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Queue: PublicMetaMap
Subject: Displaying Concept Code in Custom Metamap Dataset
Status: open
Created: Tue Apr 02 09:38:50 2013
Resolved: Not set
LastUpdated: Tue Jun 11 10:29:35 2013

Subject: 
Creator: 28
Created: 2013-04-02 13:38:50
Transaction: 1912
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         >Category: mmtxT
         >Synopsis: Displaying Concept Code in Custom Metamap Dataset
         >Confidential: no
         >Severity: non-critical
         >Priority: low
         >Class: question
         >Submitter-Id: mmtxWeb
         >Release: 
         >Environment:
         >Operating System - MetaMap: 
         >OS Version - unknown
         >Java Version - Java 1.6
         >Description:
         User at first wanted to know how to include the CODE field from MR(CON)SO in DataFileBuilder and (presumably) how to use it in MetaMap.
         
         I told him that neither DFB nor MetaMap handled the CODE field.
         
         The user then wrote back asking how to create MRCON.mesh, which DFB uses.
         
         
         >How-To-Repeat:
         There is no problem to reproduce. My response to the user was
         
         -----------------------------------------------------------------
         
         First of all, thanks for your kind words about MetaMap!
         
         MRCON.mesh (or MRCONSO.mesh in the Rich Release Format) can indeed be created using MetamorphoSys. It's simply a version of MRCON(SO) that contains data from only the MeSH source vocabulary. There are a number of ways to create this file. Here's how to do it in MetamorphoSys:
         
         In addition to generic steps in MetamorphoSys that are not specific to MeSH, the specific steps you need to follow to create a MeSH-only MRCON using MetamorphoSys are:
         (1) In "Select Default Subset Configuration", choose "Level 0", and then select "OK".
         (2) You'll next see a window called "Metathesaurus Configuration 20XXAB Data File Format".
               * In the "Input Options" tab, choose "NLM Data File Format".
               * In the "Source List" tab, make sure the "INCLUDE" radio button is checked.
               * Click on the "Source Family" column to sort all sources by source family.
               * Scroll down to "Medical Subject Headings, 20YY...", and select that vocabulary; several other vocabularies in the MSH Source Family (translations of MeSH into French, German, etc.) will be selected.
               * Make sure all and only source vocabularies in the MSH family are selected for inclusion.
               * Select any filters you want using "File --> Enable/Disable Filters", e.g., in the Unicode tab, you will probably want to choose "Convert non-ASCII Unicode characters to ASCII characters.
         
         Let me know if that works for you.
         
         
         >Unformatted:




Subject: [PublicMetamap #44] Displaying Concept Code in Custom Metamap Dataset 
Creator: 1
Created: 2013-06-11 14:29:35
Transaction: 1952
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         Tue Jun 11 10:29:35 2013: Request 44 was acted upon.
          Transaction: Given to flang by wjrogers
                Queue: PublicMetaMap
              Subject: Displaying Concept Code in Custom Metamap Dataset
                Owner: flang
           Requestors: [email redacted]
               Status: open
          Ticket 
         
         
         This transaction appears to have no content



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