SeMRA Raw Semantic Mapping Database

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

Ontologies indexed in the Bioregistry (primary)

Databases integrated in PyOBO (primary)

Biomappings (secondary)

Wikidata (primary/secondary)

Custom resources integrated in SeMRA (primary)

Processing is not performed on this database because it would require too many definitions. For processed mapping datasets, we suggest smaller domain-specific processing rules (see https://github.com/biopragmatics/semra/tree/main/notebooks/landscape for examples).

How to Run

Download all artifacts from this Record

Make sure that you have Docker running locally

Run sh run_on_docker.sh from the command line

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. Inferred mappings are distributed under the public domain CC0-1.0 license.