I second Tim's comment. Information in the link provided by Troy is really helpful, if "user guide" has this link may be in ctakes-resources downloaded section, that helps users.
Right now I am limited myself as user of ctakes and trying to understand what I may get our of the box, how much I need to customize to develop my idea into a to prototype. You guys have been really helpful with quick replies with solution pointers. Few days back, I was about to give-up, but with the help and pointers I am getting from you guys, motivated me to stay with ctakes and explore more. Now I am almost ready to finalize infrastructure and take-off for prototype development(few more things to hash-out and hoping they will be quick). Thanks again for your time and help. Thank you, Giri On Fri, Apr 12, 2013 at 12:19 PM, Tim Miller < [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]<[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]> 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]] > *Sent:* Friday, April 12, 2013 10:26 AM > *To:* [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]] > *Sent:* 12 April 2013 15:10 > *To:* <[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]> 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] 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. 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 Road, Coleraine, Co. Londonderry BT52 1SA **** > > **** > > **** > ------------------------------ > > > 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] 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. 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 Road, Coleraine, Co. Londonderry BT52 1SA **** > > >
