Hi Marcello, I am hoping that somebody will answer your question with a "Yes, I have a fhir / owl / bioc / json writer to share".
Unfortunately I am not aware of any that are publicly available for ctakes output. BioC should be fairly easy to do as an -xml- rearrangement of what ctakes can produce. Fhir seems to be gaining a lot of momentum, and I know that fhir output is possible ... but I don't know of a project that goes directly from ctakes annotations to fhir. If you do find or make a ctakes writer for one of these standards please share it. Thanks, Sean -----Original Message----- From: Marcello Bax UFMG [mailto:[email protected]] Sent: Thursday, October 26, 2017 7:48 PM To: [email protected] Subject: Re: Can cTAKES output AUI? [EXTERNAL] Hi, Lani and others, two days ago I asked a similar question to the user list @ctakes.apache.org but I realize now that dev list would be a better forum, regarding my inquiry. The question was: > Could anyone clarify me if cTAKES-generated annotations follow some standard format or ontology, like Web Annotation Ontology (W3C), BioC, and others? It would facilitate interoperability issues. I will be grateful if anyone here can send me this information. Thanks, Marcello On Thu, Oct 26, 2017 at 5:22 AM, Lani Uni <[email protected]> wrote: > Hello all, > > I am using UMLS to annotate medical forms and would like to know which > terminology (SAB in MRCONSO) is used by cTAKES for the generated annotation. > Is there a way to get this information (something like AUI)? > I see in OntologyConcept one can get terminology using > getCodingScheme, but this only gives me back info about UMLS. > On the other hand, getPreferredText in UmlsConcept seems to give me > the PN or PT of an concept but not the actual term used for annotation > generation. > Any idea to help me a step further? > > best, > Lani
