8. Ontology mapping with Ontology Xref Service (OxO)



Recipe Overview
Reading Time
30 minutes
Executable Code
No
Difficulty
Ontology mapping with Ontology Xref Service (OxO)
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Recipe Type
Hands-on
Maturity Level & Indicator
DSM-1-C0
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8.1. Main Objectives

Different ontology terms can describe the same concept, which makes it difficult for data integration. Ontology mapping, or ontology alignment, is the process of determining correspondences between equivalent concepts in alternative ontologies and distinct vocabularies.

OxO maps terms in different ontologies, vocabularies and coding standards using evidence collected mainly from the Ontology Lookup Service (OLS), Unified Medical Language System (UMLS), but also from other sources.

This recipe shows how to use the EMBL-EBI Ontology Xref Service (OxO) service to map ontology terms between source and target vocabularies 1 .

8.2. Graphical Overview

8.3. Requirements

8.4. FAIRification Objectives, Inputs and Outputs

Actions.Objectives.Tasks

Input

Output

ID mapping

Ontology term

Ontology term

Annotation

Ontology term

Ontology term

8.5. Table of Data Standards

Data Formats

Terminologies

Models

Mondo Disease ontology

Human Disease ontology

Medical Subject Headings

8.6. Using EMBL-EBI OXO

Ontology cross Ontology or OxO service is available from a web interface or a programmatic interface. The following sections show both.

8.6.1. OXO Web Interface:

8.6.1.1. Step 1: Identify source vocabulary and target vocabulary

For pathology data annotation, vocabularies, such as MeSH, NCI thesaurus, ICD-10, UMLS, Human Disease Ontology(DOID), and MONDO disease ontology, are widely used. In this example, we use MeSH and DOID as source vocabularies and MONDO as the target vocabulary to demonstrate the ontology mapping workflow.

Obviously, a target vocabulary needs to be selected before mapping. A variety of factors can influence the selection of a terminology resource for a specific purpose or curation context. For more information about this topic, more detailed guidance on how to select vocabularies can be found here.

OxO allows users to explore the mapping status between the target vocabulary and other vocabularies. Figure 1 shows how terms in MONDO are linked to terms in other ontologies. MONDO has over 16,000 mappings to terms in UMLS. It is also mapped to terms in DOID, Ophanet, OMIM, MeSH, etc.

8.6.2. Step 2: Provide the source vocabulary term ID

OxO takes ontology term IDs as inputs for ontology mapping, which assumes the (meta)data has been annotated. If the data is not annotated, please check the ontology annotation recipe first.

In this example, we use terms for type 2 diabetes from 2 distinct sources. The corresponding term IDs are listed in the table below.

Text

Corresponding term in MeSH

Corresponding term in DOID

type 2 diabetes

MeSH:D003924

DOID:9352

8.6.3. Step 3: Perform mapping

Figure 2 shows how to map the MeSH and DOID terms to the MONDO disease ontology. Users are expected to:

  • specify the target ontology

  • provide a list of source term IDs

  • indicate the expected mapping distance.

In this example, we set the mapping distance to 1, which uses high confidence mapping evidence only. Having greater mapping distance returns more mappings but decreases the mapping confidence.

Figure 3 shows the corresponding mapping results. Both terms have been mapped to ‘MONDO:0005148’. The results can be downloaded as flat-table(tsv) files.

8.6.4. Step 4: Review mapping results

To ensure the quality of the mapping, users are recommended to review the mapping results, especially when the mapping distance increases. OxO allows users to explore vocabulary term relationships (see figure 4) by providing a network view of all linked terms. Users can also find more information about each term in the Ontology lookup service.

8.7. Using OxO service programmatically

Besides the graphical user interface offered by OxO at EMBL-EBI, a REST style API is also available. It is therefore possible to invoke the mapping service from the command line. See the OxO API documentation page.

In the following code snippet, an API request invoked via curl performed the same mapping presented in the section above, at step 3:

curl 'https://www.ebi.ac.uk/spot/oxo/api/search' -i 
-X POST 
-H 'Content-Type: application/json' 
-H 'Accept: application/json' 
-d '{
  "ids" : [ "DOID:9352","MeSH:D003924"],
  "inputSource" : null,
  "mappingTarget" : [ "MONDO" ],
  "mappingSource" : [ "MONDO" ],
  "distance" : 1
}'

The corresponding results are as follows:

{
      "queryId" : "DOID:9352",
      "querySource" : null,
      "curie" : "DOID:9352",
      "label" : "type 2 diabetes mellitus",
      "mappingResponseList" : [ {
        "curie" : "MONDO:0005148",
        "label" : "type 2 diabetes mellitus",
        "sourcePrefixes" : [ "MONDO" ],
        "targetPrefix" : "MONDO",
        "distance" : 1
      } ],
      "_links" : {
        "self" : {
          "href" : "https://www.ebi.ac.uk/spot/oxo/api/terms/DOID:9352"
        },
        "mappings" : {
          "href" : "https://www.ebi.ac.uk/spot/oxo/api/mappings?fromId=DOID:9352"
        }
      }
    }

8.7.1. Common questions about OxO

  1. What about incorrect mappings?

    OxO imports term mapping information from ontologies and other curated databases. It doesn’t validate the mapping evidence. Users are recommended to check the mapping results manually, especially when the mapping distance is above 1.

  2. Why is no mapping found?

    OxO relies on the ontology and other curated databases to improve the mapping coverage. Some terms describing the same concept might not be aligned in OxO. In this case, users are recommended to identify possible mappings by searching in OLS.

    To help the ontology community improve the mapping, users can also submit an update request in corresponding ontologies. The guidance can be found here Requesting new terms

  3. Ontology mapping service for internal databases

    OxO has been dockerized for local deployment and licensed under Apache License 2.0. The source code can be found here.

8.8. Conclusion

This recipe presented OxO, EMBL-EBI tool for performing ontology mapping as an example to demonstrate the ontology mapping workflow. In the context of a FAIRification workflow, a tool such as OxO comes particurlary handy to augment a dataset with cross-references or replace an annotation set with another in a data integration exercice for instance.

8.9. References

8.10. Authors