Hi Martijn,
The UmlsConcept should be in an array in the IdentifiedAnnotation. Does your
array only contain a single concept?
When you use the gui, it should store codes in the database as a unique table
for every (target) vocabulary that you selected in the left panel. The .xml
file that it creates should list all of those types in the <conceptFactory>
section. In your .xml you should see the line:
<property key="snomedct_usTable" value="long"/>
If that line is in the .xml, you can inspect your database directly with a
hsqldb tool. I can help you do that if needed. The db should have a table
named "snomedct_us".
If all of those are ok then I will need to look at the lookup code as something
must have broken.
Sean
-----Original Message-----
From: Martijn [mailto:[email protected]]
Sent: Thursday, March 09, 2017 5:35 PM
To: [email protected]
Subject: Re: 2016AB UMLS (ctakessnorx)
Hi Sean,
Thanks! I used the GUI to generate a custom dictionary, but I still get the
UMLS code and not the SNOMED CT one.
If I print the concept that was detected it returns:
UmlsConcept
codingScheme: "custom"
code: <null>
oid: "null#custom"
oui: <null>
score: 0.0
disambiguated: false
cui: "C1281583"
tui: "T023"
preferredText: "Entire hand"
As you can see, the code is <null>. The concept is present in the UMLS subset
and there is also a SNOMED CT code listed there:
Entire hand [A3421866/SNOMEDCT_US/PT] CUI:C1281583 SCUI:302539009
Am I doing something wrong?
- Martijn
On 08/03/2017, 08:12, "Finan, Sean" <[email protected]> wrote:
Hi Martijn,
The dictionary creator gui is in sandbox just like the command line tool,
but it is newer and easier to use.
OntologyConceptUtil is in org.apache.ctakes.core.util.
Sean
-----Original Message-----
From: Martijn [mailto:[email protected]]
Sent: Tuesday, March 07, 2017 5:38 PM
To: [email protected]
Subject: Re: 2016AB UMLS (ctakessnorx)
Hi Sean,
Thanks so much for your quick reply.
I used the command line directorytool. Is that different than the gui? Can
that explain the decrease in tagged concepts?
I’m not able to find the OntologyConceptUtil class, may I ask what the path
for that class is?
- Martijn
On 07/03/2017, 14:24, "Finan, Sean" <[email protected]>
wrote:
Hi Martijn,
Since you say that you've created your own dictionary I will assume
that you used the gui in sandbox to do so. If that isn't the case then let me
know.
The any dictionary created using the default settings on the gui does
have snomedct and rxnorm codes in addition to the cuis. However, umls cui is
always used as the primary normalization code for ctakes annotations.
To obtain codes for an annotation, check the OntologyConceptUtil in
ctakes core. It has methods that will return all associated codes as well as
one to get all associated codes for a scheme/vocabulary (like snomedct_us,
etc.). It can do this for a single annotation, a collection of annotations,
the entire document, or a section of the document (sentence, paragraph,
section). It also has methods that allow you to fetch annotations found in the
document by codes other than the umls cui.
Sean
-----Original Message-----
From: Martijn [mailto:[email protected]]
Sent: Tuesday, March 07, 2017 5:13 PM
To: [email protected]
Subject: 2016AB UMLS (ctakessnorx)
Hi,
I've been using cTAKES for a bit now, but I still can't figure out how
to upgrade the UMLS version to the most recent one.
If I create my own dictionary, cTAKES only returns UMLS concepts and no
SNOMED CT ones (I'm interested in those). The amount of concepts returned is
also way less compared to the 2011 UMLS that's included with cTAKES.
Can someone help me out by providing me a proper 2016 dictionary or
clear explanation how to implement the newest version of the UMLS (with SNOMED
CT).
Thanks!
- Martijn
