Schema element mapping with LinkML-Map

Data integration

Schema element mapping with LinkML-Map Case Study Infobox

• Author: Sierra Moxon (@sierra-moxon)
• Last updated: 2025-04-02
• Mapping Type:
• Status of this case study:

Map a schema element to an external standard or model.

Domain

biomedical, biology, chemistry, industry, any!

Purpose of the mapping

Data integration

Other purpose of the mapping

No response

Type of mapped resources

biolink:Gene --> nmdc-schema:Gene biolink:PhenotypicFeature --> phenopacket:PhenotypicFeature

With detailed provenance of the mapping, including how sub-elements that are part of the mapped element are also mapped.

LinkML-Map auto-generates these nice diagrams to show how one schema element maps to another schema element:

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Links to an existing mappings

I am not quite sure of the ask here, but here are some resources to show how we map schema elements in linkml to external standards:

in biolink model: https://biolink.github.io/biolink-model/Gene/ , in the LinkML segment toward the bottom of the documentation page, you can see the per-element mappings using skos predicates like this:

exact_mappings:
- SO:0000704
- SIO:010035
- WIKIDATA:Q7187
- dcid:Gene
narrow_mappings:
- bioschemas:gene
broad_mappings:
- NCIT:C45822

in the linkml-map repo, you can see a series of tutorials and notebooks that show how this tool maps entire schemas to one another:

https://github.com/linkml/linkml-map/tree/main/docs/examples

Tools used for creating the mapping

For schema mapping, LinkML provides two kinds of tools:

1. https://linkml.io/linkml-map/ - a declarative format for mapping two schemas to one another
2. https://linkml.io/linkml/schemas/uris-and-mappings.html - model syntax for mapping a specific element in the model to another element somewhere else in a different standard or model (using either skos predicates here or via identity mappings using slot/class_uris)

Type of mapping relations

synonym, unit conversion, entity mappings, one to one, one to many, many to one

Examples (samples) of different types of mapping implementations

Lots of examples in these notebooks:

https://github.com/linkml/linkml-map/tree/main/docs/examples, in particular, the tutorial: https://github.com/linkml/linkml-map/blob/main/docs/examples/Tutorial.ipynb

e.g. for linkml-map, declaring the mapping using a transformation specification like this one from the tutorial:

class_derivations:
  Individual:
    populated_from: Person
    slot_derivations:
      family_name:
        populated_from: family_name
      given_name:
        populated_from: given_name
      age:
        populated_from: age_in_years
      height:
        populated_from: height_in_cm

with visual output of the transformation/mapping

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