+1 Sent from my iPhone
On Apr 12, 2013, at 12:19 PM, "Tim Miller" <[email protected]<mailto:[email protected]>> wrote: 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]> [mailto:[email protected]] On Behalf Of giri vara prasad nambari Sent: Friday, April 12, 2013 11:06 AM To: [email protected]<mailto:[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? ________________________________ This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at [email protected]<mailto:[email protected]> and delete 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. 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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 Road, Coleraine, Co. Londonderry BT52 1SA
