CLI fenominal application

fenominal is a Java library written in Java 17. fenominal contains a command-line interface (cli) module that demonstrates some of the functionality of the library.

See CLI fenominal app: Setup for instructions on building the application.

See CLI fenominal app: Downloading the hpo file for instructions on how to download the hp.json file that is needed for the app.

Once you have built the application, you should see this

java -jar fenominal-cli/target/fenominal.jar
    Usage: fenominal [-hV] [COMMAND]
    phenotype/disease NER
        -h, --help      Show this help message and exit.
        -V, --version   Print version information and exit.
    Commands:
        download, D  Download files for fenominal
        parse, P     Parse text

in the following we will show only fenominal.jar. Adjust the path accordingly.

Fenominal’s Matching

Fenominal can perform exact matching and fuzzy matching. See Fenominal’s Matching Algorithms for an explanation.

To see the options, run java -jar fenominal.jar parse -h.

Short option	Long option	Explanation
-e	–exact	Use exact matching algorithm
-h	–help	Show this help message and exit.
	–hp=<path>	Path to HP json file (default data/hp.json)
-i	–input=<path>	Path to HP json file (default data/hp.json)
-0	–output=<path>	Path to output file
-V	–version	Print version information and exit.
	–verbose	Show parse results in shell

Exact matching

For this example, create a file called text-exact.txt with the following contents

A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retardation, cardiomyopathy, and hypertelorism.

Run fenominal as follows.

java -jar fenominal.jar parse --exact -i text-exact.txt --verbose
(...)
Growth delay HP:0001510      growth retardation      observed        79      97      A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retardation, cardiomyopathy, and hypertelorism.
Cardiomyopathy       HP:0001638      cardiomyopathy  observed        99      113     A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retardation, cardiomyopathy, and hypertelorism.
Hypertelorism        HP:0000316      hypertelorism   observed        119     132     A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retardation, cardiomyopathy, and hypertelorism.

T-BLAT (fuzzy) Matching

For this example, create a file called text-errors.txt with the following contents.

A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retadation, cardiomyopathic, and hypertelorisn.

Run fenominal as follows.

java -jar fenominal.jar parse -i text-errors.txt --verbose
(...)
 Agnosia     HP:0010524      agnosia observed        28      37      A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retadation, cardiomyopathic, and hypertelorisn.
 Growth delay        HP:0001510      growth retardation      observed        79      96      A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retadation, cardiomyopathic, and hypertelorisn.
 Cardiomyopathy      HP:0001638      cardiomyopathy  observed        98      113     A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retadation, cardiomyopathic, and hypertelorisn.
 Hypertelorism       HP:0000316      hypertelorism   observed        119     132     A 28-year-old woman who was diagnosed with Noonan syndrome at age 4 because of growth retadation, cardiomyopathic, and hypertelorisn.

Fenominal picks up four terms. Agnosia is false postion (from the word diagnosed). The remaining three terms are inferred correctly despite the presence of spelling errors or variants. Note that T-BLAT is the default approach, and exact matching is only performed if the --exact flag is passed.