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Edge Merging Proposal #70

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Edge Merging Proposal #70

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5073caf
edge merging proposal and example
uhbrar Apr 25, 2022
d2de278
adjust attributes
uhbrar May 1, 2022
8d508b3
merging script
uhbrar May 18, 2022
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uhbrar May 19, 2022
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397 changes: 397 additions & 0 deletions amesbah_edge_merging_example.md
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# Edge Merging Example

The example will show an entire merged knowledge graph, as well as each step in the process. This shows an edge that was returned by three knowledge providers (KP_1, KP_2, KP_3) to two ARA's (ARA_1 and ARA_2), and then from the ARA's to the Workflow Runner (WR). In this, ARA_1 receives the edge from KP_1 and KP_2, and ARA_2 receives it from KP_1 and KP_3. Also, say ARA_1 actually contains KP_2 within it.

## KP output

This section shows the outputs of the three KP's.

### KP_1

```json
{
"edges": {
"e719492": {
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"provenance": {
"p0": {
"original_knowledge_source": "infores:DB"
},
"p1": {
"aggregator_knowledge_source": "infores:KP_1",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
}
},
"attributes": {
"a82984": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_1669",
"attribute_source": ["infores:KP_1"]
},
"a428959": {
"attribute_type_id": "biolink:p_value",
"value": 6375,
"value_type_id": "EDAM:data_0006",
"attribute_source": ["infores:KP_1"]
},
},
}
}
}
```

### KP_2

```json
{
"edges": {
"e719492": {
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"provenance": {
"p0": {
"original_knowledge_source": "infores:DB"
},
"p2": {
"aggregator_knowledge_source": "infores:KP_2",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
}
},
"attributes": {
"a82984": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_1669",
"attribute_source": ["infores:KP_2"]
},
"a7429403": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_6109",
"attribute_source": ["infores:KP_2"]
},
},
}
}
}
```

### KP_3

```json
{
"edges": {
"e719492": {
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"provenance": {
"p0": {
"original_knowledge_source": "infores:DB"
},
"p3": {
"aggregator_knowledge_source": "infores:KP_3",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
}
},
"attributes": {
"a7429403": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_6109",
"attribute_source": ["infores:KP_3"]
},
"a428959": {
"attribute_type_id": "biolink:p_value",
"value": 6375,
"value_type_id": "EDAM:data_1669",
"attribute_source": ["infores:KP_3"]
}
},
}
}
}
```

## ARA output

This section shows the outputs of the two ARA's.

### ARA_1

```json
{
"edges": {
"e719492": {
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"provenance": {
"p0": {
"original_knowledge_source": "infores:DB"
},
"p1": {
"aggregator_knowledge_source": "infores:KP_1",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
"p2": {
"aggregator_knowledge_source": "infores:KP_2",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
"p4": {
"aggregator_knowledge_source": "infores:ARA_1",
"adjacency_list": [
{
"parent": "p1",
"method": "query"
},
{
"parent": "p2",
"method": "contains"
}
]
}
},
"attributes": {
"a82984": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_1669",
"attribute_source": [
"infores:KP_1",
"infores:KP_2"
]
},
"a428959": {
"attribute_type_id": "biolink:p_value",
"value": 6375,
"value_type_id": "EDAM:data_0006",
"attribute_source": ["infores:KP_1"]
},
"a7429403": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_6109",
"attribute_source": ["infores:KP_2"]
},
},
}
}
}
```

### ARA_2

```json
{
"edges": {
"e719492": {
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"provenance": {
"p0": {
"original_knowledge_source": "infores:DB"
},
"p1": {
"aggregator_knowledge_source": "infores:KP_1",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
"p3": {
"aggregator_knowledge_source": "infores:KP_3",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
"p5": {
"aggregator_knowledge_source": "infores:ARA_2",
"adjacency_list": [
{
"parent": "p1",
"method": "query"
},
{
"parent": "p3",
"method": "query"
}
]
}
},
"attributes": {
"a82984": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_1669",
"attribute_source": [
"infores:KP_1",
"infores:KP_3"
]
},
"a428959": {
"attribute_type_id": "biolink:p_value",
"value": 6375,
"value_type_id": "EDAM:data_0006",
"attribute_source": ["infores:KP_1"]
},
"a7429403": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_6109",
"attribute_source": ["infores:KP_3"]
},
},
}
}
}
```

## WR

Finally, this would be the final merged output from the WR.

```json
{
"edges": {
"e719492": {
"subject": "RXCUI:1544384",
"predicate": "biolink:correlated_with",
"object": "MONDO:0008383",
"provenance": {
"p0": {
"original_knowledge_source": "infores:DB"
},
"p1": {
"aggregator_knowledge_source": "infores:KP_1",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
"p2": {
"aggregator_knowledge_source": "infores:KP_2",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
"p3": {
"aggregator_knowledge_source": "infores:KP_3",
"adjacency_list": [
{
"parent": "p0",
"method": "consumed"
}
]
},
"p4": {
"aggregator_knowledge_source": "infores:ARA_1",
"adjacency_list": [
{
"parent": "p1",
"method": "query"
},
{
"parent": "p2",
"method": "contains"
}
]
},
"p5": {
"aggregator_knowledge_source": "infores:ARA_2",
"adjacency_list": [
{
"parent": "p1",
"method": "query"
},
{
"parent": "p3",
"method": "query"
}
]
},
"p6": {
"aggregator_knowledge_source": "infores:WR",
"adjacency_list": [
{
"parent": "p4",
"method": "query"
},
{
"parent": "p5",
"method": "query"
}
]
}
},
"attributes": {
"a82984": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_1669",
"attribute_source": [
"infores:KP_1",
"infores:KP_2",
"infores:KP_3"
]
},
"a428959": {
"attribute_type_id": "biolink:p_value",
"value": 6375,
"value_type_id": "EDAM:data_0006",
"attribute_source": ["infores:KP_1"]
},
"a7429403": {
"attribute_type_id": "biolink:p_value",
"value": 0,
"value_type_id": "EDAM:data_6109",
"attribute_source": [
"infores:KP_2",
"infores:KP_3"
]
},
},
}
}
}
```
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