Thanks Pei.
Sure, that would be great, add me. Jg — Sent from Mailbox for iPhone On Fri, Apr 4, 2014 at 10:15 AM, Chen, Pei <pei.c...@childrens.harvard.edu> wrote: > John, > You should have committer rights now... I would suggest opening a Jira item > just so that it can be tracked. > But you should be able create a subdir within > https://svn.apache.org/repos/asf/ctakes/sandbox and do an svn commit. > As a side note: ctakes-vm.apache.org has been created now. John, let me know > if you would like to added as list of maintainers. > We can use that machine to host any of the demo's. > It requires passwordless ssh so you'll need to ssh-keygen and save them via > http://id.apache.org. > --Pei >> -----Original Message----- >> From: John Green [mailto:john.travis.gr...@gmail.com] >> Sent: Thursday, April 03, 2014 6:05 PM >> To: dev@ctakes.apache.org >> Cc: dev@ctakes.apache.org >> Subject: RE: ctakes-vm.apache.org >> >> 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 >> >>> >>
