Whether nucleotide is classified as a medication depends on the dictionary used. It appears nucleotide is not within the default dictionary as a medication
In order to have drugner annotations, org.apache.ctakes.drugner.ae.DrugMentionAnnotator needs to be in the pipeline. (When using xml descriptors, that's desc\ctakes-drug-ner\desc\analysis_engine\DrugMentionAnnotator.xml) However, I see that annotator listed in the AggregatePlaintextFastUMLSProcessor pipeline. I'll take a look at why the drugner annotations are not being created. When I use AggregatePlaintextFastUMLSProcessor in 3.2.2, medications *are* getting annotated - but they are being annotated as org.apache.ctakes.typesystem.type.textsem.MedicationEventMention which is found under org.apache.ctakes.typesystem.type.textsem.EventMention hope this helps -- James On Thu, Mar 23, 2017 at 9:35 AM, MAZE, Christian <[email protected]> wrote: > Hi, > > > > I am using the v3.2.2 ctakes. > > I copied the v3.2.1.1 resources. > > > > I used another tool for extracting chemical/drug entities and when > processing my input text, I got the following results: > > 1092 1107 nucleotide 1517 > > 1165 1178 aspartic acid > > 1184 1191 glycine > > 1195 1204 codon 506 > > 1254 1257 Asp > > > > My input test text is : > > A novel missense mutation Asp506Gly in Exon 13 of the F11 gene in an > asymptomatic Korean woman with mild factor XI deficiency. Factor XI (FXI) > deficiency is a rare autosomal recessive coagulation disorder most commonly > found in Ashkenazi and Iraqi Jews, but it is also found in other ethnic > groups. It is a trauma or surgery-related bleeding disorder, but > spontaneous bleeding is rarely seen. The clinical manifestation of bleeding > in FXI deficiency cases is variable and seems to poorly correlate with > plasma FXI levels. The molecular pathology of FXI deficiency is mutation in > the F11 gene on the chromosome band 4q35. We report a novel mutation of the > F11 gene in an 18-year-old asymptomatic Korean woman with mild FXI > deficiency. Pre-operative laboratory screen tests for lipoma on her back > revealed slightly prolonged activated partial thromboplastin time (45.2 > sec; reference range, 23.2-39.4 sec). Her FXI activity (35%) was slightly > lower than the normal FXI activity (reference range, 50-150%). Direct > sequence analysis of the F11 gene revealed a heterozygous A to G > substitution in nucleotide 1517 (c.1517A>G) of exon 13, resulting in the > substitution of aspartic acid with glycine in codon 506 (p.Asp506Gly). To > the best of our knowledge, the Asp506Gly is a novel missense mutation, and > this is the first genetically confirmed case of mild FXI deficiency in > Korea. > > > > When I start the same treatment using ctakes and the > AggregatePlaintextFastUMLSProcessor annotator file. > > > > No drug entity is detected inside drugner leaf ( > > For example I would have thought that nucleotide be classified in the > drugner leaf. > > > > Please could you correct me if I missed anything ? > > > > Christian > > > This message contains information that may be privileged or confidential > and is the property of the Capgemini Group. It is intended only for the > person to whom it is addressed. If you are not the intended recipient, you > are not authorized to read, print, retain, copy, disseminate, distribute, > or use this message or any part thereof. If you receive this message in > error, please notify the sender immediately and delete all copies of this > message. >
