Contact Us Copyright Privacy Accessibility Freedom of Information Act
Queue: PublicMetaMap
Subject: Utterances are returned that are not found in the document text
Status: resolved
Created: Tue Mar 19 15:01:42 2013
Resolved: Tue Jun 11 10:26:38 2013
LastUpdated: Tue Jun 11 10:26:38 2013

Subject: 
Creator: 28
Created: 2013-03-19 19:01:42
Transaction: 1872
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         >Category: mmtxT
         >Synopsis: Utterances are returned that are not found in the document text
         >Confidential: no
         >Severity: serious
         >Priority: high
         >Class: sw-bug
         >Submitter-Id: mmtxWeb
         >Release: 
         >Environment:
         >Operating System - MetaMap: 
         >OS Version - Mac 10.6.8
         >Java Version - Java 1.6
         >Description:
         Utterances returned about processing by MetaMap do not exist in the text. It appears that document text lines are sometimes joined together, giving a single line utterance that is composed of two lines.
         
         This is a problem since the utterance can not be found in the document text and calls to the API to return the utterance will not be able to return the utterance.
         
         A bugfix (hack) could be possible in the MetaMapAnnotator.java file by searching for a findable utterance string in the document text (backtracking by one) but this is a horrible and would be better to be fixed at a lower level.
         
         I did attach the entire document tested, but it is from the SharClef2013 challenge. I also modified a few numbers since distribution of the original document is restricted.
         >How-To-Repeat:
         Actual Text to Reproduce Problem in Input Document (2 lines)
         27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08 00:00:00.0 ||||  ||||  ||||  ||||
         Admission Date:  [**2015-03-28**]              Discharge Date:   [**2014-05-08**]
         
         Utterance Returned (one line)
         27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08 00:00:00.0 ||||  ||||  ||||  ||||  Admission Date:  [**2015-03-28**]              Discharge Date:   [**2014-05-08**]
         >Unformatted:




Subject: 
Creator: 28
Created: 2013-03-20 19:35:44
Transaction: 1878
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/html
ContentEncoding: none

Content: Each line will need to separated by a blank line if you want the annotator to treat them as separate lines. 

the input:

27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08 00:00:00.0 ||||  ||||  ||||  ||||

Admission Date:  [**2015-03-28**]              Discharge Date:   [**2014-05-08**]

will result in:

Utterance:
 Utterance text: 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08 00:00:00.0 ||||  ||||  ||||  ||||
Utterance:
 Utterance text: Admission Date:  [**2015-03-28**]              Discharge Date:   [**2014-05-08**]


I not sure if this is what you're looking for...

Sincerely,
Willie Rogers









On Tue Mar 19 15:01:42 2013, wjrogers wrote:
>
> >Submitter: [email redacted]
> >Category: mmtxT
> >Synopsis: Utterances are returned that are not found in the document
> text
> >Confidential: no
> >Severity: serious
> >Priority: high
> >Class: sw-bug
> >Submitter-Id: mmtxWeb
> >Originator: John Osborne ([email redacted])
> >Release:
> >Environment:
> >Operating System - MetaMap:
> >OS Version - Mac 10.6.8
> >Java Version - Java 1.6
> >Description:
> Utterances returned about processing by MetaMap do not exist in the
> text. It appears that document text lines are sometimes joined
> together, giving a single line utterance that is composed of two
> lines.
>
> This is a problem since the utterance can not be found in the document
> text and calls to the API to return the utterance will not be able
> to return the utterance.
>
> A bugfix (hack) could be possible in the MetaMapAnnotator.java file by
> searching for a findable utterance string in the document text
> (backtracking by one) but this is a horrible and would be better to
> be fixed at a lower level.
>
> I did attach the entire document tested, but it is from the
> SharClef2013 challenge. I also modified a few numbers since
> distribution of the original document is restricted.
> >How-To-Repeat:
> Actual Text to Reproduce Problem in Input Document (2 lines)
> 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
> 00:00:00.0 |||| |||| |||| ||||
> Admission Date: [**2015-03-28**] Discharge Date:
> [**2014-05-08**]
>
> Utterance Returned (one line)
> 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
> 00:00:00.0 |||| |||| |||| |||| Admission Date: [**2015-03-
> 28**] Discharge Date: [**2014-05-08**]
> >Unformatted:


Subject: [PublicMetamap #40] Utterances are returned that are not found in the document text 
Creator: 1
Created: 2013-03-20 19:35:44
Transaction: 1879
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: Each line will need to separated by a blank line if you want the annotator to
         treat them as separate lines.
         
         the input:
         
         27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08 00:00:00.0 ||||
         |||| |||| ||||
         
         Admission Date: [**2015-03-28**] Discharge Date: [**2014-05-08**]
         
         will result in:
         
         Utterance:
         Utterance text: 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         00:00:00.0 |||| |||| |||| ||||
         Utterance:
         Utterance text: Admission Date: [**2015-03-28**] Discharge Date:
         [**2014-05-08**]
         
         
         I not sure if this is what you're looking for...
         
         Sincerely,
         Willie Rogers
         
         
         
         
         
         
         
         
         
         On Tue Mar 19 15:01:42 2013, wjrogers wrote:
         >
         > >Category: mmtxT
         > >Synopsis: Utterances are returned that are not found in the document
         > text
         > >Confidential: no
         > >Severity: serious
         > >Priority: high
         > >Class: sw-bug
         > >Submitter-Id: mmtxWeb
         > >Release:
         > >Environment:
         > >Operating System - MetaMap:
         > >OS Version - Mac 10.6.8
         > >Java Version - Java 1.6
         > >Description:
         > Utterances returned about processing by MetaMap do not exist in the
         > text. It appears that document text lines are sometimes joined
         > together, giving a single line utterance that is composed of two
         > lines.
         >
         > This is a problem since the utterance can not be found in the document
         > text and calls to the API to return the utterance will not be able
         > to return the utterance.
         >
         > A bugfix (hack) could be possible in the MetaMapAnnotator.java file by
         > searching for a findable utterance string in the document text
         > (backtracking by one) but this is a horrible and would be better to
         > be fixed at a lower level.
         >
         > I did attach the entire document tested, but it is from the
         > SharClef2013 challenge. I also modified a few numbers since
         > distribution of the original document is restricted.
         > >How-To-Repeat:
         > Actual Text to Reproduce Problem in Input Document (2 lines)
         > 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         > 00:00:00.0 |||| |||| |||| ||||
         > Admission Date: [**2015-03-28**] Discharge Date:
         > [**2014-05-08**]
         >
         > Utterance Returned (one line)
         > 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         > 00:00:00.0 |||| |||| |||| |||| Admission Date: [**2015-03-
         > 28**] Discharge Date: [**2014-05-08**]
         > >Unformatted:
         



Subject: [PublicMetamap #40] Utterances are returned that are not found in the document text 
Creator: 1
Created: 2013-03-20 19:35:44
Transaction: 1880
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: Each line will need to separated by a blank line if you want the annotator to
         treat them as separate lines.
         
         the input:
         
         27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08 00:00:00.0 ||||
         |||| |||| ||||
         
         Admission Date: [**2015-03-28**] Discharge Date: [**2014-05-08**]
         
         will result in:
         
         Utterance:
         Utterance text: 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         00:00:00.0 |||| |||| |||| ||||
         Utterance:
         Utterance text: Admission Date: [**2015-03-28**] Discharge Date:
         [**2014-05-08**]
         
         
         I not sure if this is what you're looking for...
         
         Sincerely,
         Willie Rogers
         
         
         
         
         
         
         
         
         
         On Tue Mar 19 15:01:42 2013, wjrogers wrote:
         >
         > >Category: mmtxT
         > >Synopsis: Utterances are returned that are not found in the document
         > text
         > >Confidential: no
         > >Severity: serious
         > >Priority: high
         > >Class: sw-bug
         > >Submitter-Id: mmtxWeb
         > >Release:
         > >Environment:
         > >Operating System - MetaMap:
         > >OS Version - Mac 10.6.8
         > >Java Version - Java 1.6
         > >Description:
         > Utterances returned about processing by MetaMap do not exist in the
         > text. It appears that document text lines are sometimes joined
         > together, giving a single line utterance that is composed of two
         > lines.
         >
         > This is a problem since the utterance can not be found in the document
         > text and calls to the API to return the utterance will not be able
         > to return the utterance.
         >
         > A bugfix (hack) could be possible in the MetaMapAnnotator.java file by
         > searching for a findable utterance string in the document text
         > (backtracking by one) but this is a horrible and would be better to
         > be fixed at a lower level.
         >
         > I did attach the entire document tested, but it is from the
         > SharClef2013 challenge. I also modified a few numbers since
         > distribution of the original document is restricted.
         > >How-To-Repeat:
         > Actual Text to Reproduce Problem in Input Document (2 lines)
         > 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         > 00:00:00.0 |||| |||| |||| ||||
         > Admission Date: [**2015-03-28**] Discharge Date:
         > [**2014-05-08**]
         >
         > Utterance Returned (one line)
         > 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         > 00:00:00.0 |||| |||| |||| |||| Admission Date: [**2015-03-
         > 28**] Discharge Date: [**2014-05-08**]
         > >Unformatted:
         



Subject: 
Creator: 28
Created: 2013-03-22 19:58:52
Transaction: 1895
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: multipart/mixed
ContentEncoding: 

Content: 

Subject: 
Creator: 28
Created: 2013-03-22 19:58:52
Transaction: 1895
Parent: 165
MessageId: 
Filename: 
ContentType: text/plain
ContentEncoding: 

Content: 

Subject: 
Creator: 28
Created: 2013-03-22 19:58:52
Transaction: 1895
Parent: 165
MessageId: 
Filename: 
ContentType: message/rfc822
ContentEncoding: none

Content: Received: from NIHHT02.nih.gov (156.40.71.21) by CASHTV16.nih.gov
          (156.40.71.179) with Microsoft SMTP Server (TLS) id 14.2.328.9; Fri, 22 Mar
          2013 11:28:29 -0400
         Received: from mailfwd.nih.gov (128.231.90.76) by NIHHT02.nih.gov
          (156.40.71.21) with Microsoft SMTP Server id 8.3.279.5; Fri, 22 Mar 2013
          11:28:25 -0400
         Received: from [130.14.111.27] (130.14.111.27) by mailfwd.nih.gov
          (128.231.90.107) with Microsoft SMTP Server id 14.2.318.4; Fri, 22 Mar 2013
          11:28:26 -0400
         Message-ID: <[email redacted]>
         Date: Fri, 22 Mar 2013 11:28:25 -0400
         From: "Willie Rogers (NIH/NLM/LHC) [C]" <[email redacted]>
         Organization: National Library of Medicine
         User-Agent: Mozilla/5.0 (X11; Linux i686 on x86_64; rv:17.0) Gecko/20130307 Thunderbird/17.0.4
         To: "John David Osborne (Campus)" <[email redacted]>
         Subject: Re: Ticket: #40: Utterances are returned that are not found in the
          document text
         References: <[email redacted]>
         In-Reply-To: <[email redacted]>
         Content-Type: multipart/mixed;
         	boundary="------------080107010100070101050205"
         Return-Path: [email redacted]
         X-MS-Exchange-Organization-AuthSource: NIHHT02.nih.gov
         X-MS-Exchange-Organization-AuthAs: Internal
         X-MS-Exchange-Organization-AuthMechanism: 10
         X-MS-Exchange-Organization-AVStamp-Mailbox: MSFTFF;1;0;0 0 0
         MIME-Version: 1.0
         
         --------------080107010100070101050205
         Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
         Content-Transfer-Encoding: 7bit
         
         I've modified the adapter to fixed the issue of the adapter inserting -1 
         when it couldn't find the utterance or phrase text from 
         jcas.getDocumentText().   I've attached the source as well as an update 
         TypeSystem Descriptor (fixes a problem which occurs when using Java 6 or 
         7).
         
         The updated distribution for UIMA is available at:
         
         http://metamap.nlm.nih.gov/download/public_mm_uima_2012.tar.bz2
         
         Sorry for the problems, we had only tested the annotator with Journal 
         Articles not chunked text such as clinical notes.
         
         Sincerely,
         Willie Rogers
         
         
         On 03/21/13 17:29, John David Osborne (Campus) wrote:
         > Hi Will,
         >
         > Try this file, it dies for me using the UIMA annotator on both linux and
         > on mac. I'm using the 2012 MetaMap Annotator.
         >
         >   -John
         >
         >
         > On 3/21/13 1:47 PM, "Willie Rogers (NIH/NLM/LHC) [C]"
         > <[email redacted]> wrote:
         >
         >> I wasn't able to reproduce the position values of '-1' using the section
         >> of text you sent me.  I was wondering which versions of MetaMap API,
         >> MetaMap UIMA, and Apache UIMA you were using.  Also, which operating
         >> system your running the system on.
         >>
         >> Sincerely,
         >> Willie Rogers
         >>
         >> On 03/21/13 11:50, John David Osborne (Campus) wrote:
         >>> I don't think I am describing the problem very well or I am missing
         >>> something. In the file MetaMapAnnotator.java
         >>> Ina the processUtterance function the line:
         >>>
         >>> int utteranceStart = docText.indexOf(utterance.getString(),
         >>> citationStart
         >>> + utterance.getPosition().getX());
         >>>
         >>> Can yield an utteranceStart of -1 for input data in the generated
         >>> org.metamap.uima.ts.Utterance object. This can also be true for
         >>> org.metamap.uima.ts.Phrase.
         >>>
         >>> Would you expect this or would you say this is a bug? I would argue all
         >>> NO
         >>> utterances should ever have a -1 start.
         >>>
         >>> Perhaps the input I sent off is not generating the same error, as the
         >>> copy/paste text/capture didn't generate the same error for you?
         >>>
         >>>    -John
         >>>
         >>>
         >>> On 3/20/13 2:38 PM, "Willie Rogers (NIH/NLM/LHC) [C]"
         >>> <[email redacted]> wrote:
         >>>
         >>>> Each line will need to separated by a blank line if you want the
         >>>> annotator to treat them as separate lines.
         >>>>
         >>>>
         >>>> the input:
         >>>>
         >>>> 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         >>>> 00:00:00.0 ||||  ||||  ||||  ||||
         >>>>
         >>>> Admission Date:  [**2015-03-28**]              Discharge Date:
         >>>> [**2014-05-08**]
         >>>>
         >>>> will result in:
         >>>>
         >>>> Utterance:
         >>>>    Utterance text: 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY ||||
         >>>> 2015-04-08 00:00:00.0 ||||  ||||  ||||  ||||
         >>>> Utterance:
         >>>>    Utterance text: Admission Date:  [**2015-03-28**]
         >>>> Discharge Date:   [**2014-05-08**]
         >>>>
         >>>>
         >>>> I not sure if this is what you're looking for...
         >>>>
         >>>> Sincerely,
         >>>> Willie Rogers
         >>>>
         >>>>>> Submitter: [email redacted]
         >>>>>> Category: mmtxT
         >>>>>> Synopsis: Utterances are returned that are not found in the document
         >>>>>> text
         >>>>>> Confidential: no
         >>>>>> Severity: serious
         >>>>>> Priority: high
         >>>>>> Class: sw-bug
         >>>>>> Submitter-Id: mmtxWeb
         >>>>>> Originator: John Osborne ([email redacted])
         >>>>>> Release:
         >>>>>> Environment:
         >>>>>> Operating System - MetaMap:
         >>>>>> OS Version - Mac 10.6.8
         >>>>>> Java Version - Java 1.6
         >>>>>> Description:
         >>>>> Utterances returned about processing by MetaMap do not exist in the
         >>>>> text. It appears that document text lines are sometimes joined
         >>>>> together,
         >>>>> giving a single line utterance that is composed of two lines.
         >>>>>
         >>>>> This is a problem since the utterance can not be found in the document
         >>>>> text and calls to the API to return the utterance will not be able to
         >>>>> return the utterance.
         >>>>>
         >>>>> A bugfix (hack) could be possible in the MetaMapAnnotator.java file by
         >>>>> searching for a findable utterance string in the document text
         >>>>> (backtracking by one) but this is a horrible and would be better to be
         >>>>> fixed at a lower level.
         >>>>>
         >>>>> I did attach the entire document tested, but it is from the
         >>>>> SharClef2013 challenge. I also modified a few numbers since
         >>>>> distribution
         >>>>> of the original document is restricted.
         >>>>>> How-To-Repeat:
         >>>>> Actual Text to Reproduce Problem in Input Document (2 lines)
         >>>>> 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         >>>>> 00:00:00.0 ||||  ||||  ||||  ||||
         >>>>> Admission Date:  [**2015-03-28**]              Discharge Date:
         >>>>> [**2014-05-08**]
         >>>>>
         >>>>> Utterance Returned (one line)
         >>>>> 27559 |||| 211 |||| 5653 |||| DISCHARGE_SUMMARY |||| 2015-04-08
         >>>>> 00:00:00.0 ||||  ||||  ||||  ||||  Admission Date:  [**2015-03-28**]
         >>>>>           Discharge Date:   [**2014-05-08**]
         >>>>>> Unformatted:
         >>>>
         >>>>
         >>>> --
         >>>> Willie Rogers,
         >>>> Contractor, Lister Hill Center, National Library of Medicine, NIH
         >>>> email: [email redacted]
         >>>
         >>
         >>
         >> --
         >> Willie Rogers,
         >> Contractor, Lister Hill Center, National Library of Medicine, NIH
         >> email: [email redacted]
         >
         
         
         -- 
         Willie Rogers,
         Contractor, Lister Hill Center, National Library of Medicine, NIH
         email: [email redacted]
         
         --------------080107010100070101050205
         Content-Type: text/plain; charset="us-ascii"; name="MetaMapAnnotator.java"
         Content-Transfer-Encoding: 7bit
         Content-Disposition: attachment; filename="MetaMapAnnotator.java"
         
         package gov.nih.nlm.nls.metamap.uima;
         
         import java.util.List;
         import java.util.ArrayList;
         import java.io.*;
         
         import gov.nih.nlm.nls.metamap.*;
         import gov.nih.nlm.nls.metamap.uima.ts.AcronymAbbrev;
         import gov.nih.nlm.nls.metamap.uima.ts.Document;
         
         import org.apache.uima.util.Level;
         import org.apache.uima.UimaContext;
         import org.apache.uima.jcas.JCas;
         import org.apache.uima.jcas.JCasRegistry;
         import org.apache.uima.jcas.cas.FSArray;
         import org.apache.uima.jcas.cas.StringArray;
         import org.apache.uima.jcas.cas.IntegerArray;
         import org.apache.uima.analysis_component.AnalysisComponent;
         import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
         import org.apache.uima.resource.ResourceInitializationException;
         import org.metamap.uima.ts.CuiConcept;
         import org.metamap.uima.ts.Span;
         
         /**
          * Describe class MetaMapAnnotator here.
          * 
          * 
          * Created: Fri Dec 4 11:32:31 2009
          * 
          * @author Willie Rogers
          * @version 1.0
          */
         public class MetaMapAnnotator extends JCasAnnotator_ImplBase implements
         							       AnalysisComponent {
         	private static final String MESSAGE_DIGEST = "AnnotatorMessages";
         	
           public static final String MMSERVER_PATH_PARAMETER = "metamap_server_path";
           public static final String TEMPDIR_PATH_PARAMETER = "tempdir_path";
           public static final String SKRMEDPOSTCTL_PATH_PARAMETER = "skrmedpostctl_path";
           public static final String WSDSERVERCTL_PATH_PARAMETER = "wsdserverctl_path";
           public static final String METAMAP_OPTIONS_PARAMETER = "metamap_options";
           public static final String METAMAP_TIMEOUT_PARAMETER = "0";
           
           private String mmserverPath;
           private String skrmedpostctlPath;
           private String wsdserverctlPath;
           private String metamapOptions;
           private String apiTimeoutInterval;
           MetaMapApi api;
         
           /**
            * @generated
            * @ordered
            */
           public final static int typeIndexID = JCasRegistry
             .register(MetaMapAnnotator.class);
           /**
            * @generated
            * @ordered
            */
           public final static int type = typeIndexID;
         
           /** @generated */
           public int getTypeIndexID() {
             return typeIndexID;
           }
         
           /**
            * Creates a new MetaMapAnnotator instance.
            * 
            */
           public MetaMapAnnotator() {
         
           }
         
           /**
            *  Write your own initialization here 
            * 
            * @generated modifiable
            */
           //private void readObject() {
           //}
         
           /** Performs any startup tasks required by this component. */
           public void initialize(UimaContext aContext) throws ResourceInitializationException {
         	super.initialize(aContext);
         	this.getParameters();
             this.api = new MetaMapApiImpl(0);
             this.startTaggerServer();
             this.startDisambiguationServer();
             this.startMetaMapServer();
             this.setupMetaMapOptions();
           }
         
           /** Completes the processing of a batch of CASes. */
           //public void batchProcessComplete() {
           //}
         
           /**
            * Notifies this AnalysisComponent that processing of an entire collection
            * has been completed.
            */
           //public void collectionProcessComplete() {
           //}
         
           /** Frees all resources held by this AnalysisComponent. */
           public void destroy() {
         
           }
         
           /**
            * Returns the specific CAS interface that this AnalysisComponent requires
            * the framework to pass to its process(AbstractCas) method.
            */
           // public Class getRequiredCasInterface() { return null; }
         
           /** Inputs a CAS to the AnalysisComponent. */
           public void process(JCas jcas) {
             String docText = jcas.getDocumentText();
             List resultList = this.api.processCitationsFromString(docText.trim());
             int resultStartIndex = 0;
             for (Result result: resultList) {
               if (result != null) {
         	try {
         	  int citationStart = docText.indexOf(result.getInputText(), resultStartIndex);
         	  if (citationStart == -1) { citationStart = 0; }
         	  Document item = 
         	    new gov.nih.nlm.nls.metamap.uima.ts.Document(jcas, 
         							 citationStart, 
         							 citationStart + result.getInputText().length());
         	  
         	  List acronymsAbbrevs = processAcronymsAbbrevs(jcas, result.getAcronymsAbbrevsList());
         	  FSArray aaArray = new FSArray(jcas, acronymsAbbrevs.size());
         	  aaArray.copyFromArray(acronymsAbbrevs.toArray(new gov.nih.nlm.nls.metamap.uima.ts.AcronymAbbrev[0]), 0, 0, aaArray.size());
         	  item.setAcronymsAbbrevs(aaArray);
         	  aaArray.addToIndexes(jcas);
         	  
         	  List negations = processNegations(jcas, result.getNegationList(), citationStart);
         	  FSArray negationArray = new FSArray(jcas, negations.size());
         	  negationArray.copyFromArray(negations.toArray(new org.metamap.uima.ts.Negation[0]), 0, 0, negationArray.size());
         	  item.setNegations(negationArray);
         	  negationArray.addToIndexes(jcas);
         	  
         	  List utterances = processUtterances(jcas, 
         									     result.getUtteranceList(), 
         									     citationStart);
         	  FSArray utteranceArray = new FSArray(jcas, utterances.size());
         	  utteranceArray.copyFromArray(utterances.toArray(new org.metamap.uima.ts.Utterance[0]), 0, 0, utteranceArray.size());
         	  item.setUtterances(utteranceArray);
         	  utteranceArray.addToIndexes(jcas);
         	  
         	  item.addToIndexes(jcas);
         	  
         	} catch (Exception e) {
         	  e.printStackTrace();
         	}
         	resultStartIndex = resultStartIndex + result.getInputText().length();
               }
             }
           }
         
           List processAcronymsAbbrevs(JCas jcas, List acronymsAbbrevsList)
             throws Exception
           {
             List acronymAbbrevList =
               new ArrayList
               (acronymsAbbrevsList.size());
             
             for (AcronymsAbbrevs aa: acronymsAbbrevsList) {
               AcronymAbbrev currentAA =	new AcronymAbbrev(jcas);
         
               currentAA.setAcronym(aa.getAcronym());
               currentAA.setExpansion(aa.getExpansion());
         
               int i = 0;
               int[] countVector = new int[aa.getCountList().size()];
               for (Integer count : aa.getCountList()) {
             	  countVector[i] = count.intValue();
             	  i++;
               }
               IntegerArray countArray = new IntegerArray(jcas, countVector.length);      
               countArray.copyFromArray(countVector, 0, 0, countVector.length);
               currentAA.setCountList(countArray);
               countArray.addToIndexes(jcas);
         
               StringArray cuiArray = new StringArray(jcas, aa.getCUIList().size());
               cuiArray.copyFromArray(aa.getCUIList().toArray
         		      (new String[0]), 0, 0, aa.getCUIList().size());
               currentAA.setCuiList(cuiArray);
               cuiArray.addToIndexes(jcas);
               acronymAbbrevList.add(currentAA);
               currentAA.addToIndexes(jcas);
             }
             return acronymAbbrevList;
           }
         	
           List processNegations(JCas jcas, List aNegationList, int citationStart)
             throws Exception
           {
             /** uima types from metamap uima package */
             List negationList =
               new ArrayList
               (aNegationList.size());
         
             CuiConcept currentCuiConcept = null;
             List cuiConcepts = null;
         
             // System.out.println("MetaMapAnnotator: result.getNegationList(): " + result.getNegationList());
             for (Negation neg : aNegationList) {
             org.metamap.uima.ts.Negation currentNegation =
               new org.metamap.uima.ts.Negation(jcas);
               
         	cuiConcepts = new ArrayList();
         	
         	currentNegation.setNegType(neg.getType());
         	currentNegation.setNegTrigger(neg.getTrigger());
         
         	FSArray fsArray = createSpanFSArray(jcas, neg.getTriggerPositionList(), citationStart);
         	currentNegation.setNtSpans(fsArray);
         	fsArray.addToIndexes();
         
         	for (ConceptPair conceptPair : neg.getConceptPairList()) {
         	  currentCuiConcept = new CuiConcept(jcas);
         	  currentCuiConcept.setNegExConcept(conceptPair.getPreferredName());
         	  currentCuiConcept.setNegExCui(conceptPair.getConceptId());
         	  cuiConcepts.add(currentCuiConcept);
         	  currentCuiConcept.addToIndexes();
         	}
         
         	fsArray = createSpanFSArray(jcas, neg.getConceptPositionList(), citationStart);
         	currentNegation.setNcSpans(fsArray);
         	fsArray.addToIndexes();
         
         	fsArray = new FSArray(jcas, cuiConcepts.size());
         	fsArray.copyFromArray(cuiConcepts.toArray(new CuiConcept[0]), 0, 0, fsArray.size());
         	currentNegation.setCuiConcepts(fsArray);
         	fsArray.addToIndexes();
         	currentNegation.addToIndexes();
               
               negationList.add(currentNegation);
             }
             return negationList;
           }
         
           List processUtterances(JCas jcas, List anUtteranceList, int citationStart)
             throws Exception
           {
             String docText = jcas.getDocumentText().replace("\n"," ");
             /** uima types from metamap uima package */
             List utteranceList =
               new ArrayList
               (anUtteranceList.size());
         
             // System.out.println("MetaMapAnnotator: result.getUtteranceList(): " + anUtteranceList);
             for (Utterance utterance : anUtteranceList) {
               int utteranceStart = docText.indexOf(utterance.getString(), citationStart + utterance.getPosition().getX());
               /* if indexOf can't find text because of missing spaces or
                * newlines replaced by spaces then trust values UIMA is
                * providing. */
               if (utteranceStart == -1) {
         	utteranceStart = citationStart + utterance.getPosition().getX();
               }
               org.metamap.uima.ts.Utterance currentUtterance = 
         	new org.metamap.uima.ts.Utterance (jcas,
         					   utteranceStart,
         					   utteranceStart + utterance.getPosition().getY());
               currentUtterance.setPmid(utterance.getId());
               processPCMList(jcas, utterance, currentUtterance, citationStart);
               currentUtterance.addToIndexes();
               utteranceList.add(currentUtterance);
             }
             return utteranceList;
           }
         
           void processPCMList(JCas jcas,
         		      gov.nih.nlm.nls.metamap.Utterance utterance,
         		      org.metamap.uima.ts.Utterance currentUtterance,
         		      int citationStart)
             throws Exception
           {
             String docText = jcas.getDocumentText();
             org.metamap.uima.ts.Phrase currentPhrase;
             // org.metamap.uima.ts.CuiConcept currentCuiConcept = null;
             List phrases = null;
             List candidates = null;
             List mappings = null;
             phrases = new ArrayList();
             mappings = new ArrayList();
         
             // System.out.println("MetaMapAnnotator: utterance.getPCMList(): " + utterance.getPCMList());
             for (PCM pcm : utterance.getPCMList()) {
               // System.out.println("MetaMapAnnotator: pcm.getPhrase().getPhraseText(): " + pcm.getPhrase().getPhraseText());
         
               int phraseStart = docText.indexOf(pcm.getPhrase().getPhraseText(), 
         					citationStart + pcm.getPhrase().getPosition().getX());
               /* if indexOf can't find text because of missing spaces or
                * newlines replaced by spaces then trust values UIMA is
                * providing. */
               if (phraseStart == -1) {
         	phraseStart = citationStart + pcm.getPhrase().getPosition().getX();
               }
         	
               currentPhrase = new org.metamap.uima.ts.Phrase
         	(jcas,
         	 phraseStart,
         	 phraseStart + pcm.getPhrase().getPosition().getY() );
               phrases.add(currentPhrase);
         
               candidates = processCandidates(jcas, pcm.getCandidateList(), citationStart);
               FSArray fsArray = new FSArray(jcas, candidates.size());
               fsArray.copyFromArray(candidates.toArray
         			    (new org.metamap.uima.ts.Candidate[0]), 
         			    0, 0, fsArray.size());
               currentPhrase.setCandidates(fsArray);
               fsArray.addToIndexes();
         
               mappings = processMappings(jcas, pcm, citationStart);
               fsArray = new FSArray(jcas, mappings.size());
               fsArray.copyFromArray(mappings.toArray(new org.metamap.uima.ts.Mapping[0]), 0, 0, fsArray.size());
               currentPhrase.setMappings(fsArray);
               fsArray.addToIndexes();
               currentPhrase.addToIndexes();
             }
             int beginUtteranceEnd = utterance.getId().indexOf(".");
             int endUtteranceEnd = utterance.getId().lastIndexOf(".");
             currentUtterance.setLocation(utterance.getId().substring(beginUtteranceEnd,
         							     endUtteranceEnd));
             FSArray fsArray = new FSArray(jcas, phrases.size());
             fsArray.copyFromArray(phrases.toArray(new org.metamap.uima.ts.Phrase[0]), 
         			  0, 0, fsArray.size());
         
             currentUtterance.setPhrases(fsArray);
             fsArray.addToIndexes();
           }
         
           List processCandidates(JCas jcas, List candidateList, int citationStart)
             throws Exception 
           {
             String docText = jcas.getDocumentText();
             org.metamap.uima.ts.Candidate currentCandidate;
             List candidates = new ArrayList();
         
             for (Ev ev : candidateList) {
               // System.out.println("MetaMapAnnotator: ev.getScore(): " + ev.getScore());
               // System.out.println("MetaMapAnnotator: ev.getConceptId(): " + ev.getConceptId());
               int begin = 9999;
               int end = 0;
               for (Position pos : ev.getPositionalInfo()) {
         	begin = Math.min(begin, (int)pos.getX());
         	end = Math.max(end, pos.getX() + pos.getY());
         	// System.out.println("span: [" + pos.getX() + "," + pos.getX() + pos.getY() + "]");
               }
               int start = citationStart + begin;
               int finish = citationStart + end;
         
              // System.out.println("maximal span: [" + begin + "," + end + "]");
               currentCandidate = new org.metamap.uima.ts.Candidate(jcas, start, finish);
               currentCandidate.setScore(ev.getScore());
               currentCandidate.setCui(ev.getConceptId());
               currentCandidate.setConcept(ev.getConceptName());
               currentCandidate.setPreferred(ev.getPreferredName());
               currentCandidate.setHead(ev.isHead());
               currentCandidate.setOvermatch(ev.isOvermatch());
               
               List matchMaps = new ArrayList();
               gov.nih.nlm.nls.metamap.uima.ts.MatchMap currentMatchMap;
               for (MatchMap matchMap: ev.getMatchMapList()) {	
             	  currentMatchMap = new gov.nih.nlm.nls.metamap.uima.ts.MatchMap(jcas);
             	  currentMatchMap.setPhraseMatchStart(matchMap.getPhraseMatchStart());
             	  currentMatchMap.setPhraseMatchEnd(matchMap.getPhraseMatchEnd()); 
             	  currentMatchMap.setConceptMatchStart(matchMap.getConceptMatchStart());
             	  currentMatchMap.setConceptMatchEnd(matchMap.getConceptMatchEnd());
             	  currentMatchMap.setLexVariation(matchMap.getLexMatchVariation());
             	  matchMaps.add(currentMatchMap);
               }
               FSArray matchMapArray = new FSArray(jcas,ev.getMatchMapList().size());
               matchMapArray.copyFromArray(matchMaps.toArray(new gov.nih.nlm.nls.metamap.uima.ts.MatchMap[0]), 
         			  0, 0, matchMapArray.size());
               currentCandidate.setMatchMap(matchMapArray);
               matchMapArray.addToIndexes();
               
               StringArray sourceArray =	new StringArray(jcas, ev.getSources().size());
               // ev.getSources().toArray()
               sourceArray.copyFromArray(ev.getSources().toArray
         				(new String[0]), 0, 0, ev.getSources().size());
               currentCandidate.setSources(sourceArray);
               sourceArray.addToIndexes();
         
         
               StringArray semTypeArray = new StringArray
               	(jcas, ev.getSemanticTypes().size());
               // ev.getSemanticTypes().toArray()
               semTypeArray.copyFromArray(ev.getSemanticTypes().toArray
             		  (new String[0]), 0, 0, ev.getSemanticTypes().size());
               currentCandidate.setSemanticTypes(semTypeArray);
               semTypeArray.addToIndexes();
               
               StringArray matchedWordArray = new StringArray(jcas, ev.getMatchedWords().size());
               matchedWordArray.copyFromArray(ev.getMatchedWords().toArray
             		  (new String[0]), 0, 0, ev.getMatchedWords().size());
               currentCandidate.setMatchedwords(matchedWordArray);
               matchedWordArray.addToIndexes();
         
               FSArray fsArray = createSpanFSArray(jcas, ev.getPositionalInfo(), citationStart);
               currentCandidate.setSpans(fsArray);
               fsArray.addToIndexes();
         
               candidates.add(currentCandidate);
               currentCandidate.addToIndexes();
             }
             return candidates;
           }
         
           List processMappings(JCas jcas, PCM pcm, int citationStart)
             throws Exception
           {
             org.metamap.uima.ts.Mapping currentMapping;
             List candidates;
             List mappings = new ArrayList();
         
             for (gov.nih.nlm.nls.metamap.Mapping map : pcm.getMappingList()) {	
               // System.out.println("MetaMapAnnotator: map.getScore(): " + map.getScore());
               currentMapping = new org.metamap.uima.ts.Mapping(jcas);
         							
               candidates = processCandidates(jcas, map.getEvList(), citationStart);
         							
               FSArray mappedCandidatesFSArray = new FSArray(jcas, candidates.size());
               mappedCandidatesFSArray.copyFromArray(candidates.toArray
         					    (new org.metamap.uima.ts.Candidate[0]), 
         					    0, 0, mappedCandidatesFSArray.size());
               currentMapping.setCandidates(mappedCandidatesFSArray);
               mappedCandidatesFSArray.addToIndexes();
               mappings.add(currentMapping);
               currentMapping.setScore(map.getScore());
               currentMapping.addToIndexes();
             }
             return mappings;
           }
         
           public FSArray createSpanFSArray (JCas jcas, List positionList, int citationStart) {
             List spans = createSpanList(jcas, positionList, citationStart);
             FSArray fsArray = new FSArray(jcas, spans.size());
             fsArray.copyFromArray(spans.toArray(new org.metamap.uima.ts.Span[0]),
         			  0, 0, fsArray.size());
             return fsArray;
           }
         
           public List createSpanList(JCas jcas, List positionList, int citationStart) {
             List spans = new ArrayList();
             for (Position pos : positionList) {
               Span currentSpan = new Span(jcas); ;
               if (pos != null) {
         	currentSpan.setBegin(citationStart + pos.getX());
         	currentSpan.setEnd(citationStart + pos.getX() + pos.getY()); // getY() actually is the Span length (http://skr.nlm.nih.gov/Help/MMO_08_Info.html)
               } else {
         	System.err.println("Null positional information in pos: " + pos);
               }
               spans.add(currentSpan);
               currentSpan.addToIndexes();
             }
             return spans;
           }
         
         
           /*
            * Alerts this AnalysisComponent that the values of its configuration
            * parameters or external resources have changed.
            */
           //public void reconfigure() {
           //}
         
           /** Sets the ResultSpecification that this AnalysisComponent should use. */
           //public void setResultSpecification(ResultSpecification aResultSpec) {
           //}
         
           /** add any extra options (besides machine output) to be used for processing, see parameter metamap_options*/
         	private void setupMetaMapOptions() {
         		// Mandatory options.
         		if ((this.metamapOptions != null) && (! this.metamapOptions.isEmpty())) {
         		this.api.setOptions(metamapOptions); 
         		}
         	}
         
           /**
            * Modified version of getParameters() from Kai Schlamp's BasicMetaMapAnnotator.
            */
           private void getParameters() {
             this.mmserverPath = (String) getContext().getConfigParameterValue(MMSERVER_PATH_PARAMETER);
             this.skrmedpostctlPath = (String) getContext().getConfigParameterValue(SKRMEDPOSTCTL_PATH_PARAMETER);
             this.wsdserverctlPath = (String) getContext().getConfigParameterValue(WSDSERVERCTL_PATH_PARAMETER);
             // tempdirPath = (String) getContext().getConfigParameterValue(TEMPDIR_PATH_PARAMETER);
             this.metamapOptions = (String) getContext().getConfigParameterValue(METAMAP_OPTIONS_PARAMETER);
             this.apiTimeoutInterval = (String) getContext().getConfigParameterValue(METAMAP_TIMEOUT_PARAMETER);
           }
           /**
            * Taken from Kai Schlamp's BasicMetaMapAnnotator.
            *
            */
           private void startTaggerServer() {
             File skrmedpostctlFile = null;
             if (this.skrmedpostctlPath != null && !this.skrmedpostctlPath.isEmpty()) {
               skrmedpostctlFile = new File(this.skrmedpostctlPath);
               if (!skrmedpostctlFile.isFile()) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "wrong_skrmedpostctl_path");
         	skrmedpostctlFile = null;
               }
               if (!skrmedpostctlFile.canExecute()) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "not_executable_skrmedpostctl");
         	skrmedpostctlFile = null;
               }
             }
         		
             boolean taggerServerRunning = false;
             String os = System.getProperty("os.name");
             if ((skrmedpostctlFile != null) && (os.contains("Linux") || os.contains("linux"))) {
               try {
         	taggerServerRunning = checkProcess("taggerServer");
         	if (!taggerServerRunning && skrmedpostctlFile != null) {
         	  ProcessBuilder taggerServerStartProcessBuilder = new ProcessBuilder(skrmedpostctlFile.getAbsolutePath(), "start");
         	  try {
         	    taggerServerStartProcessBuilder.start().waitFor();
         	    Thread.sleep(2000);
         	  } catch (InterruptedException e) {
         	    getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "failure_tagger_server_start", e);
         	  }
         	}
               }
               catch (IOException e) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "failure_searching_server_processes", e);
               }
             }
           }
         
         
           /**
            * Taken from Kai Schlamp's BasicMetaMapAnnotator.
            *
            */
           private void startDisambiguationServer() {
             File wsdserverctlFile = null;
             if (this.wsdserverctlPath != null && !this.wsdserverctlPath.isEmpty()) {
               wsdserverctlFile = new File(this.wsdserverctlPath);
               if (!wsdserverctlFile.isFile()) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "wrong_wsdserverctl_path");
         	wsdserverctlFile = null;
               }
               if (!wsdserverctlFile.canExecute()) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "not_executable_wsdserverctl");
         	wsdserverctlFile = null;
               }
             }
         		
             boolean disambiguatorServerRunning = false;
             String os = System.getProperty("os.name");
             if ((wsdserverctlFile != null) && (os.contains("Linux") || os.contains("linux"))) {
               try {
         	disambiguatorServerRunning = checkProcess("wsd.server.DisambiguatorServer");
         	if (!disambiguatorServerRunning && wsdserverctlFile != null) {
         	  ProcessBuilder disambiguatorStartProcessBuilder = new ProcessBuilder(wsdserverctlFile.getAbsolutePath(), "start");
         	  try {
         	    disambiguatorStartProcessBuilder.start().waitFor();
         	    Thread.sleep(2000);
         	  } catch (InterruptedException e) {
         	    getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "failure_disambiguator_server_start", e);
         	  }
         	}
               }
               catch (IOException e) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "failure_searching_server_processes", e);
               }
             }
           }
         	
           /**
            * Taken from Kai Schlamp's BasicMetaMapAnnotator.
            *
            */
           private boolean checkProcess(String processName) throws IOException {
             ProcessBuilder processBuilder = new ProcessBuilder("ps", "-ef");
             Process psProcess = processBuilder.start();
             BufferedReader input = new BufferedReader(new InputStreamReader(psProcess.getInputStream()));
             String line;
             while ((line = input.readLine()) != null) {
               if (line.contains(processName)) {
         	return true;
               }
             }
             input.close();
             return false;
           }
         	
           private void startMetaMapServer() {
             File mmserverFile = null;
             if (this.mmserverPath != null && !this.mmserverPath.isEmpty()) {
               mmserverFile = new File(this.mmserverPath);
               if (!mmserverFile.isFile()) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "wrong_mmserver_path");
         	mmserverFile = null;
               }
               if (mmserverFile != null && !mmserverFile.canExecute()) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "not_executable_mmserver");
         	mmserverFile = null;
               }
             }
         		
             boolean disambiguatorServerRunning = false;
             String os = System.getProperty("os.name");
             if ((mmserverFile != null) && (os.contains("Linux") || os.contains("linux"))) {
               try {
         	disambiguatorServerRunning = checkProcess("mmserver");
         	if (!disambiguatorServerRunning && mmserverFile != null) {
         	  ProcessBuilder disambiguatorStartProcessBuilder = new ProcessBuilder(mmserverFile.getAbsolutePath(), "start");
         	  try {
         	    disambiguatorStartProcessBuilder.start().waitFor();
         	    Thread.sleep(2000);
         	  } catch (InterruptedException e) {
         	    getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "failure_disambiguator_server_start", e);
         	  }
         	}
               }
               catch (IOException e) {
         	getContext().getLogger().logrb(Level.WARNING, null, null, MESSAGE_DIGEST, "failure_searching_server_processes", e);
               }
             }
           }
         
         
         }
         
         --------------080107010100070101050205
         Content-Type: text/xml; name="MetaMapApiTypeSystem.xml"
         Content-Transfer-Encoding: 7bit
         Content-Disposition: attachment; filename="MetaMapApiTypeSystem.xml"
         
         
         
           Document
           Document Representation
           1.0
           
           
             
               org.metamap.uima.ts.Candidate
               The meta elements found in the text. Those are then used as candidates and mappings.
               uima.tcas.Annotation
               
                 
                   score
                   The score of this meta element (0 <= x <= 1000).
                   uima.cas.Integer
                 
                 
                   spans
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Span
                 
                 
                   cui
                   
                   uima.cas.String
                 
                 
                   concept
                   
                   uima.cas.String
                 
                 
                   preferred
                   
                   uima.cas.String
                 
                 
                   head
                   
                   uima.cas.Boolean
                 
                 
                   overmatch
                   
                   uima.cas.Boolean
                 
                 
                   sources
                   
                   uima.cas.StringArray
                 
                 
                   semanticTypes
                   
                   uima.cas.StringArray
                 
                 
                   matchedwords
                   
                   uima.cas.StringArray
                 
                 
                   matchMap
                   
                   uima.cas.FSArray
                   gov.nih.nlm.nls.metamap.uima.ts.MatchMap
                 
               
             
             
               org.metamap.uima.ts.Mapping
               A meta mapping.
               uima.cas.TOP
               
                 
                   score
                   The score of this mapping.
                   uima.cas.Integer
                 
                 
                   candidates
                   An array of elements of this mapping.
                   uima.cas.FSArray
                   org.metamap.uima.ts.Candidate
                 
               
             
             
               org.metamap.uima.ts.Phrase
               
               uima.tcas.Annotation
               
                 
                   candidates
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Candidate
                 
                 
                   mappings
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Mapping
                 
               
             
             
               org.metamap.uima.ts.Span
               
               uima.tcas.Annotation
             
             
               org.metamap.uima.ts.Utterance
               
               uima.tcas.Annotation
               
                 
                   pmid
                   
                   uima.cas.String
                 
                 
                   phrases
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Phrase
                 
                 
                   location
                   
                   uima.cas.String
                 
               
             
             
               org.metamap.uima.ts.Negation
               
               uima.tcas.Annotation
               
                 
                   negType
                   
                   uima.cas.String
                 
                 
                   negTrigger
                   
                   uima.cas.String
                 
                 
                   ntSpans
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Span
                 
                 
                   cuiConcepts
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.CuiConcept
                 
                 
                   ncSpans
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Span
                 
               
             
             
               org.metamap.uima.ts.CuiConcept
               
               uima.cas.TOP
               
                 
                   negExCui
                   
                   uima.cas.String
                 
                 
                   negExConcept
                   
                   uima.cas.String
                 
               
             
             
               gov.nih.nlm.nls.metamap.uima.ts.MatchMap
               
               uima.tcas.Annotation
               
                 
                   phraseMatchStart
                   
                   uima.cas.Integer
                 
                 
                   phraseMatchEnd
                   
                   uima.cas.Integer
                 
                 
                   conceptMatchStart
                   
                   uima.cas.Integer
                 
                 
                   conceptMatchEnd
                   
                   uima.cas.Integer
                 
                 
                   lexVariation
                   
                   uima.cas.Integer
                 
               
             
             
               gov.nih.nlm.nls.metamap.uima.ts.AcronymAbbrev
               Container for MetaMap Acronym or Abbreviation annotation.
               uima.tcas.Annotation
               
                 
                   acronym
                   Acronym or Abbreviation
                   uima.cas.String
                 
                 
                   expansion
                   expansion of the acronym or abbreviation
                   uima.cas.String
                 
                 
                   countList
                   count list
                   uima.cas.IntegerArray
                 
                 
                   cuiList
                   list of concept id for acronym or abbreviation
                   uima.cas.StringArray
                 
               
             
             
               gov.nih.nlm.nls.metamap.uima.ts.Document
               A citation or item of free-text
               uima.tcas.Annotation
               
                 
                   acronymsAbbrevs
                   acronym and abbreviations
                   uima.cas.FSArray
                   gov.nih.nlm.nls.metamap.uima.ts.AcronymAbbrev
                 
                 
                   negations
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Negation
                 
                 
                   utterances
                   
                   uima.cas.FSArray
                   org.metamap.uima.ts.Utterance
                 
               
             
           
         
         
         --------------080107010100070101050205--



Back to MetaMap Trouble Report Page