Kostee / NCBO-REST-Annotator

Java application for using BioPortal annotator locally in the console

NCBO-REST-Annotator

Java application for using BioPortal annotator locally in the console

Sources

The program has been implemented according to the documentation: http://data.bioontology.org/documentation

Inspirated by: https://github.com/ncbo/ncbo_rest_sample_code

Also noteworthy - REST API example in R: https://github.com/muntisa/RNCBO

Example URL for GET: https://data.bioontology.org/annotator?text=My+biomedical+text+for+annotation

Sample use (run in /src dir; with examples below):

1. Just plain text, with standard API key - output in console

java -classpath ".;../lib/*" AnnotateText <text to anotate>
java -classpath ".;../lib/*" AnnotateText "Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body"

2. Plain text to output file (with standard API key)

java -classpath ".;../lib/*" AnnotateText <text to anotate> > <outputfile> | type <outputfile>
java -classpath ".;../lib/*" AnnotateText "Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body" > "..\output\exampleOutput1.txt" | type "..\output\exampleOutput1.txt"

3. Plain text to output file with own API key

java -classpath ".;../lib/*" AnnotateTextAdvanced <text to anotate> <API key> > <outputfile> | type <outputfile>
java -classpath ".;../lib/*" AnnotateTextAdvanced "Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body" "ddbc0f31-8c9e-4a77-bd04-b146ae01baa0"  > "..\output\exampleOutput2.txt" | type "..\output\exampleOutput2.txt"

4. Text from .txt file (with standard API key, output in console)

java -classpath ".;../lib/*" AnnotateText `cat <file>`
java -classpath ".;../lib/*" AnnotateText `cat ../examples/exampleInput.txt`

Commands above processed on Windows - similarly on Linux