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Posted to dev@ctakes.apache.org by Pei Chen <ch...@apache.org> on 2014/03/18 16:15:12 UTC
ctakes-vm.apache.org
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
RE: ctakes-vm.apache.org
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Andy,
Let me know if you're able to ssh -l -v to andymc@ctakes-vm.apache.org
I believe all you would need to do is run ssh-keygen and then copy your public key to id.apache.org.
James:
opiekey is only required for sudo access. I see you're able to log in successfully already.
Nethertheless, Jan reset opiekey so you can try again if needed.
https://issues.apache.org/jira/browse/INFRA-7451
--Pei
> -----Original Message-----
> From: andy mcmurry [mailto:mcmurry.andy@gmail.com]
> Sent: Monday, April 07, 2014 5:43 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctakes-vm.apache.org
>
> On a mac here, also having trouble logging in to the VM.
> Looking more into the keys situation.
>
> On mac, there is this problem: "no support for PKCS#11"
> Which I'm working to resolve.
>
>
>
>
> On Sat, Apr 5, 2014 at 12:15 PM, John Green
> <jo...@gmail.com>wrote:
>
> > 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.Chen@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.green@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
> > >> <Pe...@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.green@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
> > >> <mc...@gmail.com>
> > >> > wrote:
> > >> >> Yes! Impeccable timing. Where can we find the python source?
> > >> >> On Apr 2, 2014 8:33 AM, "John Green"
> > >> >> <jo...@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
> > >> >>> <mc...@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
> > >> >>> > <ch...@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
> > >> >>> >>
> >
Re: ctakes-vm.apache.org
Posted by andy mcmurry <mc...@gmail.com>.
On a mac here, also having trouble logging in to the VM.
Looking more into the keys situation.
On mac, there is this problem: "no support for PKCS#11"
Which I'm working to resolve.
On Sat, Apr 5, 2014 at 12:15 PM, John Green <jo...@gmail.com>wrote:
> 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.Chen@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.green@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
> >> <Pe...@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.green@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
> >> <mc...@gmail.com>
> >> > wrote:
> >> >> Yes! Impeccable timing. Where can we find the python source?
> >> >> On Apr 2, 2014 8:33 AM, "John Green" <jo...@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
> >> >>> <mc...@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 <ch...@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
> >> >>> >>
>
RE: ctakes-vm.apache.org
Posted by John Green <jo...@gmail.com>.
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 <Pe...@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.green@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
>> <Pe...@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.green@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
>> <mc...@gmail.com>
>> > wrote:
>> >> Yes! Impeccable timing. Where can we find the python source?
>> >> On Apr 2, 2014 8:33 AM, "John Green" <jo...@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
>> >>> <mc...@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 <ch...@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
>> >>> >>
RE: ctakes-vm.apache.org
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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.green@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
> <Pe...@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.green@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
> <mc...@gmail.com>
> > wrote:
> >> Yes! Impeccable timing. Where can we find the python source?
> >> On Apr 2, 2014 8:33 AM, "John Green" <jo...@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
> >>> <mc...@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 <ch...@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
> >>> >>
RE: ctakes-vm.apache.org
Posted by John Green <jo...@gmail.com>.
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 <Pe...@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.green@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 <mc...@gmail.com>
> wrote:
>> Yes! Impeccable timing. Where can we find the python source?
>> On Apr 2, 2014 8:33 AM, "John Green" <jo...@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 <mc...@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 <ch...@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
>>> >>
RE: ctakes-vm.apache.org
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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.green@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 <mc...@gmail.com>
wrote:
> Yes! Impeccable timing. Where can we find the python source?
> On Apr 2, 2014 8:33 AM, "John Green" <jo...@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 <mc...@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 <ch...@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
>> >>
Re: ctakes-vm.apache.org
Posted by John Green <jo...@gmail.com>.
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 <mc...@gmail.com>
wrote:
> Yes! Impeccable timing. Where can we find the python source?
> On Apr 2, 2014 8:33 AM, "John Green" <jo...@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 <mc...@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 <ch...@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
>> >>
Re: ctakes-vm.apache.org
Posted by andy mcmurry <mc...@gmail.com>.
Yes! Impeccable timing. Where can we find the python source?
On Apr 2, 2014 8:33 AM, "John Green" <jo...@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 <mc...@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 <ch...@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
> >>
Re: ctakes-vm.apache.org
Posted by John Green <jo...@gmail.com>.
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 <mc...@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 $$$ are invested in getting phenotype concepts --
> indications, diseases, problem lists -- linked to patient test results
> including DNA / RNA / etc. In industry, most of the curation work is done
> manually because platforms like cTAKES are not yet immediately accessible.
> I have written code to
> A) start automating the installer tasks for cTAKES on Ubuntu 13
> B) install UMLS NLP tools metamap, semrep, semmed
> C) mirror NLM content that extends UMLS annotation
> *SO THAT : *
> Mentions of diseases relationships -- SNOMED-CT, HPO, OMIM, GTR, UMLS --
> reference the same semantic relationships in UMLS Clinical Terms and
> Genetic Test Reference. This is powerful and all credit to the NLM for
> creating MedGen and GTR, new crucial additions to the UMLS. To my
> knowledge, these new sources have not been fully utilized by the medical
> NLP community.
> *I'm strongly advocating for a cTAKES VM that indexes UMLS concepts in the
> same say that NCBI indexes UMLS linked Medical Genetics terms.*
> Towards this goal, if other committers are interested, I'm 100% time
> committed to this problem.
> *TL;DR*: at minimum, having a demo site makes cTAKES more accessible. We
> should demonstrate rather than explain every feature of cTAKES. I'm working
> 100% on the Clinical Text +BioNLP problem. If that interests you, let me
> know I'm convinced this area has huge, understudied potential.
> --AndyMC
> On Tue, Mar 18, 2014 at 8:15 AM, Pei Chen <ch...@apache.org> wrote:
>> FYI:
>> ASF Infra is setting up our VM for demo purposes.
>> INFRA-7451
>>
>> If you need access, feel free to let us now.
>> Initial maintainers: james-masanz, andymc,chenpei
>> --Pei
>>
Re: ctakes-vm.apache.org
Posted by andy mcmurry <mc...@gmail.com>.
Yes! I have been working full time on the "apt-get install" task specific
to medical genetics: http://www.ncbi.nlm.nih.gov/medgen
Right now, millions of $$$ 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 <ch...@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
>