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Phenotypic annotation

As explained in Knowledge Graphs and LLMs in Action

A phenotypic annotation is an assertion associating a disease with a phenotypic feature and potentially recording metadata about that assertion.

A phenotypic annotation associates a disease with a phenotypic feature while preserving provenance such as source, author, and creation date. section 3.2.2

Represent the association and retrieve its metadata through several graph-modeling patterns:

  • Model an RDF n-ary relation with a typed annotation resource, including OMIM:222100, HP:0410050, PMID:9357814, author, and date. section 3.2.2
  • Represent the same assertion with an RDF named graph, RDF-star statement, or LPG edge properties. section 3.2.2
  • Query provenance by disease and feature using SPARQL or Cypher. section 3.2.2
Listing 3.11 Example LPG representation
(d { id: "OMIM:222100" })
-[:HAS_PHENOTYPIC_FEATURE {
        source: "PMID:9357814"
        createdBy: "Nicole Vasilevsky";
        creationDate: "2018-02-23}]->
(p { id: "HP:0410050" })

Inspect an LPG edge-property representation connecting a disease to an HPO feature and carrying annotation provenance. section 3.2.2

How Knowledge Graphs and LLMs in Action covers it

How deep it goes
Compares RDF n-ary relations, named graphs, RDF-star, and LPG edge properties with corresponding queries.
Examples
Uses OMIM:222100, HP:0410050, PMID:9357814, an author, and a creation date.
What it assumes
Assumes familiarity with disease and HPO identifiers, RDF or LPG graph modeling, and graph query syntax.
What you can do after
Apply via SPARQL or Cypher to retrieve annotation source, author, and creation date.
How it connects
Connects disease, phenotypic feature, RDF, LPG, SPARQL, Cypher, named graphs, RDF-star, and provenance tracking.
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