UMLS SemRep and Semantic Medline are probably better resources for parsing papers with respect to Subject, Predicate, Object.
https://semrep.nlm.nih.gov/ https://skr3.nlm.nih.gov/SemMed On Mon, Jun 18, 2018 at 2:40 AM, Don Flinn <fl...@alum.mit.edu> wrote: > I want to parse medical research papers and am looking at using Ctakes. I > do realize that Ctkes is aimed at Clinical Reports, but I would like to see > if I can use it for my purposes. I'm initially looking to get a tuple of > Subject, Predicate, Object for each sentence and later additional semantic > information.. > > I modified ClinicalPipelineFactory.java to use the following portion of a > research report - > > "A research team based in Houston has developed a prototype for a > “bionic” heart replacement. Other designs all mimic the beating of > a heart, but due to many moving parts, the mechanical hearts > would quickly wear out. The heart developed by BiVACOR does not > beat, and instead has one moving part which propels the blood > throughout the body. The bionic heart has been safely and > successfully transplanted into animals leading to very promising > results." > > I got the following result - > Entity: heart === Polarity: 1 === Uncertain? false === Subject: patient === > Generic? false === Conditional? false === History? false > Entity: replacement === Polarity: 1 === Uncertain? false === Subject: > patient === Generic? false === Conditional? false === History? false > Entity: mimic === Polarity: 0 === Uncertain? false === Subject: null === > Generic? false === Conditional? false === History? false > Entity: heart === Polarity: 1 === Uncertain? false === Subject: patient === > Generic? false === Conditional? false === History? false > Entity: heart === Polarity: 1 === Uncertain? false === Subject: patient === > Generic? false === Conditional? false === History? false > Entity: heart === Polarity: 1 === Uncertain? false === Subject: patient === > Generic? false === Conditional? false === History? false > > I assume my problem is related to the Snomed database, which is not trained > for what I want. > > My questions - > Is my assumption correct? > Should I attempt to modify/extend Snomed? > Is there a better/different way to query Snomed to meet my needs? > Is there an existing database that I could use with Ctakes that would more > meet my needs? > Should I instead use the Stanford Java NLP system or the Apache OpenNLP? > I'll still need a database. > > Thank you for any suggestions > Don >
