Hi all, I’m glad that there continues to be interest in the fast alternative to the dictionary lookup and I welcome all testing.
GBM actually is Glioblastoma Multiforme – hence the “M”. The WHO name is the abbreviated “Glioblastoma”, but they are actually not (as far as I can discern) different things. If you check the metathesaurus 2011ab, GBM brings up both Glioblastoma C0017636 and Glioblastoma Multiforme C1621958. The first comes from Mesh and NCI, the second from CSP. If you look at the definitions they are synonymous: “malignant form of astrocytoma histologically characterized by pleomorphism of cells, nuclear atypia, microhemorrhage and necrosis; may arise in any region of the central nervous system, with a predilection for the cerebral hemispheres, basal ganglia, and commissural pathways.” Mapping to a different CUI in the UMLS does not always mean that they are truly different concepts. It often means that they came from 2 different source dictionaries (such as in this case). Also check https://en.wikipedia.org/wiki/Glioblastoma_multiforme But I am a little confused: are you saying that you got only Glioblastoma Multiforme C1621958 and not Glioblastoma C0017636 ? When I run it I get both returns … Britt is correct (thank you) in that if you change the default minimum span from 3 to 2 you will get Cutaneous Mastocytosis C1136033 within “5.5 cm”. The minimum span is 3 (not 2) to prevent things like the obviously garbage return of Cutaneous Mastocytosis for every “cm”. However, feel free to change it to fit your purposes. 2 characters is the minimum – you cannot lookup 1 character terms with the default dictionary. You can do so with a custom dictionary if you like – which might be useful if you just have 1 or 2 single-character terms. Sean From: britt fitch [mailto:britt.fi...@wiredinformatics.com] Sent: Monday, June 22, 2015 9:24 AM To: dev@ctakes.apache.org Subject: Re: The fast dictionary pipeline vs. the regular one Regarding the miss on “cm” in #2, you might want to check out the dictionary xml descriptor or uimafit wiring, depending on which you are using, for the parameter “minimumSpan”. If I recall correctly the default minimum span is 3 characters, however you can reduce it to 2 if desired. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com<mailto:britt.fi...@wiredinformatics.com> On Jun 21, 2015, at 2:45 PM, Miller, Timothy <timothy.mil...@childrens.harvard.edu<mailto:timothy.mil...@childrens.harvard.edu>> wrote: Sean wrote the fast version and may be able to answer your specific questions. But in general, the fast dictionary does not match performance exactly -- it is not implementing an equivalent search and it has different indexing methods. We are happy to receive reports of what seem like bugs, though, any new software is likely to have some. What I will say is that I know Sean has run some (as yet unpublished) experiments and we believe that in the aggregate the new system output is at least as high quality as the older one. Tim ________________________________________ From: Oranit Dror [ora...@algotec.co.il<mailto:ora...@algotec.co.il>] Sent: Sunday, June 21, 2015 4:37 AM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: The fast dictionary pipeline vs. the regular one Hello, I am using ctakes 3.2.2 with the regular pipeline. Recently, I have tested the fast dictionary pipeline and indeed it is much faster. However, I have encountered with several quality differences in the returned annotations. For example: 1. With the fast pipeline, the term "GBM" is annotated as "glioblastoma multiforme", while in the regular pipeline it is annotated as "glioblastoma". Note that according to the UMLS DB, the concept of "GBM" is "glioblastoma" and "glioblastoma multiforme" is mapped to a narrower concept. 2. The word "cm" in a phrase like "5.5 cm X 2.6 cm" is annotated by the regular pipeline as "Cutaneous Mastocytosis", while in the fast pipeline it is not annotated as a medical term (as expected and as in UMLS). Any explanation for the differences? Thank you, Oranit.
