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Knowledge source

Biolink.

The shared grammar that lets a knowledge graph make sense.

Invisible on the page, load-bearing underneath it.

Why Biolink exists

A graph is only as useful as the agreement about what its nodes and edges mean.

Connect enough biomedical databases and you hit a wall that is not about data, it is about grammar. One resource calls something a "gene," another a "gene product." One says "causes," another "associated with," and they do not mean the same thing. Without a shared vocabulary for the categories and the relationships, you cannot merge two sources without quietly corrupting both.

The Biolink Model, from the Monarch Initiative and the NCATS Biomedical Data Translator, is that shared grammar. It defines the categories (gene, disease, phenotypic feature, variant), the predicates that connect them, and the identifier conventions that name them, so that knowledge from many sources can live in one graph and be queried as one thing. It is the schema the modern biomedical knowledge-graph world has largely agreed to speak.

What Biolink contributes to Sniff

Biolink is why Sniff is a graph and not a pile of tables.

Every entity in Sniff, a gene, a disease, a variant, a breed, a phenotype, and every relationship between them is typed and identified in the Biolink idiom. That is what lets OMIA, VBO, Mondo, uPheno, and Ensembl coexist in one coherent graph instead of a stack of incompatible spreadsheets, and it is what makes the graph queryable by a tool or an agent without a custom key for every source.

It is the least visible of Sniff's sources and one of the most important. Speaking the same grammar as the wider biomedical knowledge-graph world is also what makes Sniff interoperable with it, rather than a private dialect nobody else can read.

Credit

The Biolink Model is developed openly by the Monarch Initiative and the NCATS Biomedical Data Translator program. Sniff is not affiliated with either. We build on Biolink, credit it here, and link back to the source.

Visit the Biolink Model ↗

Citation: Unni DR, Moxon SAT, et al. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci 2022. doi:10.1111/cts.13302.

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Sources: Biolink Model (biolink.github.io/biolink-model) · Unni et al. 2022, doi:10.1111/cts.13302