Would love to! Ive only submitted those example notes I did though to a jira ticket. How do I push to the sandbox dir? Any special permissions I need?
JG — Sent from Mailbox for iPhone On Wed, Apr 2, 2014 at 10:51 PM, Chen, Pei <pei.c...@childrens.harvard.edu> wrote: > 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 >>> >>
