Guilt is such a powerful motivator ... The problem is that ctakes traditionally identifies a bunch of those terms as Medications, not Labs. So, I added a parameter named "useDrugs" to the LabValueFinder. If you set that to "true" then the Lab/Medication values come through shining.
I also added some (commented out) code to the LabValueFinderTester to use the default dictionary instead of the test dictionary. By default the test dictionary is used and all counts match. If you use the default dictionary you can expect the test to fail because it finds 23 labs instead of 24 - but Kean's test code kindly prints the labs and values found so you can look at the test results. The code just went into trunk. Enjoy, Sean -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, March 28, 2018 9:03 AM To: dev@ctakes.apache.org Subject: Re: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS] Hi Gandhi, I know that I just sent an email to the devlist, but that seemed like an item that had wide-impact. Because of some critical work (job that pays the bills) I am still "dark" as far as ctakes goes - no free nights and only partial weekends. My apologies. I know that there are a lot of issues building up, and I will try to try to address them asap; I don't know when I'll have the time and energy to get back to the devlist. Feeling a bit guilty, Sean ________________________________________ From: Gandhi Rajan Natarajan <gandhi.natara...@arisglobal.com> Sent: Wednesday, March 28, 2018 8:56 AM To: dev@ctakes.apache.org Subject: RE: Query on LabValueFinder [EXTERNAL] Hi Sean, Can you throw some light on this? Regards, Gandhi -----Original Message----- From: Kean Kaufmann [mailto:k...@recordsone.com] Sent: Monday, March 19, 2018 8:35 PM To: dev@ctakes.apache.org Subject: Re: Query on LabValueFinder Gandhi, at first blush, I can't replicate your result using the code I submitted... but my code and config differ from trunk, so Sean is probably the best person to ask. I included unit tests with a mini-dictionary for ProcedureMentions, but they probably didn't play nicely with the rest of the framework. Sean, any insight? On Mon, Mar 19, 2018 at 10:31 AM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi All, > > I'm using LabValueFinder annotator in my piper file and when I analyze > the following text: > > > "HEPATIC FUNCTION PANEL Result Value Ref Range Albumin 2.2 (*) 3.7 - > 5.1 g/dL Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844 > (*) 42 - > 121 IU/L" as mentioned in > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D441&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JMvtiTFymmqWfE6zZ1z5oPfqlSFrG0nZKJ0bhEBltrc&s=2EcJhW06YyWZpdLla-yruHEw4Il9CyHMLBrKoHaDVlc&e= > > > > The resulted XML generated using XmiCasSerializer contains only one > LabMention as mentioned below: > > > <textsem:LabMention xmi:id="3876" sofa="1" begin="0" end="22" id="9" > ontologyConceptArr="1089 1109 1079 1099 1069" typeID="0" > discoveryTechnique="3" confidence="0.0" polarity="0" uncertainty="0" > conditional="false" generic="false" historyOf="0" labValue="3907" /> > > <relation:RelationArgument xmi:id="3922" id="0" argument="537" /> > > <relation:RelationArgument xmi:id="3917" id="0" argument="3876" /> > > <relation:ResultOfTextRelation xmi:id="3907" id="0" discoveryTechnique="0" > confidence="0.0" polarity="0" uncertainty="0" conditional="false" > arg1="3917" arg2="3922" /> > > <textsem:FractionAnnotation xmi:id="537" sofa="1" begin="56" end="59" > id="0" typeID="0" discoveryTechnique="0" confidence="0.0" polarity="0" > uncertainty="0" conditional="false" generic="false" historyOf="0" /> > > > But as per the comments in the issue, it is supposed to identify 3 lab > mentions. Any thoughts on this on how to achieve it ? > > Regards, > Gandhi > > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they are > addressed. > If you are not the named addressee you should not disseminate, > distribute or copy this e-mail. Please notify the sender or system > manager by email immediately if you have received this e-mail by > mistake and delete this e-mail from your system. If you are not the > intended recipient you are notified that disclosing, copying, > distributing or taking any action in reliance on the contents of this > information is strictly prohibited and against the law. > This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
