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es-ontology-annotator-core
es-ontology-annotator-es1.3 Add handling for parent paths to Mapper instances. Feb 25, 2016
es-ontology-annotator-es1.4 Add handling for parent paths to Mapper instances. Feb 25, 2016
es-ontology-annotator-es1.5 Add handling for parent paths to Mapper instances. Feb 25, 2016
es-ontology-annotator-es2.0
es-ontology-annotator-es2.1
es-ontology-annotator-es2.2
.gitignore
README.md
pom.xml Use OntologyHelperBuilder in ElasticOntologyHelperFactory. Feb 24, 2016

README.md

ElasticSearch Ontology Annotator plugin

This directory contains a plugin for enriching records with ontology annotations by adding further data from the ontology where available. It adds a new field type for the ontology annotation which is then expanded with additional data.

There are currently five versions of the module:

  • es-ontology-annotator-es1.3 - this version should work with ElasticSearch versions prior to 1.4, although it has not been extensively tested against versions earlier than 1.3

  • es-ontology-annotator-es1.4 - this version works with ElasticSearch versions 1.4.x.

  • es-ontology-annotator-es1.5 - this version works with ElasticSearch versions 1.5.x - 1.7.x.

  • es-ontology-annotator-es2.0 - this version works with ElasticSearch versions 2.0.x

  • es-ontology-annotator-es2.1 - this version works with ElasticSearch versions 2.1.x

Installation

To build the versions of the plugin, use maven:

mvn clean package

This will create a zip file for each version of the module, containing the full plugin. Once this is complete, it needs to be added to your local ElasticSearch instance. The easiest way to do this is using ElasticSearch's own plugin manager, although usage of this varies between ElasticSearch 1.x and 2.x.

Note: These plugins now depend on the Ontology Annotator Core module, which should be built and installed to your local maven repository before building this module.

Installing to ElasticSearch 1.x

In the ElasticSearch install directory, use the following command:

bin/plugin -u file:///path/to/plugin.zip -i ontology-annotator

Use the plugin version most appropriate to your version of ElasticSearch.

To re-install the plugin, you will first need to remove the previous version, using the following command:

bin/plugin -r ontology-annotator

Installing to ElasticSearch 2.x

In the ElasticSearch install directory, use the following command:

bin/plugin install file:///path/to/plugin.zip

Use the plugin version most appropriate to your version of ElasticSearch.

To re-install the plugin, you will first need to remove the previous version, using the following command:

bin/plugin remove ontology-annotator

The plugin manager for ElasticSearch 2.x does strict checks between the version of the ElasticSearch library used to build the plugin, and that currently in use on your system - for example, the plugin may be built using the ElasticSearch 2.1.1 libraries, but you may be running 2.1.2. To work around this, open the pom.xml file in the ElasticSearch module directory (ie. es-ontology-annotator-es2.1/pom.xml) and change the elasticsearch.version property to that which matches your version of ElasticSearch. Re-build the plugin, and try installing again. If the plugin won't build with the altered version, please file an issue.

Usage

The plugin creates a new field mapping type, which is then used to expand an ontology reference by retrieving additional details from the ontology. The plugin can be configured to use either an ontology file (ie. an OWL file), which may be local or remote, or it can use the EBI Ontology Lookup Service (OLS) as its reference. For both methods, the ontology details need to be included in the field mappings.

Using an ontology file

Example mappings for using an ontology file are:

{
	"test":{
		"properties": {
			"annotation": {
				"type": "ontology",
				"ontology": {
					"ontologyURI": "./ontologyUpdate/owl/test.owl",
					"labelURI": "http://www.w3.org/2000/01/rdf-schema#label",
					"synonymURI": "http://www.ebi.ac.uk/efo/alternative_term",
					"definitionURI": [
						"http://www.ebi.ac.uk/efo/definition",
						"http://purl.obolibrary.org/obo/IAO_0000115"
					],
					"includeIndirect": true,
					"includeRelations": true,
					"includeParentPaths": false,
					"includeParentPathLabels": true
				}
			}
		}
	}
}

The ontologyURI value is mandatory. The label, synonym and definition URI fields have default values:

  • labelURI: http://www.w3.org/2000/01/rdf-schema#label
  • synonymURI: http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
  • definitionURI: http://purl.obolibrary.org/obo/IAO_0000115

Each of the above can be given as a single string or an array (as shown by definitionURI in the mapping example).

The includeIndirect property indicates whether or not the field should include all ancestors and descendants in the data (indirect parent/child relationships), or just the direct parent and child nodes. If true, sub-fields called ancestor_uris, ancestor_labels, descendant_uris and descendant_labels will be created, as well as the parent/child fields.

The includeRelations property indicates whether or not additional relationships between nodes should be included with the data. If true, relationships such as "has disease location", "participates in", etc., will be included with the annotation data.

The includeParentPaths property indicates whether or not the parent paths from the annotated node to the root should be generated and added to the data. If this is set to true, you can also set the includeParentPathLabels property to add the parent node labels to the parent paths string. These will be added to a sub-field called parent_paths. Note that this property is set to false by default.

Using the Ontology Lookup Service

Example mappings for using OLS are:

{
	"test":{
		"properties": {
			"annotation": {
				"type": "ontology",
				"ontology": {
					"olsBaseURL": "http://www.ebi.ac.uk/ols/beta/api",
					"olsOntology": "efo",
                    "includeIndirect": true,
                    "includeRelations": true
				}
			}
		}
	}
}

The olsBaseURL property is mandatory if using OLS, and should point to the API endpoint to be used.

The olsOntology property is optional, and should contain the ontology code, as used in OLS. This is then added to the base URL to carry out term lookups

When an ontology is not specified, the plugin will use the OLS field is_defining_ontology to attempt to find the best version of a record to use. If no defining ontology can be found, it will usually default to the first instance of the record returned by the search for its label, synonym and definitions. The parent, child and other relationship fields will be generated using all of the records, which can take a long time and result in a lot of data being indexed.

The includeIndirect and includeRelations properties have the same function as when using an ontology file - see above for further details.

Searching ontology data

The plugin adds subfields to your nominated ontology field, but these are not added to the document's _source field. This means that they won't appear by default when searching the data.

To carry out a search returning the new ontology annotation fields, they need to be added to the field list, either individually, or by returning all of the fields for each record.

GET biosolr/documents/_search
{
  "fields": "*",
  "_source": true,
  "query": {
    "match_all": {}
  }
}

The above query will return the _source and all of the fields added to the returned documents:

"_source": {
  "study": 23633212,
  "title": "Genome-wide association of single-nucleotide polymorphisms ...",
  ...
},
"fields": {
  "annotation.uri": [
    "http://www.ebi.ac.uk/efo/EFO_0005245"
  ],
  "annotation.label": [
    "body weight loss"
  ],
  ...
}

NOTE: To do the same search in ElasticSearch 2.0, you need to specify all of the _source subfields as well:

GET biosolr/documents/_search
{
  "_source": [ "*" ],
  "fields": [ "*" ],
  "query": {
    "match_all": {}
  }
}

The full mapping, including the new fields that have been added for the ontology annotations, is available using the _mapping endpoint:

GET biosolr/documents/_mapping

The output from the mapping list can be used to get a list of fields. Dynamically generated fields, for additional relationships, will always have the suffixes _rel_labels (for label fields) and _rel_uris (for URI fields).

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