wiki/index.php/Importing_UMLS_To_Virtual_Appliance
>
> Thanks!
>
> Michael
>
>
>> On Nov 23, 2015, at 19:15, David Donohue <drdonohue at gmail.com 
>> <mailto:drdonohue at gmail.com>> wrote:
>>
>> Great Michael it's working again! Could I ask you a quick question?  
>> We hope to use Bioportal for our personal health record app.  We have 
>> installed the Bioportal Virtual Appliance and find it works pretty 
>> well.  Does the Bioportal Virtual Appliance support batch querying?
>>
>> Also I would like to load some UMLS ontologies into our Virtual 
>> Appliance (ICD10CM, MEDLINEPLUS, RXNORM, SNOMEDCT). But we have 
>> trouble converting them into TTL syntax and loading them into 
>> bioportal.  Can you recommend any simpler way to load UMLS ontologies 
>> into the Bioportal?
>>
>> Thanks!
>> Dave Donohue
>>
>> On Mon, Nov 23, 2015 at 9:26 PM, Michael Dorf <mdorf at stanford.edu 
>> <mailto:mdorf at stanford.edu>> wrote:
>>
>>     Hi David,
>>
>>     Thank you for getting in touch with us. It looks like RxNorm
>>     didn't get indexed properly during our latest re-run of the
>>     indexer. The problem is now fixed. You should be able to use both
>>     the UI or the REST service to retrieve terms from RxNorm. Let me
>>     know if you experience further issues.
>>
>>     Thanks!
>>
>>     Michael Dorf
>>
>>
>>
>>>     On Nov 22, 2015, at 06:09, David Donohue <drdonohue at gmail.com
>>>     <mailto:drdonohue at gmail.com>> wrote:
>>>
>>>     Hello!  We are using Bioportal for our prototype PHR
>>>     http://biolog.io <http://biolog.io/>
>>>     Many thanks for this fine tool!
>>>
>>>     I find that the RXNORM ontology is not working for some weeks now?
>>>     Best regards
>>>
>>>     -- 
>>>     /David Donohue, MD, FACP/
>>>     /Progressive Health of Delaware/
>>>     /302-543-5454/
>>>     /3519 Silverside Rd, Ste 200/
>>>     /Wilmington, DE 19810/
>>>     /Fax 302-327-4200/
>>>     /www.progressivehealthofde.com <http://progressivehealthofde.com/>/
>>>     invent.healthcare <http://invent.healthcare/>
>>>     biolog.io <http://biolog.io/>
>>>     Twitter: @PhatLoser <https://twitter.com/phatloser>
>>>     Healthgrades
>>>     <http://www.healthgrades.com/physician/dr-david-donohue-2lb9n>
>>>
>>>     PRIVILEGED AND CONFIDENTIAL:  This document and the information
>>>     contained herein are confidential and protected from disclosure
>>>     pursuant to federal law.  This message is intended only for the
>>>     use of the Addressee(s) and may contain information that is
>>>     PRIVILEGED and CONFIDENTIAL. If you are not the intended
>>>     recipient, you are hereby notified that the use dissemination,
>>>     or copying of this information is strictly prohibited.  If you
>>>     have received this communication in error, please erase all
>>>     copies of the message and its attachments and notify the sender
>>>     immediately.  Thanks!
>>>     _______________________________________________
>>>     bioontology-support mailing list
>>>     bioontology-support at lists.stanford.edu
>>>     <mailto:bioontology-support at lists.stanford.edu>
>>>     https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>>
>> -- 
>> /David Donohue, MD, FACP/
>> /Progressive Health of Delaware/
>> /302-543-5454/
>> /3519 Silverside Rd, Ste 200/
>> /Wilmington, DE 19810/
>> /Fax 302-327-4200/
>> /www.progressivehealthofde.com <http://progressivehealthofde.com/>/
>> invent.healthcare <http://invent.healthcare/>
>> biolog.io <http://biolog.io/>
>> Twitter: @PhatLoser <https://twitter.com/phatloser>
>> Healthgrades 
>> <http://www.healthgrades.com/physician/dr-david-donohue-2lb9n>
>>
>> PRIVILEGED AND CONFIDENTIAL:  This document and the information 
>> contained herein are confidential and protected from disclosure 
>> pursuant to federal law.  This message is intended only for the use 
>> of the Addressee(s) and may contain information that is PRIVILEGED 
>> and CONFIDENTIAL. If you are not the intended recipient, you are 
>> hereby notified that the use dissemination, or copying of this 
>> information is strictly prohibited.  If you have received this 
>> communication in error, please erase all copies of the message and 
>> its attachments and notify the sender immediately.  Thanks!
>
>
>
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