Hi Akhilesh, For Eclipse Luna, where did you download required SCM connectors (Subversion team provider connectors 1.7+.), and "m2e - Maven Integration for Eclipse"?
Thanks, Justin On Wed, Jul 15, 2015 at 10:52 AM, Akhilesh Patel < [email protected]> wrote: > Luna > > > Sent from Samsung Mobile > > > -------- Original message -------- > From: Justin Zhang > Date:15/07/2015 8:54 PM (GMT+05:30) > To: [email protected] > Subject: Re: corresponding versions ctakes and stakes-resource > > Which Eclipse package did you use? > > Mars Packages <https://eclipse.org/downloads/packages/release/Mars/R> > Luna Packages <https://eclipse.org/downloads/packages/release/Luna/SR2> > Kepler Packages > <https://eclipse.org/downloads/packages/release/Kepler/SR2> > Juno Packages <https://eclipse.org/downloads/packages/release/Juno/SR2> > Indigo Packages > <https://eclipse.org/downloads/packages/release/Indigo/SR2> > Helios Packages > <https://eclipse.org/downloads/packages/release/Helios/SR2> > Galileo Packages > <https://eclipse.org/downloads/packages/release/Galileo/SR2> > Ganymede Packages > <https://eclipse.org/downloads/packages/release/Ganymede/SR2> > Europa Packages > <https://eclipse.org/downloads/packages/release/Europa/WINTER> > All Releases <https://eclipse.org/downloads/packages/all> > > > > On Wed, Jul 15, 2015 at 9:36 AM, Akhilesh Patel < > [email protected]> wrote: > >> Yes I ran using source code as well as using cvd provided by them >> >> >> Sent from Samsung Mobile >> >> >> -------- Original message -------- >> From: Justin Zhang >> Date:15/07/2015 8:02 PM (GMT+05:30) >> To: [email protected] >> Subject: Re: corresponding versions ctakes and stakes-resource >> >> Did you run from source code? >> Any successful experience with binary ctakes? >> >> >> On Wed, Jul 15, 2015 at 9:27 AM, Akhilesh Patel < >> [email protected]> wrote: >> >>> You can download it from their svn repository. Please use following url >>> to get latest version >>> >>> http://ctakes.apache.org/downloads.cgi >>> >>> Sent from Samsung Mobile >>> >>> >>> -------- Original message -------- >>> From: Justin Zhang >>> Date:15/07/2015 7:45 PM (GMT+05:30) >>> To: [email protected] >>> Subject: Re: corresponding versions ctakes and stakes-resource >>> >>> Hello Akhilesh, >>> >>> Thank you for quick response. >>> >>> What is the link to download 3.2.2-SNAPSHOT? and What version of ctakes >>> resource did you use? >>> >>> >>> Is it different from >>> https://www.apache.org/dist/ctakes/ctakes-3.2.2/apache-ctakes-3.2.2-bin.tar.gz >>> ? >>> >>> I tried this one and with ctakes resource 3.2.1.1. It did not for these >>> 3 pipelines. >>> >>> Justin >>> >>> >>> On Wed, Jul 15, 2015 at 9:03 AM, Akhilesh Patel < >>> [email protected]> wrote: >>> >>>> Hi Justin, >>>> >>>> >>>> >>>> I have not worked on smoking status however I am able to capture “Side >>>> effects” and “Drug annotation” information from clinical notes. Both the >>>> module working form me. >>>> >>>> I am using following xml files to extract the information >>>> >>>> >>>> >>>> <delegateAnalysisEngine key=*"DrugMentionAnnotator"*> >>>> >>>> <import location= >>>> *"../../ctakes/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"* >>>> /> >>>> >>>> </delegateAnalysisEngine> >>>> >>>> >>>> >>>> <delegateAnalysisEngine key=*"SideEffect"*> >>>> >>>> <import location= >>>> *"../../ctakes/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml"* >>>> /> >>>> >>>> </delegateAnalysisEngine> >>>> >>>> >>>> >>>> Ctakes version I am using is 3.2.2-SNAPSHOT. >>>> >>>> >>>> >>>> Thanks, >>>> >>>> Akhilesh >>>> >>>> >>>> >>>> *From:* Justin Zhang [mailto:[email protected]] >>>> *Sent:* Wednesday, July 15, 2015 7:22 PM >>>> *To:* [email protected] >>>> *Subject:* Re: corresponding versions ctakes and stakes-resource >>>> >>>> >>>> >>>> Hello again, >>>> >>>> For the same purpose as the first email: I have put a lot of efforts in >>>> order to run this few pipelines with different versions ctakes/resources >>>> and different computer systems, and did not succeed. Most errors are "URIs" >>>> or "File (xml) not found". >>>> >>>> I am so eager to move forward. Could anyone help me through the steps >>>> for "Smoking Status", and then "Side effects"/"Drug Annotations"? I would >>>> need the information of specific ctakes binary version and correct match >>>> resources, and relevant necessary steps. >>>> >>>> Great appreciation!!! >>>> >>>> Justin >>>> >>>> >>>> >>>> On Tue, Jul 14, 2015 at 4:04 PM, Justin Zhang <[email protected]> >>>> wrote: >>>> >>>> Hello Everyone, >>>> >>>> >>>> >>>> I am looking to load following AE (analysis engine) from runctakesCVD.sh >>>> >>>> >>>> >>>> · >>>> <cTAKES_HOME>/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml >>>> (The annotator to obtain document or patient-level smoking status) >>>> >>>> · >>>> <cTAKES_HOME>/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml >>>> (The annotator to find side effect mentions and sentences from clinical >>>> documents) >>>> >>>> · >>>> <cTAKES_HOME>/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcesor.xml >>>> (The annotator to obtain drug annotations) >>>> >>>> >>>> >>>> What corresponding ctakes binary and ctakes resource should I use? >>>> >>>> >>>> >>>> In download page, current resource versions are 3.0.1, 3.10, 3.13, >>>> 3.2.0, 3.2.1.1 >>>> >>>> >>>> >>>> current ctakes versions are 3.1.0, 3.1.1, 3.2.0, 3.2.1, 3.2.2 >>>> >>>> >>>> >>>> thanks, >>>> >>>> >>>> >>>> -- >>>> >>>> Justin >>>> >>>> >>>> >>>> >>>> -- >>>> >>>> Justin >>>> =========================================================================================================================================================================================== >>>> DISCLAIMER: The information contained in this message (including any >>>> attachments) is confidential and may be privileged. If you have received it >>>> by mistake please notify the sender by return e-mail and permanently delete >>>> this message and any attachments from your system. Any dissemination, use, >>>> review, distribution, printing or copying of this message in whole or in >>>> part is strictly prohibited. Please note that e-mails are susceptible to >>>> change. CitiusTech shall not be liable for the improper or incomplete >>>> transmission of the information contained in this communication nor for any >>>> delay in its receipt or damage to your system. CitiusTech does not >>>> guarantee that the integrity of this communication has been maintained or >>>> that this communication is free of viruses, interceptions or interferences. >>>> ==================================================================================================================================================================== >>>> >>>> >>> >>> >>> >>> -- >>> Justin >>> >>> =========================================================================================================================================================================================== >>> DISCLAIMER: The information contained in this message (including any >>> attachments) is confidential and may be privileged. If you have received it >>> by mistake please notify the sender by return e-mail and permanently delete >>> this message and any attachments from your system. Any dissemination, use, >>> review, distribution, printing or copying of this message in whole or in >>> part is strictly prohibited. Please note that e-mails are susceptible to >>> change. CitiusTech shall not be liable for the improper or incomplete >>> transmission of the information contained in this communication nor for any >>> delay in its receipt or damage to your system. CitiusTech does not >>> guarantee that the integrity of this communication has been maintained or >>> that this communication is free of viruses, interceptions or interferences. >>> ==================================================================================================================================================================== >>> >>> >> >> >> >> -- >> Justin >> >> =========================================================================================================================================================================================== >> DISCLAIMER: The information contained in this message (including any >> attachments) is confidential and may be privileged. If you have received it >> by mistake please notify the sender by return e-mail and permanently delete >> this message and any attachments from your system. Any dissemination, use, >> review, distribution, printing or copying of this message in whole or in >> part is strictly prohibited. Please note that e-mails are susceptible to >> change. CitiusTech shall not be liable for the improper or incomplete >> transmission of the information contained in this communication nor for any >> delay in its receipt or damage to your system. CitiusTech does not >> guarantee that the integrity of this communication has been maintained or >> that this communication is free of viruses, interceptions or interferences. >> ==================================================================================================================================================================== >> >> > > > > -- > Justin > > =========================================================================================================================================================================================== > DISCLAIMER: The information contained in this message (including any > attachments) is confidential and may be privileged. If you have received it > by mistake please notify the sender by return e-mail and permanently delete > this message and any attachments from your system. Any dissemination, use, > review, distribution, printing or copying of this message in whole or in > part is strictly prohibited. Please note that e-mails are susceptible to > change. CitiusTech shall not be liable for the improper or incomplete > transmission of the information contained in this communication nor for any > delay in its receipt or damage to your system. CitiusTech does not > guarantee that the integrity of this communication has been maintained or > that this communication is free of viruses, interceptions or interferences. > ==================================================================================================================================================================== > > -- Justin
