Re: UMLS Integration
Praveen, The error looks specific to UMLS metamorphosys rather than cTAKES. I am assuming you are trying to install UMLS locally from scratch rather than using the bundled cTAKES resources. Did you confirm that all of the files have been downloaded correctly per Metamorphosys instructions: http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html The error seems to be related to incomplete or corrupted zip files? Pei Chen Wired Informatics http://www.wiredinformatics.com 265 Franklin St Ste 1702 Boston, MA 02110 tel: (617) 433-7544 pei.c...@wiredinformatics.com -- Forwarded message -- From: Jay_Ram pandupraveen...@gmail.com Date: Tue, Dec 16, 2014 at 12:07 AM Subject: UMLS Integration To: dev@ctakes.apache.org Hi All, I downloaded UMLS resource, to use them offline by loading in mysql. I followed them which are mentioned to load data into mysql. But I am unable to do it show error Loading MetamorphoSys ... [Please be patient and wait for MetamorphoSys to begin] java.util.zip.ZipException: invalid LOC header (bad signature) at java.util.zip.ZipFile.read(Native Method) at java.util.zip.ZipFile.access$1400(Unknown Source) at java.util.zip.ZipFile$ZipFileInputStream.read(Unknown Source) at java.util.zip.ZipFile$ZipFileInflaterInputStream.fill(Unknown Source) at java.util.zip.InflaterInputStream.read(Unknown Source) at java.util.zip.InflaterInputStream.read(Unknown Source) at java.util.zip.CheckedInputStream.read(Unknown Source) at java.util.zip.GZIPInputStream.readUByte(Unknown Source) at java.util.zip.GZIPInputStream.readUShort(Unknown Source) at java.util.zip.GZIPInputStream.readHeader(Unknown Source) at java.util.zip.GZIPInputStream.init(Unknown Source) at gov.nih.nlm.umls.meta.io.RRFMetadataInputStream.openSourceFile(RRFMetadataInputStream.java:390) at gov.nih.nlm.umls.meta.io.RRFConceptInputStream.open(RRFConceptInputStream.java:175) at gov.nih.nlm.umls.meta.io.RRFMetathesaurusInputStream.open(RRFMetathesaurusInputStream.java:125) at gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysInputStream.open(RRFMetamorphoSysInputStream.java:629) at gov.nih.nlm.umls.mmsys.subset.gui.MetamorphoSysGUI.validateGUIConfigurables(MetamorphoSysGUI.java:1097) at gov.nih.nlm.umls.mmsys.subset.gui.BeginSubsetAction.actionPerformed(BeginSubsetAction.java:110) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$200(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at
Re: revamping the Apache cTAKES website
Looks great. Bootstrap provides most of the css/layout natively. There are augmentations freely available like http://bootswatch.com/ that can add flare to the packaged css. Design is easy with templating incorporated into systems like django ;-) (not another plug!) Bootstrap also has some designs as examples on its website that would probably be safe to use as a base. JG On Mon, Dec 15, 2014 at 11:17 PM, Pei Chen chen...@apache.org wrote: the template was borrowed from spark... we should put in our own design/css/layout/skin to suit our needs. Perhaps Michelle or others familiar with bootstrap could help us out here? On Mon, Dec 15, 2014 at 7:32 PM, jay vyas jayunit100.apa...@gmail.com wrote: this is gorgeous ! Thanks pei ! i let the bigtop folks know as well ! On Mon, Dec 15, 2014 at 6:21 PM, Murali mmin...@gmail.com wrote: Looks great. +1 On Dec 15, 2014, at 4:29 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Check out a mockup of a new website proposal: http://svn.apache.org/repos/asf/ctakes/site/new/index.html Based off bootstrap (Idea borrowed from the Spark folks..). Couple of key pieces of info: - 10% of visitors are on mobile/tablets - The most currently visited pages are: downloads.cgi, gettingstarted.html. I suggest we focus our attention on those 2 items. (Putting a Downloads link right on the front page, etc.) svn co http://svn.apache.org/repos/asf/ctakes/site/new if you want to checkout the code of the site. --Pei -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Friday, December 05, 2014 6:34 PM To: dev@ctakes.apache.org Cc: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website I would like to second the bootstrap recommendation, with the additional recommendation of django for the backend. It is an amazing platform for rapid development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original Message- From: Savova, Guergana [mailto: guergana.sav...@childrens.harvard.edu] Sent: Friday, December 05, 2014 11:56 AM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES website Wonderful, thank you, Michelle! There will be a flurry of emails the week of Dec 15 followed by actual work, so book your calendar if possible... --Guergana -Original Message- From: Michelle Chen [mailto:michelle1919c...@gmail.com] Sent: Friday, December 05, 2014 11:48 AM To: dev@ctakes.apache.org Subject: Re: revamping the Apache cTAKES website Hello Guergana, I don't know that much about cTakes, but would be interested in contributing to the effort. I'm not sure if there is an interest in matching the website design of other Apache projects, but it seems that the two main designs that are being used from my arbitrary search on http://projects.apache.org/indexes/alpha.html is 1. the current design that cTakes is using and 2. a Bootstrap approach. I've done a little bit of work on Bootstrap and would be interested in helping with that. Let me know how I can be helpful. Sincerely, Michelle Chen :) Be strong and of good courage; do not be afraid, nor be dismayed, for the Lord your God is with you wherever you go. ~Joshua 1:9 On Fri, Dec 5, 2014 at 11:21 AM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: cTAKES-ers, we would like to start working on updating the Apache cTAKES website - some of the information there is already stale and needs refreshing. Do you have ideas on website design, content, etc.? Would you like to contribute to the effort? We are planning to start working on the website the week of Dec 15. Cheers, --Guergana -- jay vyas
drug ner in ctakes 3.2.1
I'm getting an error when I try to load the Drug NER pipeline in the ctakes 3.2.1 CVD. I received a similar error in ctakes 3.2.0 for the clinical pipeline, but the clinical pipeline is working for me now in 3.2.1. :-) Is Drug NER supported in 3.2.1 and can it use the new fast dictionary lookup? Or is there more work required there? FYI... I'm loading desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcessor.xml Here's the error message: java.lang.IllegalArgumentException: URI is not hierarchical More detailed information is in the log file. Here's the stack trace: 12/15/14 4:57:45 PM - 15: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: URI is not hierarchical java.lang.IllegalArgumentException: URI is not hierarchical at java.io.File.init(File.java:418) at org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44) at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603) at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442) at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476) at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6525) at javax.swing.JComponent.processMouseEvent(JComponent.java:3321) at java.awt.Component.processEvent(Component.java:6290) at java.awt.Container.processEvent(Container.java:2234) at java.awt.Component.dispatchEventImpl(Component.java:4881) at java.awt.Container.dispatchEventImpl(Container.java:2292) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) at java.awt.Container.dispatchEventImpl(Container.java:2278) at java.awt.Window.dispatchEventImpl(Window.java:2739) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:746) at java.awt.EventQueue.access$400(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:697) at java.awt.EventQueue$3.run(EventQueue.java:691) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:719) at java.awt.EventQueue$4.run(EventQueue.java:717) at java.security.AccessController.doPrivileged(Native Method) at
Re: intro video and ctakes youtube : Youtube Apache cTakes Channel Direct Link
How do we upload videos we wish to contribute? I dont have any experience with youtube other than as a watcher. JG On Mon, Dec 15, 2014 at 11:43 AM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hmmm, I can't find it in a search. However, here is a direct link: https://www.youtube.com/channel/UC8hQoOKz3v4PNEf6cqSkjbQ Maybe it needs a few videos to register in the search engine ? Sean -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Monday, December 15, 2014 11:32 AM To: dev@ctakes.apache.org Subject: Re: intro video and ctakes youtube John, I presume you this thread: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201408.mbox/%3c393252f14c42f946952f1ed75d316cad39158...@chexmbx4a.chboston.org%3E Strange, I couldn't find it anymore either... The place holder could have been auto deleted because it was empty? I think it's worth it if you're willing to create and add to it again... ---Pei On Fri, Dec 12, 2014 at 11:46 PM, John Green john.travis.gr...@gmail.com wrote: I was going to post some basic how to videos that help with the learning curve I've walked over the last year and a half. I went looking for ctakes youtube channel mentioned awhile back and I did not find it... Anyone know where it went? Best, JG
ApacheCon 2015 (April) UIMA Track
We are planning a UIMA Track at the next ApacheCon conference (being held in Austin Texas, April 13-17th, 2015). Topics / areas where talks are solicited include: - UIMA itself (including its subprojects), new features, directions, etc., which could be of interest to people using UIMA. - Interesting Applications built using UIMA, including how UIMA is of benefit, of interest to people exploring UIMA and its uses - Demos of UIMA tooling, to appeal to users who want to become more effective in their unstructured analysis work - Connections with other Apache projects - what they are and how they're using UIMA in their analytics - Experiences with UIMA scaleout - to share with others who are scaling out UIMA pipelines The official call for papers is here: http://events.linuxfoundation.org/events/apachecon-north-america/program/cfp. Please consider submitting talks; the deadline is February 1st. Questions? Please email d...@uima.apache.org -Marshall Schor, for the Apache UIMA project
RE: intro video and ctakes youtube : Youtube Apache cTakes Channel Direct Link
Hi John, Look for an Upload button in the upper-left corner next to a blue Sign in button. Sean -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Tuesday, December 16, 2014 11:12 AM To: dev@ctakes.apache.org Subject: Re: intro video and ctakes youtube : Youtube Apache cTakes Channel Direct Link That is, how do we upload videos *to the channel. * On Tue, Dec 16, 2014 at 11:09 AM, John Green john.travis.gr...@gmail.com wrote: How do we upload videos we wish to contribute? I dont have any experience with youtube other than as a watcher. JG On Mon, Dec 15, 2014 at 11:43 AM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hmmm, I can't find it in a search. However, here is a direct link: https://www.youtube.com/channel/UC8hQoOKz3v4PNEf6cqSkjbQ Maybe it needs a few videos to register in the search engine ? Sean -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Monday, December 15, 2014 11:32 AM To: dev@ctakes.apache.org Subject: Re: intro video and ctakes youtube John, I presume you this thread: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201408.mbox/%3C39 3252f14c42f946952f1ed75d316cad39158...@chexmbx4a.chboston.org%3E Strange, I couldn't find it anymore either... The place holder could have been auto deleted because it was empty? I think it's worth it if you're willing to create and add to it again... ---Pei On Fri, Dec 12, 2014 at 11:46 PM, John Green john.travis.gr...@gmail.com wrote: I was going to post some basic how to videos that help with the learning curve I've walked over the last year and a half. I went looking for ctakes youtube channel mentioned awhile back and I did not find it... Anyone know where it went? Best, JG
