Working with the model API¶
The model package provides classes for building common sets of triples based on our modeling patterns.
For an example see the notebook on this topic: Building graphs with the model API
Basics¶
The model class provides methods for building common RDF and OWL statements
For a list of methods, see the API docs.
Building associations¶
We use the RDF Reification [1] pattern to create ternary statements, for example, adding frequency data to phenotype to disease associations. We utilize the Open Biomedical Association ontology [2] to reify statements, and the SEPIO ontology to add evidence and provenance.
For a list of classes and methods, see the API docs.
Building genotypes¶
We use the GENO ontology [4] to build complex genotypes and their parts.
For a list of methods, see the API docs.
GENO docs: The Genotype Ontology (GENO)
Building complex evidence and provenance graphs¶
We use the SEPIO ontology to build complex evidence and provenance. For an example see the IMPC source ingest.
For a list of methods, see the API docs for evidence and provenance.
SEPIO docs: The Scientific Evidence and Provenance Information Ontology (SEPIO)
References¶
[1] | RDF Reification: https://www.w3.org/TR/rdf-primer/#reification |
[2] | OBAN: https://github.com/EBISPOT/OBAN |
[3] | SEPIO: https://github.com/monarch-initiative/SEPIO-ontology |
[4] | GENO: https://github.com/monarch-initiative/GENO-ontology |