Troy,
My vote would be to mention in the user guide that "real" entity
recognition requires the umls component, and maybe a link to the
developers guide where that is explained? Probably there are some people
who wouldn't know what to expect out of the box and will be disappointed
that it doesn't find much. (Luckily some of them email our lists and we
can help them figure it out, but there may be people who just figure it
doesn't work very well and give up.)
Btw, the guides are really nice, great job on that.
Tim
On 04/12/2013 12:12 PM, Bleeker, Troy C. wrote:
The Developer install guide talks about UMLS integration:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
Search for UMLS. It is described for Eclipse and for command line.
Users that are just trying out cTAKES don't have those instructions.
Do you think they should be part of the User Guide?
Troy
*From:*[email protected]
[mailto:[email protected]] *On
Behalf Of *giri vara prasad nambari
*Sent:* Friday, April 12, 2013 11:06 AM
*To:* [email protected]
*Subject:* RE: concept identification query
Hi All,
Where do we need to update this UMLS key in ctakes?
Thanks for your time and help.
Thank you,
Giri
On Apr 12, 2013 10:59 AM, "Savova, Guergana"
<[email protected]
<mailto:[email protected]>> wrote:
You would need to get a UMLS license to get the full functionality. It
takes 2-3 days to be approved for it.
Hope this helps.
--Guergana
*From:*Rooney, Niall [mailto:[email protected]
<mailto:[email protected]>]
*Sent:* Friday, April 12, 2013 10:26 AM
*To:* [email protected] <mailto:[email protected]>
*Subject:* RE: concept identification query
Pei,
I don't have a UMLS license yet but thanks for looking into this.
*From:*Chen, Pei [mailto:[email protected]
<mailto:[email protected]>]
*Sent:* 12 April 2013 15:10
*To:* <[email protected] <mailto:[email protected]>>
*Subject:* Re: concept identification query
Thanks Tim for confirming...
AggregatePlaintextUMLSProcessor.xmlshould pick up stomach and aphasia etc.
Sent from my iPhone
On Apr 12, 2013, at 9:25 AM, "Tim Miller"
<[email protected]
<mailto:[email protected]>> wrote:
Niall,
I'm sure Pei will get back to you soon, but just wanted to let you
know, many of those entities will be found by the standard ctakes
installation. I get aphasia and stomach. It does not get blood
pressure, I think because this is filtered out by UMLS semantic
class - I think it is categorized as a "measurement," and cTAKES
will find things like disease/disorder, signs/symptoms, and a few
others, which this does not fit into exactly. It may be worth
thinking about how to include it if it will be useful. In this
example it looks like it's linked to some assessment "HB +20%", I
assume that is some measurement that would be useful to extract?
Tim
On 04/12/2013 07:05 AM, Rooney, Niall wrote:
Hi,
I have question concerning concept identification. I have
modifying the example text given in the installation
instructions to demonstrate the use of CAS Visual Debugger.
My text is:
Dr. Nutritious
Medical Nutrition Therapy for Hyperlipidemia and Aphasia
Referral from: Julie Tester, RD, LD, CNSD
Phone contact: (555) 555-1212
Height: 144 cm Current Weight: 45 kg Date of current
weight: 02-29-2001 Admit Weight: 53 kg BMI: 18 kg/m2
Diet: General
Daily Calorie needs (kcals): 1500 calories, assessed as HB +
20% for activity and blood pressure.
Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
Pt has been on a 3-day calorie count and has had an average
intake of 1100 calories. She was instructed to drink 2-3 cans
of liquid supplement to help promote weight gain.
She agrees with the plan and has my number for further
assessment. May want a Metabolic Rate as well. She takes
Codeine a day for knee and stomach pain.
Original entities and concepts are identified such as
"Hyperlidemia" , "knee","pain". However concepts associated
with addition to the text are not identified such as
"Aphasia", "blood pressure", "stomach". Also "metabolic rate"
is not identified. Does anyone know why this is?
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this email immediately. Any views or opinions expressed are solely
those of the author and do not necessarily represent those of the
University of Ulster. The University's computer systems may be
monitored and communications carried out on them may be recorded to
secure the effective operation of the system and for other lawful
purposes. The University of Ulster does not guarantee that this email
or any attachments are free from viruses or 100% secure. Unless
expressly stated in the body of a separate attachment, the text of
email is not intended to form a binding contract. Correspondence to
and from the University may be subject to requests for disclosure by
3rd parties under relevant legislation. The University of Ulster was
founded by Royal Charter in 1984 and is registered with company number
RC000726 and VAT registered number GB672390524.The primary contact
address for the University of Ulster in Northern Ireland is,Cromore
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