John, If there are no other objections, you can also put it directly in sandbox https://svn.apache.org/repos/asf/ctakes/sandbox/ It may make it easier in the future if folks decided to integrate into cTAKES... and possibly save any potential IP/License questions...
--Pei ________________________________________ From: John Green [john.travis.gr...@gmail.com] Sent: Wednesday, April 02, 2014 6:24 PM To: dev@ctakes.apache.org Subject: Re: ctakes-vm.apache.org Great! Let me clean it up this weekend and ill throw it out onto my github. Will post link soon; nlt cob this weekend. JG — Sent from Mailbox for iPhone On Wed, Apr 2, 2014 at 1:53 PM, andy mcmurry <mcmurry.a...@gmail.com> wrote: > 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 >> >>
