curies4j

A Java implementation of the curies Python package, which enables idiomatic conversion between URIs and compact URIs (CURIEs).

Note that this package returns null when it gets content it can't handle instead of throwing errors.

import org.biopragmatics.curies.Converter;
import org.biopragmatics.curies.Reference;

class CuriesDemo1 {
    public static void main(String[] args) {
        Converter converter = Converter.getExampleConverter();

        String curie = "CHEBI:1234";
        String uri = "http://purl.obolibrary.org/obo/CHEBI_1234";

        String reference = new Reference("CHEBI", "1234");
        String prefix = reference.getPrefix();  // "CHEBI"
        String identifier = reference.getIdentfier();  // "1234"

        // 2 ways to expand a CURIE into a URI
        String uri1 = converter.expand("CHEBI:1234");
        String uri2 = converter.expand("CHEBI", "1234");
        // "http://purl.obolibrary.org/obo/CHEBI_1234"

        // Expand a reference into a URI
        String uri3 = converter.expand(reference);
        // "http://purl.obolibrary.org/obo/CHEBI_1234"

        // Compress a URI to a CURIE string
        String curie1 = converter.compress(uri);
        // CHEBI:1234

        // Parse a URI into a reference
        Reference reference1 = converter.parseURI(uri);
        // new Reference("CHEBI", "1234")

        // Parse a CURIE into a reference
        Reference reference2 = converter.parseCURIE(curie);
        // new Reference("CHEBI", "1234")
    }
}

Loading a Prefix Map

import java.util.HashMap;
import java.util.Map;
import org.biopragmatics.curies.Converter;
import org.biopragmatics.curies.Loader;

class AdHocResourceDemo {
    public static void main(String[] args) {
        Map<String, String> prefixMap = new HashMap<>();
        prefixMap.put("OMIM", "https://omim.org/entry/");
        prefixMap.put("OMIMPS", "https://omim.org/phenotypicSeries/PS");
        prefixMap.put("Orphanet", "http://www.orpha.net/ORDO/Orphanet_");

        Converter converter = new Converter(prefixMap);
        converter.compress("http://www.orpha.net/ORDO/Orphanet_85163");
        // Orphabet:85163
    }
}

Loading an Extended Prefix Map

If you have the URL for an extended prefix map, you can do the following:

import org.biopragmatics.curies.Converter;
import org.biopragmatics.curies.Loader;

class RemoteResourceDemo {
    public static void main(String[] args) {
        String url = "https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/bioregistry.epm.json";
        Converter converter = new Converter(Loader.getRecords(url));
        converter.compress("https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:1234");
        // doid:1234
    }
}

Similarly, if you have a file object, you can do:

import java.io.*;
import org.biopragmatics.curies.Converter;
import org.biopragmatics.curies.Loader;

class LocalResourceDemo {
    public static void main(String[] args) {
        File file = new File("/Users/cthoyt/dev/bioregistry/exporst/contexts/bioregistry.epm.json")
        Converter converter = new Converter(Loader.getRecords(file));
        converter.compress("https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:1234");
        // doid:1234
    }
}

Bioregistry Integration

The Bioregistry can be loaded over the web.

import org.biopragmatics.curies.Converter;

class CuriesDemo2 {
    public static void main(String[] args) {
        Converter converter = Converter.loadBioregistry();
        converter.compress("https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:1234");
        // doid:1234
    }
}

Installation

See https://central.sonatype.com/artifact/org.biopragmatics.curies/curies

Acknowledgements