Installing MetaMap on CentOS 6.4

由於工作要做text mining去取得UML's CONCEPT_ID，因此就將安裝的過程記錄下來

請至MetaMap網頁下載public_mm_linux_main_2013v2.tar.gz

自行解壓縮

# tar -zxvf public_mm_linux_main_2013v2.tar.gz

進入主目錄

# cd public_mm

# ./bin/install.sh

Enter basedir of installation [/home/ben/public_mm]

/home/ben/public_mm

Basedir is set to /home/ben/public_mm.

The WSD Server requires Sun's Java Runtime Environment (JRE);

Sun's Java Developer Kit (JDK) will work as well. if the

command: "which" java returns /usr/local/jre1.4.2/bin/java, then the

JRE resides in /usr/local/jre1.4.2/.

Where does your distribution of Sun\'s JRE reside?

Enter home path of JRE (JDK) [/usr/java/jdk1.7.0_45]:

/usr/java/jdk1.7.0_45

Using /usr/java/jdk1.7.0_45 for JAVA_HOME.

PS. 藍色字為安裝過程自行輸入的部分

啟用MetaMap Server

# ./bin/skrmedpostctl start

# ./bin/wsdserverctl start

測試MetaMap

# echo "lung cancer" | ./bin/metamap13 -I

/home/ben/public_mm/bin/SKRrun.13 /home/ben/public_mm/bin/metamap13.BINARY.Linux -L 2013 --lexicon db -Z 2013AB -I

libgcc_s.so.1 must be installed for pthread_cancel to work

/home/ben/public_mm/bin/metamap2013.TEMPLATE: line 135: 23683 Aborted                 (core dumped) $COMMAND

出現錯誤訊息

安裝libgcc_s.so.1

# yum provides */libgcc_s.so.1

# yum install libgcc.i686

重啟Server，先關閉，在啟用

# ./bin/skrmedpostctl stop

# ./bin/wsdserverctl stop

# ./bin/skrmedpostctl start

# ./bin/wsdserverctl start

測試MetaMap

# echo "lung cancer" | ./bin/metamap13 -I

metamap13.BINARY.Linux (2013)

Control options:

 composite_phrases=4

 lexicon_year=2013

 lexicon=db

 mm_data_year=2013AB

 show_cuis

Processing 00000000.tx.1: lung cancer

Phrase: "lung cancer"

Meta Candidates (Total=11; Excluded=3; Pruned=0; Remaining=8)

 1000   C0242379:Lung Cancer (Malignant neoplasm of lung) [Neoplastic Process]

 1000   C0684249:LUNG CANCER (Carcinoma of lung) [Neoplastic Process]

  861   C0006826:Cancer (Malignant Neoplasms) [Neoplastic Process]

  861   C0024109:Lung [Body Part, Organ, or Organ Component]

  861   C0819757:LUNG (Structure of parenchyma of lung) [Tissue]

  861   C0998265:Cancer (Cancer Genus) [Eukaryote]

  861   C1278908:Lung (Entire lung) [Body Part, Organ, or Organ Component]

  861   C1306459:Cancer (Primary malignant neoplasm) [Finding]

  805 E C2707265:Pulmonary (Pulmonary:-:Point in time:^Patient:-) [Clinical Attribute]

  805 E C2709248:Pulmonary (Pulmonary (qualifier value)) [Qualitative Concept]

  768 E C0032285:Pneumonia [Disease or Syndrome]

Meta Mapping (1000):

 1000   C0684249:LUNG CANCER (Carcinoma of lung) [Neoplastic Process]

Meta Mapping (1000):

 1000   C0242379:Lung Cancer (Malignant neoplasm of lung) [Neoplastic Process]

測試OK~