mbrush
commented
4 years ago Hi Andrew, and thanks for moving this question this over from our Slack chat - as I think it speaks to a common question about what relationships to create as Associations vs Slots, and how these are related.
First, I do think that the types of relationships you describe would be in scope for the Biolink Model (BLM). W.r.t. where/how to created them in the BLM, a distinction to keep in mind is that between an Association (aka an edge) and a Slot (aka a property).
Associations in the BLM are relationship reifications that provide schema for representing the semantics of what is stated as true in the association, and also the provenance/evidence supporting it. Associations are instantiated in the data (e.g. an edge in a KG) to capture an assertion of domain knowledge, and the E/P supporting it. The schema for a GenetoDiseaseAssociation is here.
Slots/properties, by contrast, are simply named predicates used to capture properties of an Entity or an Association. They are used to capture the semantics of the relationship asserted in an Association instance.
I think for your example, we would want to create new Biolink slots for each gene-disease relationship we think might be useful to describe in a GenetoDiseaseAssociation instance. These slots would descend from the root BLM slot/property 'related to'. And more specifically, they might be direct children of the 'gene associated with condition' slot that itself is a child of 'related to'. Also, these BLM slots could be mapped where possible to properties in the Relation Ontology that may already cover some of the relationships you have in mind (e.g. here).
Then, in the context of a GenetoDiseaseAssociation instance, one of these slots/properties (e.g. 'gene_mutated_in_disease') would be used as the value of the Association's 'relation' slot - to indicate that this is the specific type of gene-disease relationship being asserted. For example:
ex:associationinstance001
- association_type: biolink:GeneToDiseaseAssociation
- subject: ex:gene001
- relation: 'gene_mutated_in_disease'
- object: ex:disease001When useful, a more generic Association type such as GenetoDiseaseAssociation can be specialized to provide a schema for representing a more specific type of gene-disease relationship (e.g. https://biolink.github.io/biolink-model/docs/GeneHasVariantThatContributesToDiseaseAssociation.html). But in general I think the granularity that BLM advocates for Association type specialization is not as fine as that for slots. The idea being that Associations define general categories of associations (e.g. GenetoDiseaseAssociation), and the 'relation' slot of such associations can take one of possibly many slots/properties that describe a more specific relationship asserted in the association instance (e.g. gene_mutations_cuasal_for, gene_overexpressed_in_disease, gene_mutations_increase_susceptability_to, etc.)
andrewsu
nlharris
sierra-moxon
This is likely a very naive question... I can imagine a few ways that genes could be related to diseases. For example:
Genemutated_inDisease,Geneoverexpressed_inDisease,Geneunderexpressed_inDisease. Would those types of relationships be in scope of the Biolink model? If so, would they theoretically be added as children of https://biolink.github.io/biolink-model/docs/GeneToDiseaseAssociation.html or somewhere else?