golr-loader

Convert SciGraph query results into JSON that can be loaded by a Golr instance.

Example

golr-loader applies conventions to a Cypher execution result and produces Golr loadable JSON facilitating the creation of "Golr quads":

node ID
node ID closure
node rdfs:label
node rdfs:label closure

Processing resolves around the Cypher RETURN clause.

Literals are mapped directly to JSON literals with the same name as the Cypher projection
Nodes are mapped to Golr quads with the same root name as the Cypher projection
Relationships are resolved to their object property nodes and mapped to Golr quads
Paths are combined with any property container above to produce "evidence" which is then stored as a Golr quad and materialized as a JSON graph

By default golr-load traverses rdf:type and rdf:subClassOf when calculating closures.

The executable JAR produced by mvn package takes the following arguments:

The location of SciGraph YAML file
The location of a golr-loader query YAML file
An optional location to save the generated JSON
An optional Solr server to POST the generated JSON

Here's an example configuration:

query: |
        MATCH path = (subject:gene)-[relation:RO_HOM0000001!]-(object:gene) 
        RETURN path, 
        subject, object, relation, 
        'gene' AS subject_category, 'gene' AS object_category, 'direct' AS qualifier

which results in the following JSON structure:

[
    {
        "evidence": [
            "MONARCH:b0246c04ec0245c5c32e88f79dea1b8b"
        ],
        "evidence_closure": [
            "MONARCH:b0246c04ec0245c5c32e88f79dea1b8b",
            "Annotation:"
        ],
        "evidence_closure_label": [
            "MONARCH:b0246c04ec0245c5c32e88f79dea1b8b",
            "Annotation:"
        ],
        "evidence_graph": "", // Omitted for brevity
        "evidence_label": [
            ""
        ],
        "object": "ENSEMBL:ENSG00000183304",
        "object_category": "gene",
        "object_closure": [
            "ENSEMBL:ENSG00000183304"
        ],
        "object_closure_label": [
            "ENSEMBL:ENSG00000183304"
        ],
        "object_label": "",
        "qualifier": "direct",
        "relation": "RO:HOM0000017",
        "relation_closure": [
            "RO:HOM0000017",
            "RO:HOM0000007",
            "RO:HOM0000001",
            "RO:HOM0000000",
            "RO:0002158",
            "RO:0002320"
        ],
        "relation_closure_label": [
            "in orthology relationship with",
            "in historical homology relationship with",
            "in homology relationship with",
            "in similarity relationship with",
            "shares ancestor with",
            "evolutionarily related to"
        ],
        "relation_label": "in orthology relationship with",
        "subject": "ENSEMBL:ENSMUSG00000096881",
        "subject_category": "gene",
        "subject_closure": [
            "ENSEMBL:ENSMUSG00000096881"
        ],
        "subject_closure_label": [
            "ENSEMBL:ENSMUSG00000096881"
        ],
        "subject_label": ""
    }
]

kevinschaper/golr-loader

golr-loader

Example