This package validates a list of relationships between two terms against the specified ontologies.
Reason this release was yanked:
Package changed name to verificado, please check the new lib on https://pypi.org/project/verificado/
Project description
Relationship validator
Validation process using Ubergraph as source of truth.
Ubergraph is an RDF triplestore with 39 OBO ontologies merged, precomputed OWL classification and materialized class relationship from existential properties restriction.
Install
pip install relation-validator
Configure YAML file
In the config file, it is defined the list of relationships the validation should run on. The order is essential.
The yaml file needs to have the keys relationships
and filename
. Check an example below:
relationships:
sub_class_of: rdfs:subClassOf
part_of: BFO:0000050
connected_to: RO:0001025
has_soma_location: RO:0002100
...
filename: path/to/filename.csv
The filename should have the following columns:
s | slabel | user_slabel | o | olabel | user_olabel |
---|---|---|---|---|---|
the subject term ID | the label of the term in the column s | optional label for the term given by user | the object term ID | the label of the term in the column s | optional label for the term given by user |
Run relation-validator CLI
relation-validator validate --input path/to/config.yaml --output path/to/output.csv
The output.csv
file will be in the same format as the filename.csv
. It will return the cases where a triple (subject, relationship, object) with the relationships listed in the yaml file was not found in Ubergraph.
List of ontologies available
To know which ontologies and their version are available in Ubergraph, use the following CLI:
relation-validator ontologies_version --output filename.json
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