SeMRA Raw Semantic Mappings Database

An automatically assembled dataset of raw semantic mappings produced by python -m semra.database. This incorporates mappings from the following places:

1. Ontologies indexed in the Bioregistry (primary)
2. Databases integrated in PyOBO (primary)
3. Biomappings (secondary)
4. Wikidata (primary/secondary)
5. Custom resources integrated in SeMRA (primary)

This is a database of raw mapping without further processing. For processed mapping datasets, we suggest smaller domain-specific processing rules (see https://github.com/biopragmatics/semra/tree/main/notebooks/landscape for examples). It can be accessed directly via:

• mappings.sssom.tsv.gz - loadable through any tools supporting SSSOM
• mappings.jsonl.gz - loadable through SeMRA using semra.from_jsonl

How to Run the Web App

1. Download all artifacts from this Record
2. Make sure that you have Docker running locally
3. Run sh run_on_docker.sh from the command line
4. Navigate to http://localhost:8773 to see the SeMRA dashboard or to http://localhost:7474 for direct access to the Neo4j graph database

Licensing

Mappings are licensed according to their primary resources. These are explicitly annotated in the SSSOM file on each row (when available) and on the mapping set level in the Neo4j graph database artifacts.