Ah. So it will get CIN 2 (in SNOMED) CIN III (in SNOMED) CIN 3 (in SNOMED) but the rest are not in SNOMED?
I wonder why it doesn't get CIN I? It looks like that exists in SNOMED (though I don't fully understand what all the symbols mean in the umls browser). > CIN I - Cervical intraepithelial neoplasia 1 > [A3002690/SNOMEDCT/SY/285836003] On 09/03/2013 09:55 PM, Pei Chen wrote: > It has the correct parse (POS, chunks, and lookupwindow)- but some of > the terms do not exist in SNOMED- > CIN 2 - Cervical intraepithelial neoplasia 2 > [A3002688/SNOMEDCT/SY/285838002] exists but not CIN II. > CIN III [A3333965/SNOMEDCT/SY/20365006] also exists that's why it was > able to perform the lookup successfully. > Note that CIN II synonyms do exist in other umls thersauses such as > MEDCIN, CCPSS though. However, the bundled cTAKES dictionaries only > contain (MeSH, SNOMEDCT, RxNORM, NCI, ICD9) IRRC. > > --Pei > > On Tue, Sep 3, 2013 at 9:44 PM, Miller, Timothy > <timothy.mil...@childrens.harvard.edu> wrote: >> That is a good question, Ted! >> >> I tried it with a simple context: "The patient has a CIN III." I'm not >> sure if that is a correct context but I was able to duplicate your >> findings. (Finds a CUI for CIN III but not if you change it to CIN II) >> >> My first thought was that it is the chunker. But the chunker seems to >> get it right, as CIN II and CIN III are both called NPs, and similarly >> the LookupWindowAnnotator handles them both identically. So that >> suggests it is a problem with the actual lookup of the tokens in the >> LookupWindow. >> >> That's all I can do for now but maybe someone else who knows more about >> its behavior offhand will have an idea. >> >> Tim >> >> >> >> >> On 09/03/2013 08:24 PM, Assur, Ted wrote: >>> I'm trying to understand what would prevent the >>> AggregatePlaintextUMLSProcessor AE from correctly parsing specific problems >>> that are defined in the UMLS version used by cTAKES. >>> >>> For example, >>> CIN (Cervical Intraepithelial Neoplasia) in its general usage is parsed out >>> as UMLS CUI C0206708. >>> >>> CIN comes in 3 grades, 1, 2 and 3. Sometimes this is reported with Roman >>> Numerals, I,II, and III. >>> >>> cTAKES correctly identifies "CIN 3" and "CIN III" with UMLS CUI C0851140: >>> "Carcinoma in situ of uterine cervix." >>> >>> However, I cannot get it to recognize CIN 1, CIN I, CIN 2, or CIN II as >>> their correct concepts, "Cervical intraepithelial neoplasia grade 1" and >>> "Cervical intraepithelial neoplasia grade 2" respectively. >>> >>> Is there a way to tune the detection of UMLS concepts? >>> >>> >>> >>> >>> -------------------------------------------- >>> Ted Assur >>> IT Solutions Architect for Cancer Research >>> Providence Health & Services >>> ted.as...@providence.org >>> 503-215-6476 >>> >>> Crede, ut intelligas. >>> Intellego, ut credam. >>> >>> >>> >>> >>> ________________________________ >>> >>> This message is intended for the sole use of the addressee, and may contain >>> information that is privileged, confidential and exempt from disclosure >>> under applicable law. If you are not the addressee you are hereby notified >>> that you may not use, copy, disclose, or distribute to anyone the message >>> or any information contained in the message. If you have received this >>> message in error, please immediately advise the sender by reply email and >>> delete this message. >>>
