fenominal library

To use fenominal as a library for Java 17 or higher applications, add the following to the POM file.

<dependency>
    <groupId>org.monarchinitiative.fenominal</groupId>
    <artifactId>fenominal-core</artifactId>
    <version>...</version>
</dependency>
<dependency>
    <groupId>org.monarchinitiative.phenol</groupId>
    <artifactId>phenol-core</artifactId>
    <version>...</version>
</dependency>
<dependency>
    <groupId>org.monarchinitiative.phenol</groupId>
    <artifactId>phenol-io</artifactId>
    <version>...</version>
</dependency>

Using the latest versions of fenominal and phenol.

TODO explain how to use GRAIL.

Imports

Use the following imports

import org.monarchinitiative.fenominal.core.FenominalRunTimeException;
import org.monarchinitiative.fenominal.core.TermMiner;
import org.monarchinitiative.fenominal.model.MinedSentence;
import org.monarchinitiative.fenominal.model.MinedTermWithMetadata;
import org.monarchinitiative.phenol.io.OntologyLoader;
import org.monarchinitiative.phenol.ontology.data.Ontology;
import org.monarchinitiative.phenol.ontology.data.TermId;

Initialize with the path to the hp.json file

Ontology ontology = OntologyLoader.loadOntology(new File(hpoJsonPath));

Decide whether to do exact or T-BLAT (fuzzy) matching

boolean doExactMatching = ....// your code decides
TermMiner miner;
if (exact) {
    miner = TermMiner.defaultNonFuzzyMapper(this.ontology);
} else {
    miner = TermMiner.defaultFuzzyMapper(this.ontology);
}

You can use fenominal to retrieve three types of objects.

sentences

Retrieve a collection of MinedSentence objects that represent each of the sentences in the input string in which at least one HPO term is indentified. Each MinedSentence object has a collection of MinedTermWithMetadata objects.

String inputString = ....// your code provides input String
Collection<MinedSentence> setences = miner.mineSentences(inputString);

MinedTermWithMetadata

Returns a collection of MinedTermWithMetadata objects, each of which provides the following methods

String getMatchingString(): the matching string in the original text
double getSimilarity() the similaroty score for the match
TermId getTermId(): the HPO TermId
int getTokenCount(): - the number of matching tokens

Additionally, all of the methods of MinedTerm are provided (see below)

String inputString = ....// your code provides input String
Collection<MinedTermWithMetadata> setences = miner.mineTermsWithMetadata(inputString);

MinedTerm

Returns a collection of MinedTerm objects, each of which provides the following methods

int getBegin(): zero-based start coordinate of the match in the original text
int getEnd(): zero-based end coordinate (included) of the match in the original text
String getTermIdAsString(): String version of the HPO term id.
boolean isPresent(): true of the HPO term was observed, false if it was excluded according to the original text

String inputString = ....// your code provides input String
Collection<MinedTerm> sentences = miner.mineTerms(inputString);