https://github.com/jervenbolleman/sapfhir

Join genomic variation graphs with public data or internal medical data e.g. FHIR. by having a FAIR data access, using W3C sparql as a standard protocol.
https://github.com/jervenbolleman/sapfhir

biohackeu20 graph-database rdf sparql

Last synced: 19 days ago
JSON representation

Join genomic variation graphs with public data or internal medical data e.g. FHIR. by having a FAIR data access, using W3C sparql as a standard protocol.

• Host: GitHub
• URL: https://github.com/jervenbolleman/sapfhir
• Owner: JervenBolleman
• License: gpl-3.0
• Created: 2020-11-17T18:46:54.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2024-03-27T20:26:28.000Z (9 months ago)
• Last Synced: 2024-05-18T07:42:15.392Z (8 months ago)
• Topics: biohackeu20, graph-database, rdf, sparql
• Language: Java
• Homepage:
• Size: 234 KB
• Stars: 3
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# SapFhir

Join genomic variation graphs with public data or internal medical data e.g. FHIR.

by having a FAIR data access, using W3C sparql as a standard protocol.

# Status

This is a [RDF4j](https://rdf4j.org/) SAIL implementation that can take any handlegraph4j 

implementation and represent it as a [W3C sparql 1.1](https://www.w3.org/TR/sparql11-query/) endpoint. 

It is functionally complete. Performance depends hugly on the specific handlegraph implementation.

It is currently read-only, but could be made read/write.

There is a query optimizer that is active that can significantly rewrite queries for the best

performance.

# Example queries

```sparql

#Find the ten most forward to forward connected nodes (needs a lot of RAM)

PREFIX vg: 

SELECT ?node 

WHERE 

{

  ?node vg:linksForwardToForward ?node2 .

} 

GROUP BY ?node 

ORDER BY (COUNT(?node2)) 

LIMIT 10

```

```sparql

# Counts the number of sequences of length 1 in the graph

PREFIX vg:

SELECT 

  (COUNT(?n) AS ?c)

WHERE {

  ?n rdf:value ?sequence .

  FILTER(strlen(?sequence) ==1)

}

```

```sparql

# Counts the number of sequences with an R ambiguous nucleotide code

# handlegraph4j lower cases all dna sequences.

PREFIX vg:

SELECT 

  (COUNT(?n) AS ?c)

WHERE {

  ?n rdf:value ?sequence .

  FILTER(contains(?sequence, 'r'))

}

```

```sparql

# List all the Paths in the variation graph

PREFIX vg:

PREFIX rdfs:

SELECT 

  ?path 

  ?pathLabel

WHERE {

  ?path a vg:Path ;

        rdfs:label ?pathLabel .

}

```