gmane.comp.apache.uima.general

Lucene cas consumer

Roberto Franchini — 2008-12-03T15:06:23

Hi, I'm going to write a Lucene CAS consumer. The porpouse is to create a Lucene document, or more than one, for each CAS. Last year (2007) the JENA university lab (JULIE lab? is it right?) delivered such a component, named LUCAS. Then it disappeared. LUCAS seems a good piece of software. The Technische Universität Darmstadt developed one too: http://www.ukp.tu-darmstadt.de/projects/dkpro/. (I will write to them). There's anybody interested to share knowledge and/or code to do that component? I think that Lucene and UIMA can be very good friends :) Roberto PS: I apologize for my bad English.

Setting Aggregate AE Parameters

Niels Ott — 2008-11-26T17:02:11

Hello everybody, I'm new to this mailing list, however I'm not so new to UIMA. Here's my issue: I am trying to set the parameters of an Aggregate AE from within my Java program. I tried the following the solution I found here: http://www.mail-archive.com/uima-user-d1GL8uUpDdXTxqt0kkDzDmD2FQJk+8+b< at >public.gmane.org/msg01241.html# which is basically to produce an annotator and then to configure it using annotator.setConfigParameterValue("ParamName","NewValue"); This does not work for me as annotator = UIMAFramework.produceAnalysisEngine(specifier); which I'm using before to produce the Aggregate initializes its AEs with the default parameters. These default parameters are of course not suitable for use in the given scenario, causing the initialization to fail before I correct the configuration. I tried to use produceAnalysisEngine(ResourceSpecifier aSpecifier, Map aAdditionalParams) instead but the additional parameters don't do the job. Perhaps I misunderstood the purpose of these additional parameters in the function. How can I specify the parameteres of an (Aggregate) AE before it is initialized? Thank you very much for your assistance. Best, Niels Ott

Additional Runtime Arguments

Thomas Polzin — 2008-11-25T21:11:51

I probably missed something in the documentation but here is my problem: I'm trying to process a pretty complex structured document and I do not want to translate the entire structure into annotations. Instead I would like to pass some object containing this additional structure to the respective analysis engines. Note that a static object will not work. Also, I do not want pass this object to the engines when they are constructed/initialized. The best solution I came up with so far is to subclass the CAS object and then to downcast to it in the process( CAS cas) function. Does this make sense? Is there a better solution? Thanks so much in advance Thomas

Assistant Scientist position available at the MBLWHOI library

Hamed, Ahmed A. — 2008-11-24T22:16:46

Apologies for cross-listing! Go to : https://mbl.simplehire.com/applicants/jsp/shared/frameset/Frameset.jsp Under Scientist link: *Assistant Scientist* View 01-10-2008 Scientist MBLWHOI library Posting Details Posting Number: 0000005 Reference Code: Department: MBLWHOI library Position Type: Scientist Position Title: Assistant Scientist Position Summary: The MBLWHOI Library at the Marine Biological Laboratory seeks highly motivated information scientists to join a growing team of library-based researchers. The successful candidate will join a community of librarians and researchers that are internationally recognized as defining the current trends and practices in marine information sciences and biological/biomedical informatics. Additional Information: In addition to providing leadership in advancing current research projects at the Library (such as the uBio and MBLWHOI Library Herbarium projects), the successful candidate will develop an extramurally funded research program that furthers the core missions of the library in addition to capitalizing on the highly collaborative environment in the Woods Hole scientific community. S/he will also evaluate the existing and anticipated needs of the MBLWHOI patrons and collaborators to motivate the development of novel tools and resources that can be used by the scientific community at-large. Expertise will be provided by the successful candidate towards for the development of tools and techniques for natural language processing, indexing, ontologies, data mining, and knowledge integration across a range of biological and biomedical resources. S/he will stay abreast of current developments in information science, informatics, and related disciplines through the participation and representation at international meetings and committees. The successful candidate will help guide the direction of an Ellison Medical Foundation (EMF) funded initiative to develop a web portal for aging. In this capacity, s/he will also serve as a liaison between the EMF-funded initiative and the biodiversity informatics group of the Encyclopedia of Life initiative, which is also located at the Marine Biological Laboratory. Basic Qualifications: The successful candidate will have a PhD in Informatics, Information Science or a related field, as well as least two years of relevant experience in biological/biomedical informatics and/or library science, a publication record within relevant informatics journals, and the ability to attract extramural funding. Formal training in biological science (e.g., molecular biology, biochemistry, biophysics) is highly desirable. Demonstrable experience with database management systems (such as MySQL), programming (e.g., Perl, PHP, Ruby, C/C++, and Java) is required. Preferred Qualifications: Physical Requirements Required Applicant Documents: Resume/CV Cover Letter References Special Instructions to Applicants:

Mailing list in a forum

Eric Quinn — 2008-11-23T18:19:34

Hello, this is Eric Quinn. I am working with Marshall Schor to find a way to view things sent to the mailing list without being forced to subscribe to the mailing list. This is a test to see whether it is also possible to send the things to the mailing list using Gmane, the website we are testing with this message. Gmane has been mirroring the mailing list since approximately May 2007, and you can view it here: http://news.gmane.org/gmane.comp.apache.uima.general/ Thank you.

Donation of a widely used type system for multi-modal text analysis

Burn Lewis — 2008-11-18T16:21:13

NOTE: This was foolishly posted to just uima-dev in September. The type system and some of the sample code are used in the recently mentioned UCC tool from CMU. We would like to add a UIMA type system and sample annotators to the Apache Incubator project as an example of a rich multimodal application. Our hope is that others will find the techniques and types useful, and will find it a good starting point for developing other multimodal applications. GTS is a type system designed for multi-modal applications that combine analytics from multiple sources and modalities, such as speech recognition, language translation, entity detection. etc. It is currently used by 10 cooperating groups participating in the Darpa GALE project ( http://www.darpa.mil/ipto/programs/gale/gale.asp) to transcribe, translate, and extract information from foreign language news broadcasts. This application requires that all the data is cross-referenced so that, for example, any English sentence can be traced back to the precise region of foreign language audio that generated it. The CAS organization and type system have been designed to allow each analytic to easily work on data of the appropriate modality. Speech recognition engines annotate an audio view with words aligned to a time axis; machine translation annotates a text view of foreign sentences with their English translation; entity detection annotates a text view of the English sentences. Multiple analytics of each type may be employed to improve the overall accuracy. The sample code includes data reorganization components that are inserted between the different analytics to perform the necessary bookkeeping of creating views and cross-reference links from one view back to an earlier one. e.g. after all speech recognition analytics have run, a reorg module creates a source-language text view for each STT engine, along with cross-reference annotations from each word in the new view back to the appropriate time span in the audio view. One reorg component is a CAS Multiplier that resegments the initial fixed-length audio segments at likely story boundaries so that later components can treat each CAS as a complete story. The STT and MT analytics are simulated analytics that read their results from a file, so that a complete pipeline of components can be tested. We welcome any comments or suggestions or questions! - Burn.

granting code to Apache UIMA project

Eric Riebling — 2008-11-18T15:48:25

Greetings, Carnegie Mellon would like to grant code to the Apache UIMA project, in the form of two support tools we have created: * UIMA Component Repository (UCR): A web portal for upload/download/review of UIMA components, type systems, etc. Based on Java and existing tools (e.g. Tomcat). * UIMA Component Container (UCC): A Java system that supports server-side execution of distributed UIMA services on data supplied from a client web browser. This message is intended to initiate discussion about whether such a grant makes sense, and if so, what the concrete next steps should be in preparing the software. (On the legal side, we have engaged CMU's tech transfer office regarding the grant letter from CMU, and we are working out the details with them now.) Thank you for your consideration, Eric Riebling, Senior Research Programmer Eric Nyberg, Professor School of Computer Science Carnegie Mellon University

U-Compare first public release announcement

Yoshinobu Kano — 2008-11-14T16:05:29

Dear UIMA users, The U-Compare Initiative is pleased to announce the first public release of U-Compare system ( http://u-compare.org/ ); an easy-to-use system for the construction and comparison of NLP workflows. U-Compare is an integrated text mining/natural language processing system based on the UIMA Framework which provides access to the worlds largest repository of type system compatible UIMA components. The components come from a wide range of different research groups, and currently include corpus readers, syntactic parsers, semantic entity recognizers, as well as a variety of other tools. New components are being added all the time, and we expect to be adding a selection of more resources like relation extraction tools in the near future. From these, or any UIMA components, U-Compare allows users to build complex NLP workflows by simply dragging-and-dropping components into order. These workflows may then be run from within the U-Compare system which automatically makes available a range of data visualization and comparison tools. The workflows created in U-Compare can also easily be exported and shared with other U-Compare users and because any UIMA component can be included in workflows, U-Compare also functions as a general UIMA workflow creation tool. Comparison of components and workflows is a central feature of the system, which was a task difficult to achieve with only the original Apache UIMA tools. U-Compare allows sets of components to be run in parallel on the same inputs and automatically generates statistics for all possible combinations of these components. This ability allows user to not only compare the performance of various components, but also to find optimal combinations for a given task. The system can be launch directly from the web by clicking the "Launch U-Compare" button on the U-Compare homepage: http://u-compare.org/ U-Compare is a joint project between the University of Tokyo, the Center for Computational Pharmacology at the University of Colorado Health Science Center, and the National Centre for Text Mining at the University of Manchester. Please refer to the documentation on the U-Compare web site for further details. We are looking forward to receiving feedback and contributions of compatible UIMA components from developers. Respectfully, U-Compare Initiative

undeployAsyncService?

Eric Riebling — 2008-11-13T20:33:56

I have a strange use case which requires taking down as well as starting up remote services. Is there a mechanism which allows removal, or de-registration of a service with a particular broker? My only idea on how to achieve this is to kill the service process brute force, and let the broker "figure out" that the service has gone away, I'm assuming by way of a timeout, or a getMeta failure. Any ideas? Is there a way to tell a broker directly to stop using a particular service, once it's been deployed? Thanks, -er

OpenCalais Annotator

Howard G. — 2008-11-07T19:14:26

Is anybody out there using the OpenCalais Annotator from the UIMA Sandbox? Is it still an active project? I am trying to use it, but it is not behaving as expected. Any help would be welcomed.

OpenCalais Annotator -- contact developer

Howard G. — 2008-11-07T17:46:32

I am trying to use the OpenCalais Annotator from the UIMA Sandbox and it is not behaving as I expected. Is there any way I can contact the developer(s)? I have not seen any activity for it since July; is it still being worked on? A UIMA user

OpenCalais Annotator -- Contact developer?

Howard G. — 2008-11-07T17:41:53

CAS Viewer/Editor for HTML

Peter Klügl — 2008-11-04T12:11:13

Hello, you can maybe remember that one of my students, Marco Nehmeier, developed a CAS viewer and editor especially for HTML documents. The work is now completed and was done in a practical course, more precisely in a "Studienarbeit". The report is written in german and is uploaded (temporary) to http://ki.informatik.uni-wuerzburg.de/~pkluegl/misc/CEV-Ausarbeitung. If there is more interest in this work, then I can maybe provide an english version of the handbook part of the report. The possibility to view or render annotation directly in interpreted HTML is extremely important for us since we are processing converted word processing documents in the majority of the cases. The work started before the issue about code donation of the UIMA CAS viewer has started. If you are interested what we are doing here in Würzburg and how we are using UIMA, then just ask me, take a look at a short paper of mine: Integrating the Rule-Based IE Component TextMarker into UIMA (LWA08 FGIR) or in near future at the project itself (homepage will follow this month, source code early next year): https://sourceforge.net/projects/textmarker/ best regards Peter

CAS Viewer/Editor for HTML

Peter Klügl — 2008-11-04T13:55:39

Hello, maybe you can remember that one of my students, Marco Nehmeier, developed a CAS viewer and editor especially for HTML documents. The work is now completed and was done in a practical course, more precisely in a "Studienarbeit". The report is written in german and I will send you the pdf on request. If there is more interest in this work, then I can maybe provide an english version of the handbook part of the report. The possibility to view or render annotation directly in interpreted HTML is extremely important for us since we are processing converted word processing documents in the majority of the cases. The work started before the issue about code donation of the UIMA CAS viewer has started. If you are interested what we are doing here in Würzburg and how we are using UIMA, then just ask me, take a look at a short paper of mine: Integrating the Rule-Based IE Component TextMarker into UIMA (LWA08 FGIR) or in near future at the TextMarker sourceforge project itself (homepage will follow this month, source code early next year) best regards Peter PS: Sorry for possible multiple posts.

Question on Capabilities of AE descriptor

Bart Mellebeek — 2008-11-03T09:39:11

Hello, I have a question on the exact role of the output types in the Capabilities of an AE descriptor that I couldn't find in the documentation. A strange thing happens when I try to manipulate the descriptors of ex4/ of the tutorial in uimaj-examples. I am running ex4/MeetingDetectorTAE.xml with UIMA Document Analyzer. When I delete the output type RoomNumber in the Capabilities of ex2/RoomNumberAnnotator.xml and I run ex4/MeetingDetectorTAE.xml, the RoomNumber type is still visible in the analysis results. Likewise, when I delete the output types TimeAnnot and DateAnnot in the capabilities of ex3/TutorialDateTime.xml, these types are still visible in the analysis results. Only deleting the output type DateTimeAnnot in the capabilities of ex3/TutorialDateTime.xml seems to have an impact on the analysis results. Why is it that deleting some output types have no impact on analysis results, while deleting other output types do have an impact? Aren't all output types supposed to have this impact? Any help appreciated. Thanks, Bart

Unit testing CollectionReaders

Isabel Drost — 2008-10-29T08:10:07

Hello, I am about to do my first steps using UIMA. I started out with the tutorial and am about to write my first CollectionReader (extending CollectionReader_ImplBase). As the tutorial says, I implemented initialize() to init the reader from its config parameters: In order to test the class I created a unit test. I thought it might be a good idea to set the parameters of the reader in the setUp method of my test like this: ... Unfortunately this gives me a null pointer exception in the line setting the config parameter that comes from inside UIMA: org.apache.uima.resource.ConfigurableResource_ImplBase.getConfigParameterValue(ConfigurableResource_ImplBase.java:37) org.apache.mahout.clustering.webkb.kmeans.WebKbReader.initialize(WebKbReader.java:58) I had a look at the UIMA code, the line throwing the exception is the following: I guess I am just making some stupid beginners mistake - forgot to initialize some internal UIMA object before calling my reader? Unfortunately I have no clue what could have gone wrong. Any help would be appreciated. Thanks, Isabel

Getting AE performance stats

Jörn Kottmann — 2008-10-24T14:24:08

Hello, I am trying to retrieve performance stats from an AnalysisEngine with the AnalysisEngineManagement object instance I got via the AE.getManagementInterface method, but all stats are 0 e.g. for AEM.getNumberOfCasProcessed(). I created the AE from a pear. And then this small loop drives the processing: CAS cas = ae.newCAS(); while (colReader.hasNext()) { colReader.getNext(cas); ae.process(cas); cas.reset(); } If I now try to use the management interface I do not get correct stats, only zero as described above. What do I am doing wrong ? Is there a switch to explicitly enable performance monitoring ? I have one more question. Is it safe to use a second thread to retrieve the performance stats ? Thanks, Jörn

UIMA repsotory

2008-10-24T04:29:23

Hi all. I tried to upload my PEAR file to CMU repository, but after the checking process I didn't get any response (and upload seemed to fail). In this mailing list, someone tells the repository is designed for older version of UIMA, so latest PEAR cannot be uploaded and update of the repository for current UIMA version is not planed. Does any one know are there any other repository for UIMA? Thank you Osamu Masutani Denso IT Laboratory,Inc.

[UIMA] How to get the element type from a TypeSystem Object

Manuel Fiorelli — 2008-10-18T00:45:20

I need to get the element type of a feature from a TypeSystem object. I didn't find any method in the Feature interface. However, when I have a definition like that foo uima.cas.FSArray uima.cas.Boolean then, foo.getRange().getComponentType() gives uima.cas.Boolean, as I expected. But, if the range type is uima.cas.FSList I know no way to get the element type. I tried the code TypeSystemUtil.feature2FeatureDescription(base_foo).getElementType() but it returns null. Manuel Fiorelli

AUTO: Benjamin Sznajder/Haifa/Contr/IBM is out of the office. (returning 22/10/2008)

Benjamin Sznajder — 2008-10-17T04:39:35

I am out of the office until 22/10/2008. Note: This is an automated response to your message "?RE: Imports with '_pear.xml' in aggregate prevent annotators to work on the right Sofa" sent on 16/10/08 21:01:52. This is the only notification you will receive while this person is away.

UIMA CPE GUI issue

Matt McClain — 2008-10-13T19:12:48

I'm using the collection processing engine GUI (main method in: org.apache.uima.tools.cpm.CpmFrame), and I'm having some issues in which saving the CPE XML descriptor file fails to record all of the analysis engine parameters correctly. So, if I edit a configuration, save it, and then immediately load it, some of the configuration parameters are changed (the edits are lost). This doesn't happen all of the time - the only correlation I can find so far is that it happens when I've changed a value from the default and then try to change it back to the default. Has anyone else seen this behavior and are there any known solutions? I didn't see a similar issue in JIRA. Thanks, Matt Matthew McClain Lead Scientist 21st Century Technologies, Inc. 4515 Seton Center Parkway Suite 320 Austin, TX 78759 Phone: 512 342 0010 Extension 240 Email: mmcclain-HzfYWs6XNgQNcFTW2g63AdBPR1lH4CV8< at >public.gmane.org public.gmane.org> URL: http://www.21technologies.com The information in this email and in any attachments is confidential and may be privileged. If you are not the intended recipient, please destroy this message, delete any copies held on your systems and notify the sender immediately. You should not retain, copy or use this email for any purpose, nor disclose all or any part of its content to any other person.