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Posted to user@ctakes.apache.org by "Das, Tanmay" <ta...@optum.com> on 2017/06/21 07:47:08 UTC
Medication attributes, confidence finding problem in ctakes
Hi,
Whenever I use the AggrigatePlainTextFastUMLSProcessor.xml, the confidence of all the
Identified annotations are 0.0 and none of the drug dosage is annotated. They just appear
Separately as numeric Annotations. And the laboratory reports are not annotated under test/ ..
But are included in medication.
Does anyone know how to recognize drug attributes and what does the 0.0 confidence mean ??
Is there any annotator for lab report reorganization in cTAKES ??
-TANMAY
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Re: Medication attributes, confidence finding problem in ctakes
Posted by Narayan Bhat <bn...@manuhsolutions.com>.
Hi Tanmay
Look into DrugMentionAnnotator.java source file, you will get some idea as
to how to access drug attributes.
Regards
Narayan
On Wed, Jun 21, 2017 at 4:28 PM, Das, Tanmay <ta...@optum.com> wrote:
> Hi Narayan,
>
> Thanks for your reply !
>
>
>
> I understand now how to extract drug mention annotaion from cas, but the
> values are still
>
> Turing out to be null (I have included DrugMentionAnnotator as well). Any
> idea what I have to do ?
>
>
>
> Can you give me some idea why the confidence values are 0 all over ?? or
> how could I get the right values.
>
> And what annotator to use to extract labaratory info from the text:
>
> Hemoglobin 10.6, hematocrit 31.7, white cell count 5.8, platelet 377.
>
> Magnesium 2.6, glucose 98, BUN 13, creatinine 0.5, sodium 138, potassium
> 3.9,
>
> chloride 103. INR is 1.5.
>
> {These get annotated as medication}
>
>
>
> Thanks again
>
> -Tanmay
>
> *From:* Narayan Bhat [mailto:bnarayan@manuhsolutions.com]
> *Sent:* Wednesday, June 21, 2017 1:32 PM
> *To:* user@ctakes.apache.org
> *Subject:* Re: Medication attributes, confidence finding problem in ctakes
>
>
>
> Hi
>
>
>
> Drug mention annotation (MedicationMention.type) captures drug attributes.
>
>
>
> Regards
>
> Narayan
>
>
>
> On Wed, Jun 21, 2017 at 1:17 PM, Das, Tanmay <ta...@optum.com> wrote:
>
> Hi,
>
>
>
> Whenever I use the AggrigatePlainTextFastUMLSProcessor.xml, the
> confidence of all the
>
> Identified annotations are 0.0 and none of the drug dosage is annotated.
> They just appear
>
> Separately as numeric Annotations. And the laboratory reports are not
> annotated under test/ ..
>
> But are included in medication.
>
>
>
> Does anyone know how to recognize drug attributes and what does the 0.0
> confidence mean ??
>
> Is there any annotator for lab report reorganization in cTAKES ??
>
>
>
>
>
> -TANMAY
>
>
> This e-mail, including attachments, may include confidential and/or
> proprietary information, and may be used only by the person or entity
> to which it is addressed. If the reader of this e-mail is not the intended
> recipient or his or her authorized agent, the reader is hereby notified
> that any dissemination, distribution or copying of this e-mail is
> prohibited. If you have received this e-mail in error, please notify the
> sender by replying to this message and delete this e-mail immediately.
>
>
>
>
>
> --
>
> Thanks and Regards
>
> Narayan L Bhat
>
> +91 9740237967
>
>
> This e-mail, including attachments, may include confidential and/or
> proprietary information, and may be used only by the person or entity
> to which it is addressed. If the reader of this e-mail is not the intended
> recipient or his or her authorized agent, the reader is hereby notified
> that any dissemination, distribution or copying of this e-mail is
> prohibited. If you have received this e-mail in error, please notify the
> sender by replying to this message and delete this e-mail immediately.
>
--
Thanks and Regards
Narayan L Bhat
+91 9740237967
RE: Medication attributes, confidence finding problem in ctakes
Posted by "Das, Tanmay" <ta...@optum.com>.
Hi Narayan,
Thanks for your reply !
I understand now how to extract drug mention annotaion from cas, but the values are still
Turing out to be null (I have included DrugMentionAnnotator as well). Any idea what I have to do ?
Can you give me some idea why the confidence values are 0 all over ?? or how could I get the right values.
And what annotator to use to extract labaratory info from the text:
Hemoglobin 10.6, hematocrit 31.7, white cell count 5.8, platelet 377.
Magnesium 2.6, glucose 98, BUN 13, creatinine 0.5, sodium 138, potassium 3.9,
chloride 103. INR is 1.5.
{These get annotated as medication}
Thanks again
-Tanmay
From: Narayan Bhat [mailto:bnarayan@manuhsolutions.com]
Sent: Wednesday, June 21, 2017 1:32 PM
To: user@ctakes.apache.org
Subject: Re: Medication attributes, confidence finding problem in ctakes
Hi
Drug mention annotation (MedicationMention.type) captures drug attributes.
Regards
Narayan
On Wed, Jun 21, 2017 at 1:17 PM, Das, Tanmay <ta...@optum.com>> wrote:
Hi,
Whenever I use the AggrigatePlainTextFastUMLSProcessor.xml, the confidence of all the
Identified annotations are 0.0 and none of the drug dosage is annotated. They just appear
Separately as numeric Annotations. And the laboratory reports are not annotated under test/ ..
But are included in medication.
Does anyone know how to recognize drug attributes and what does the 0.0 confidence mean ??
Is there any annotator for lab report reorganization in cTAKES ??
-TANMAY
This e-mail, including attachments, may include confidential and/or
proprietary information, and may be used only by the person or entity
to which it is addressed. If the reader of this e-mail is not the intended
recipient or his or her authorized agent, the reader is hereby notified
that any dissemination, distribution or copying of this e-mail is
prohibited. If you have received this e-mail in error, please notify the
sender by replying to this message and delete this e-mail immediately.
--
Thanks and Regards
Narayan L Bhat
+91 9740237967
This e-mail, including attachments, may include confidential and/or
proprietary information, and may be used only by the person or entity
to which it is addressed. If the reader of this e-mail is not the intended
recipient or his or her authorized agent, the reader is hereby notified
that any dissemination, distribution or copying of this e-mail is
prohibited. If you have received this e-mail in error, please notify the
sender by replying to this message and delete this e-mail immediately.
Re: Medication attributes, confidence finding problem in ctakes
Posted by Narayan Bhat <bn...@manuhsolutions.com>.
Hi
Drug mention annotation (MedicationMention.type) captures drug attributes.
Regards
Narayan
On Wed, Jun 21, 2017 at 1:17 PM, Das, Tanmay <ta...@optum.com> wrote:
> Hi,
>
>
>
> Whenever I use the AggrigatePlainTextFastUMLSProcessor.xml, the
> confidence of all the
>
> Identified annotations are 0.0 and none of the drug dosage is annotated.
> They just appear
>
> Separately as numeric Annotations. And the laboratory reports are not
> annotated under test/ ..
>
> But are included in medication.
>
>
>
> Does anyone know how to recognize drug attributes and what does the 0.0
> confidence mean ??
>
> Is there any annotator for lab report reorganization in cTAKES ??
>
>
>
>
>
> -TANMAY
>
>
> This e-mail, including attachments, may include confidential and/or
> proprietary information, and may be used only by the person or entity
> to which it is addressed. If the reader of this e-mail is not the intended
> recipient or his or her authorized agent, the reader is hereby notified
> that any dissemination, distribution or copying of this e-mail is
> prohibited. If you have received this e-mail in error, please notify the
> sender by replying to this message and delete this e-mail immediately.
>
--
Thanks and Regards
Narayan L Bhat
+91 9740237967
Re: Medication attributes, confidence finding problem in ctakes
Posted by Gandhi Rajan <ga...@apache.org>.
On 2017/06/21 07:47:08, "Das, Tanmay" <ta...@optum.com> wrote:
> Hi,
>
> Whenever I use the AggrigatePlainTextFastUMLSProcessor.xml, the confidence of all the
> Identified annotations are 0.0 and none of the drug dosage is annotated. They just appear
> Separately as numeric Annotations. And the laboratory reports are not annotated under test/ ..
> But are included in medication.
>
> Does anyone know how to recognize drug attributes and what does the 0.0 confidence mean ??
> Is there any annotator for lab report reorganization in cTAKES ??
>
>
> -TANMAY
>
> This e-mail, including attachments, may include confidential and/or
> proprietary information, and may be used only by the person or entity
> to which it is addressed. If the reader of this e-mail is not the intended
> recipient or his or her authorized agent, the reader is hereby notified
> that any dissemination, distribution or copying of this e-mail is
> prohibited. If you have received this e-mail in error, please notify the
> sender by replying to this message and delete this e-mail immediately.
>
Hi Tanmay,
An annotator for finding out lab values was introduced few months back on cTAKES. Its called LabValueFInder. Please have a look at the ctakes core module for more info on this.
Revert for queries.
Regards,
Gandhi