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Concordia University
Montréal, Canada

OrganismTagger error message

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I am interested in you previous publication:OrganismTagger, and I would like to use this to anntate species mention. But I met a error messgae as follow:

HashGazetteer is being initialized!
HashGazetteer is being initialized!
Exception in thread "LoadResourceFromFileAction" java.lang.NoClassDefFoundError: com/ontotext/kim/KIMConstants
at com.ontotext.kim.gate.KimGazetteer.(KimGazetteer.java:38)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
at java.lang.Class.newInstance0(Class.java:372)
at java.lang.Class.newInstance(Class.java:325)
at gate.Factory.createResource(Factory.java:233)
at gate.util.persistence.ResourcePersistence.createObject(ResourcePersistence.java:83)
at gate.util.persistence.PRPersistence.createObject(PRPersistence.java:76)
at gate.util.persistence.LanguageAnalyserPersistence.createObject(LanguageAnalyserPersistence.java:51)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:356)
at gate.util.persistence.CollectionPersistence.createObject(CollectionPersistence.java:74)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:356)
at gate.util.persistence.ControllerPersistence.createObject(ControllerPersistence.java:58)
at gate.util.persistence.SerialAnalyserControllerPersistence.createObject(SerialAnalyserControllerPersistence.java:53)
at gate.util.persistence.PersistenceManager.getTransientRepresentation(PersistenceManager.java:356)
at gate.util.persistence.PersistenceManager.loadObjectFromUrl(PersistenceManager.java:765)
at gate.util.persistence.PersistenceManager.loadObjectFromFile(PersistenceManager.java:679)
at gate.gui.MainFrame$LoadResourceFromFileAction$1.run(MainFrame.java:3544)
at java.lang.Thread.run(Thread.java:722)

thanks for your attention!

rene's picture

GATE and Java version?

Hi,

Could you provide us with some more information on your setup:

  • operating system used
  • version of GATE
  • version of Java

Also, did you see any error messages when downloading the libraries through the "ant" task (in the gate/ directory)?

Dear OganismTagger authors

Dear OganismTagger authors,
Thanks for your response. I can use it now. But I meet two additional problems.
1. Can GATE import a set of files by one time? I tried to import articles for annotation, but I found the “GATE document” can only load one file by one time.
2. I tried to export the annotation result for an xml file. But the output result is strange. You may take a look for the file as followed. Every character is spited. Is that correct?
http://140.116.245.194/OrganismTagger_result/test.zip
Besides, our group has a related project to Species normalization. I would like to get the corpus (articles) you mentioned in paper (OT-A and OT-B). But I did not found it in OrganismTagger folders, and I just found the annotation results. May you provide them?
Thanks for your help.

rene's picture

GATE Documentation

Regarding 1, yes, you need to create a corpus, which you can then populate with a set of documents. The pipeline will then process all documents in that corpus. If you are not familiar with GATE, you should look at the excellent documentation, in particular the users' guide, the GATE Training Course material, and the gate-users mailing list for general GATE questions.

Regarding 2, please also check the GATE documentation regarding the internal document format and its representation (GATE uses stand-off markup). GATE also has multiple components that allow you to export the results in different formats, like the Flexible Exporter.

Finally, we only distribute our manual annotations due to copyright reasons. Please contact us through the form if you need access to the original documents for evaluation purposes.

Dear authors

Dear authors,

Thanks for your response. I would like to evaulate by your OT corpus. May I have your contact E-mail?

Thank you very much.

rene's picture

See "Contact" link

Simply use the "Contact" link on the top or bottom of each page!