Ah - you meant best way to test. Sorry, I misread your inquiry as a best way to write output.
Yes, that is a great introduction document for ctakes and early tests. There are a few small test classes in ctakes that read anafora files, run ctakes and run agreement numbers. You can find some in the ctakes-temporal module. I didn't write them, and I think that they are built-to-fit purpose-driven classes, but you could try to adapt them to a general purpose case. That would be a great thing to have in ctakes! Sean -----Original Message----- From: Leander Melms [mailto:me...@students.uni-marburg.de] Sent: Friday, March 17, 2017 1:46 PM To: dev@ctakes.apache.org Subject: Re: Evaluate cTAKES perfomance Hi Sean, thank you (again) for your help and feedback! I'll give it a try! Seems like the authors of the publication "Mayo clinical Text analysis and Knowledge Extraction System" (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC2995668_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=PZ0f8s12PJA8W5B4hMlw-0F83VAM9m6E1ypWVaT2hcM&s=Isgii7k_fUy_qLsyqEdh15wKLAnFT6_KeE7zN1dE73Q&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC2995668_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=PZ0f8s12PJA8W5B4hMlw-0F83VAM9m6E1ypWVaT2hcM&s=Isgii7k_fUy_qLsyqEdh15wKLAnFT6_KeE7zN1dE73Q&e= >) did this as well. Thank you Leander > On 17 Mar 2017, at 18:33, Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Hi Leander, > > There is no single correct way to do this, but a couple of similar > classes exist. Well, one sat in my sandbox for two years until about 5 > seconds ago as I only just checked it in. Anyway, take a look at two classes > in ctakes-core org.apache.ctakes.core They are TextSpanWriter and > CuiCountFileWriter. > > TextSpanWriter writes annotation name | span | covered text in a file, one > per document. > > CuiCountFileWriter writes a list of discovered cuis and their counts. > > It sounds like you are interested in a combination of both - basically > TextSpanWriter with the added output of CUIs. > > You can also have a look at EntityCollector of > org.apache.ctakes.core.pipeline. It has an annotation engine that keeps a > running list of "entities" for the whole run, doc ids, spans, text and cuis. > > Sean > > > -----Original Message----- > From: Leander Melms [mailto:me...@students.uni-marburg.de] > Sent: Friday, March 17, 2017 1:09 PM > To: dev@ctakes.apache.org > Subject: Re: Evaluate cTAKES perfomance > > Sorry for writing again. I just have a quick question: My idea is to parse > the cTAKES output to a text file with a structure like this > DocName|Spans|CUI|CoveredText|ConceptType and do the same with the cold > standart (from anafora). > > Is this a correct way to do this? > > I'm new to the subject and happy about the tiniest information on the topic. > > Thanks > Leander > > I >> On 17 Mar 2017, at 12:05, Leander Melms <me...@students.uni-marburg.de> >> wrote: >> >> Hi, >> >> I've integrated a custom dictionary, retrained some of the OpenNLP models >> and would like to evaluate the changes on a gold standard. I'd like to >> calculate the precision, the recall and the f1-score to compare the results. >> >> My question is: Does cTAKES ship with some evaluation / test scripts? What >> is the best strategry to do this? Has anyone dealt with this topic before? >> >> I'm happy to share the results afterwards if there is interest for it. >> >> Thanks >> Leander >> > >
