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2013-09-30 Thread Vogel, James
No concept or annotation is created for "Birbeck granule deficiency" when I run the clinical pipeline in the CVD. I see it in the UMLS Metathesaurus Browser at https://uts.nlm.nih.gov//metathesaurus.html#C3150657;0;1;CUI;2012AB;EXACT_MATCH;*

Common Type System across systems?

2013-09-30 Thread Pei Chen
Richard, I, and few others had an interesting bar conversation... In the spirit of interoperability, What if we had a baseline common type system that could be reused across UIMA compatible NLP systems? Imagine for a moment that OpenNLP, ClearTK, ClearNLP, DKPro, cTAKES etc. if we could come up wit

RE: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor

2013-09-30 Thread Chen, Pei
Hi James, Glad you were able to make cTAKES work for your use case. The UMLS subset that is currently included in the resources should be: * International Classification of Diseases, Ninth Revision, Clinical Modification, 2012 ICD9CM_2012 ICD9CM ENG 0 20997 * Intern

RE: cTAKES DATA DICTIONARY

2013-09-30 Thread Chen, Pei
It's fixed: https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml Thanks to infra- I just had to set the mime:types in svn... Now we just need to beef up the docs a bit :) > -Original Message- > From: Masanz,

RE: cTAKES DATA DICTIONARY

2013-09-30 Thread Masanz, James J.
I think it's a bad idea to have a copy on the website. Too easy to get out of sync with SVN. I can view the copy in SVN OK with IE 8, but not with Chrome (only 2 browsers I've tried). -Original Message- From: dev-return-2058-Masanz.James=mayo@ctakes.apache.org [mailto:dev-return-20

RE: cTAKES DATA DICTIONARY

2013-09-30 Thread Chen, Pei
http://ctakes.apache.org/docs/TypeSystem.xml It's kind of weird that the xls works behind the apache site/web servers, but not within the svn repo. Does it ring a bell to anyone? I have a feeling that the svn web servers are doing something weird and not allowing the transformation. But either

Re: sentence number in WordToken

2013-09-30 Thread samir chabou
thanks for the feed back it's a good point, I did it also with selectCovering but as Richard mention I'll changed to indexCovering since it's faster. Samir From: "Chen, Pei" To: "dev@ctakes.apache.org" ; samir chabou Sent: Monday, September 30, 2013 12:10:

RE: sentence number in WordToken

2013-09-30 Thread Chen, Pei
Samir, I think Richard has a good point here. What is the use to require adding sentenceNumber() to BaseToken in the TypeSystem? If it's only temporary, It may be a good idea to do it programmatically with local variable rather than modifying the type system and having it stored in the CAS...?

Re: cTAKES DATA DICTIONARY

2013-09-30 Thread Richard Eckart de Castilho
Sounds cool, unfortunately as it is, it doesn't seem to work in Safari, Firefox, or Chrome :( (OS X) -- Richard On 30.09.2013, at 18:01, "Chen, Pei" wrote: > Thanks Murali! > It's actually pretty cool to have a quick reference to lookup what all the > different fields mean. > FYI: I've made t

RE: cTAKES DATA DICTIONARY

2013-09-30 Thread Chen, Pei
Thanks Murali! It's actually pretty cool to have a quick reference to lookup what all the different fields mean. FYI: I've made the commits to: http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml which references the

Re: sentence number in WordToken

2013-09-30 Thread Richard Eckart de Castilho
Hi, if you do many selectCovering calls, you may be faster using indexCovering once and then using the lookup index it produces. IMHO type systems should not contain information that can easily be calculated at runtime (e.g. sentence number, token number, etc.). Mind, I have no say here ;) Just

RE: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor

2013-09-30 Thread Vogel, James
That worked and I see how I can change the code to do both SNOMED and ICD9. I added an index by doing: CREATE INDEX 'umls_ms_2011ab_cui' ON umls_ms_2011ab (cui); I needed to change the database from 'read-only', is that going to cause any other problems? What subset of ICD9 is in the dictionary

sentence number in WordToken

2013-09-30 Thread samir chabou
Hi Pei, I though this may be have some use …   Because I need to know if two or more words tokens belong to the same sentence; and since WordToken does not define the feature sentence number. I added it to the TypeSystem. These are the steps:   1)  I added the sentence number features for the