Yes! Impeccable timing. Where can we find the python source? On Apr 2, 2014 8:33 AM, "John Green" <john.travis.gr...@gmail.com> wrote:
> Andy: this is very interesting and exciting. > > > > > I hacked out a script that makes a visually appealing representation of > the aggregate pipeline in d3js that, at least for a clinician, is a nice > overall summary of the meta data generated from the pipeline. Its really no > more than a parser of the xml through the type system spitted out into > json, but when I was talking to my informatics department who didnt know > much at all about ctakes, it was a great visual summary. Its in python. I > dont know if youd want it but it might be worth having the "demo site" spit > out a visually appealing graphic like this automatically. If not in python > it might be worth adapting it to whatever your using for a platform to spit > out the json for the d3js graphic im using. > > > > > John > > -- > Sent from Mailbox for iPhone > > On Thu, Mar 20, 2014 at 5:31 AM, andy mcmurry <mcmurry.a...@gmail.com> > wrote: > > > Yes! I have been working full time on the "apt-get install" task specific > > to medical genetics: http://www.ncbi.nlm.nih.gov/medgen > > Right now, millions of $$$ are invested in getting phenotype concepts -- > > indications, diseases, problem lists -- linked to patient test results > > including DNA / RNA / etc. In industry, most of the curation work is done > > manually because platforms like cTAKES are not yet immediately > accessible. > > I have written code to > > A) start automating the installer tasks for cTAKES on Ubuntu 13 > > B) install UMLS NLP tools metamap, semrep, semmed > > C) mirror NLM content that extends UMLS annotation > > *SO THAT : * > > Mentions of diseases relationships -- SNOMED-CT, HPO, OMIM, GTR, UMLS -- > > reference the same semantic relationships in UMLS Clinical Terms and > > Genetic Test Reference. This is powerful and all credit to the NLM for > > creating MedGen and GTR, new crucial additions to the UMLS. To my > > knowledge, these new sources have not been fully utilized by the medical > > NLP community. > > *I'm strongly advocating for a cTAKES VM that indexes UMLS concepts in > the > > same say that NCBI indexes UMLS linked Medical Genetics terms.* > > Towards this goal, if other committers are interested, I'm 100% time > > committed to this problem. > > *TL;DR*: at minimum, having a demo site makes cTAKES more accessible. We > > should demonstrate rather than explain every feature of cTAKES. I'm > working > > 100% on the Clinical Text +BioNLP problem. If that interests you, let me > > know I'm convinced this area has huge, understudied potential. > > --AndyMC > > On Tue, Mar 18, 2014 at 8:15 AM, Pei Chen <chen...@apache.org> wrote: > >> FYI: > >> ASF Infra is setting up our VM for demo purposes. > >> INFRA-7451 > >> > >> If you need access, feel free to let us now. > >> Initial maintainers: james-masanz, andymc,chenpei > >> --Pei > >>
