https://github.com/cthoyt/curies4j

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs)
https://github.com/cthoyt/curies4j

curies java obofoundry semantic-web uris

Last synced: 23 days ago
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🐸 Idiomatic conversion between URIs and compact URIs (CURIEs)

• Host: GitHub
• URL: https://github.com/cthoyt/curies4j
• Owner: cthoyt
• License: mit
• Created: 2023-05-08T10:12:07.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-10-25T15:38:58.000Z (about 1 year ago)
• Last Synced: 2024-05-02T02:19:23.533Z (6 months ago)
• Topics: curies, java, obofoundry, semantic-web, uris
• Language: Java
• Homepage:
• Size: 37.1 KB
• Stars: 9
• Watchers: 3
• Forks: 0
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# curies4j

A Java implementation of the [`curies`](https://github.com/cthoyt/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.

```java

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

```java

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 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:

```java

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:

```java

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.

```java

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

Special thanks to [Jonas Schaub](https://github.com/JonasSchaub) for helping with packaging and deployment to Maven Central.