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README.md
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README.md

STRING DB example

Getting the data

First, we fetch the data from STRING DB: https://stringdb-static.org/download/protein.links.v11.0/9606.protein.links.v11.0.txt.gz

For the sake of an example, we will be using just a small subset from the file:

protein1 protein2 combined_score
9606.ENSP00000000412 9606.ENSP00000225275 195
9606.ENSP00000000412 9606.ENSP00000299767 222
9606.ENSP00000000412 9606.ENSP00000416097 474
9606.ENSP00000000412 9606.ENSP00000363458 902
9606.ENSP00000000412 9606.ENSP00000354376 161
9606.ENSP00000000412 9606.ENSP00000303366 285
9606.ENSP00000000412 9606.ENSP00000369981 900
9606.ENSP00000000412 9606.ENSP00000218548 210
9606.ENSP00000000412 9606.ENSP00000418915 267

From the above we know the following,

  • These are human ENSEMBL proteins
  • There are 10 interacting proteins
  • Each interaction is qualified with a score

For modeling the above data we will make the following assumptions,

  • Each protein is a node in the graph
  • Each interaction is an edge in the graph
  • Each identifier can be prefixed with ENSEMBL to yield a compact URI
  • 9606 means NCBITaxon:9606

Mapping to Biolink Model

  • Each protein is of type biolink:Protein
  • Each interaction is of type biolink:GeneToGeneAssociation
  • The predicate/relationship that link two protein nodes is biolink:interacts_with
  • The relation that further qualifies the interaction is RO:0002434
  • The interaction score can be represented as a property on the edge

Putting it all together

nodes.tsv represents all the nodes in a graph in a TSV format.

A snippet of nodes.tsv,

id	category	in_taxon
ENSEMBL:ENSP00000000412	biolink:Protein	NCBITaxon:9606
ENSEMBL:ENSP00000225275	biolink:Protein	NCBITaxon:9606
...

edges.tsv represents all the edges in a graph in a TSV format.

A snippet of edges.tsv,

subject	predicate	object	relation	association_type	combined_score
ENSEMBL:ENSP00000000412	biolink:interacts_with	ENSEMBL:ENSP00000225275	RO:0002434	biolink:GeneToGeneAssociation	195
ENSEMBL:ENSP00000000412	biolink:interacts_with	ENSEMBL:ENSP00000299767	RO:0002434	biolink:GeneToGeneAssociation	222
...