Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Clement Jonquet jonquet at lirmm.fr
Wed Nov 25 08:27:57 PST 2015


Indeed, this will be perfect to have this merge in the Wiki doc.

 

Thanks Vincent

Clement

 

De : bioontology-support
[mailto:bioontology-support-bounces at lists.stanford.edu] De la part de Emonet
Envoyé : mercredi 25 novembre 2015 08:24
À : bioontology-support at lists.stanford.edu
Objet : Re: [bioontology-support] RXNORM (how to generate RDF from UMLS)

 

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_Applianc
e 
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.h
tml
*	Unzip mmsys.zip
*	Put the following files in the now unzipped mmsys directory : 

*	2015AB-1-meta.nlm
*	2015AB-2-meta.nlm
*	2015AB-otherks.nlm
*	mmsys.zip (why not?)
*	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

*	Select database > MySQL 5.6

*	Go to the "Source List" and select the sources (aka ontologies in
bioportal) you want

*	hold ctrl to select many
*	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

*	> create database umls2015ab; 

*	Configure database character encoding to UTF-8

*	> 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/>
"http://purl.bioontology.org/ontology/"

*	Define the ontology you want to generate in umls.conf

*	Example for LNC-RU-RU: "LNC-RU-RU,LNC-RU-RU.ttl,load_on_codes"
*	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_Applianc
e

 

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 

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://www.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

 <http://progressivehealthofde.com/> www.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

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20151125/e69f0f4b/attachment-0001.html>


More information about the bioontology-support mailing list