Semantic Knowledge Representation project in Lister Hill Center for National Institute of Health.
To run source code, you need to either add all of the jar files in lib directory to your building path or compile them through maven and add them as maven dependencies in the pom file.
Maven Compilation E.G.:
mvn install:install-file -Dfile=lib/metamaplite-3.6.2rc1.jar -DgroupId=gov.nih.nlm.nls -DartifactId=metamaplite -Dversion=3.6.2rc1 -Dpackaging=jar
mvn install:install-file -Dfile=lib/bioscores-2.0.1.jar -DgroupId=gov.nih.nlm -DartifactId=bioscores -Dversion=2.0.1 -Dpackaging=jar
mvn install:install-file -Dfile=lib/lvg2016dist-0.0.1.jar -DgroupId=gov.nih.nlm.nls.lvg -DartifactId=lvg2016dist -Dversion=0.0.1 -Dpackaging=jar
mvn install:install-file -Dfile=lib/gnormplus-1.0.0.jar -DgroupId=gov.nih.nlm -DartifactId=gnormplus -Dversion=1.0.0 -Dpackaging=jar
mvn install:install-file -Dfile=lib/aec_mrd_wsd-1.0-SNAPSHOT.jar -DgroupId=gov.nih.nlm.nls -DartifactId=aec_mrd_wsd -Dversion=1.0-SNAPSHOT -Dpackaging=jar
mvn install:install-file -Dfile=lib/lexCheck2011dist-1.0.0.jar -DgroupId=gov.nih.nlm -DartifactId=lexCheck2011dist -Dversion=1.0.0 -Dpackaging=jar
You have to run it from top level:
sh bin/semrepjava.sh
Please specify the following options:
--inputformat=? (either "dir" or "singlefile") --inputtextformat=? (either "plaintext" or "medline" or "medlinexml") --inputpath=? (the input directory path or single file path) --outputpath=? (the output directory name or a file name) --outputFormat=? ("human-readable" or "brat" or "simplified" or "json") --includes=? (optional, whether to include addition infos in the output, can be "chunk" or "tag")
e.g. to test with plaintext:
sh bin/semrepjava.sh --inputformat=singlefile --inputtextformat=plaintext --inputpath=TestFiles/test.plain --outputpath=TestFiles/out.plain --outputFormat=human-readable --includes=chunk
e.g. to test with medline:
sh bin/semrepjava.sh --inputformat=singlefile --inputtextformat=medline --inputpath=TestFiles/test.ml --outputpath=TestFiles/out.ml --outputFormat=human-readable --includes=chunk