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Merge pull request #115 from bcgsc/release/v6.3.3
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Release/v6.3.3
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@mathieulemieux
mathieulemieux authored Feb 10, 2023
2 parents fa51f39 + e078d69 commit f8a4f8b
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27 changes: 24 additions & 3 deletions data/vocab.json
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Expand Up @@ -979,6 +979,14 @@
}
]
},
"likely protective": {
"links": [
{
"class": "SubClassOf",
"target": "protective"
}
]
},
"likely resistance": {
"links": [
{
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}
]
},
"no neomorphic": {
"deprecated": true,
"links": [
{
"class": "AliasOf",
"target": "no switch of function"
},
{
"class": "OppositeOf",
"target": "neomorphic"
}
]
},
"no protein expression": {
"links": [
{
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}
]
},
"unaltered function": {
"unaltered function": {
"description": "event is not associated with a change in protein function",
"links": [
{
"class": "AliasOf",
"target": "no functional effect"
}
]
},
},
"underexpression": {
"deprecated": true,
"links": [
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"name": "moa"
}
}
}
}
89 changes: 35 additions & 54 deletions package-lock.json
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4 changes: 2 additions & 2 deletions package.json
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@@ -1,7 +1,7 @@
{
"name": "@bcgsc-pori/graphkb-loader",
"main": "src/index.js",
"version": "6.3.2",
"version": "6.3.3",
"repository": {
"type": "git",
"url": "https://github.com/bcgsc/pori_graphkb_loader.git"
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"start:signatures": "node bin/load.js file ontology data/signatures.json",
"start:vocabulary": "node bin/load.js file ontology data/vocab.json"
}
}
}
43 changes: 27 additions & 16 deletions src/civic/README.md
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> :warning: Since this loader produces statements, ontology and vocabulary data should be loaded first
Loads statements into GraphKB using the [CIViC](https://civicdb.org/) REST API.
Loads statements into GraphKB using the [CIViC](https://civicdb.org/) GraphQL API.

```bash
node bin/load.js civic
```

## About

The `variant.js` module handles all parsing/processing of variant records in CIViC for entry into GraphKB. The corresponding tests are under `test/civic.test.js`.
The `variant.js` module handles all parsing/processing of variant records in CIViC for entry into GraphKB. The corresponding tests are under `test/civic.variant.test.js`.

In general this loader attempts to update existing records based on their CIViC evidence ID, however when the mapping from CIViC evidence record to GraphKB statement is not 1 to 1 then the statement is sometimes recreated and the old version soft-deleted instead since we cannot resolve tracking between the 2 for these cases.

Expand All @@ -24,10 +24,10 @@ node bin/load.js civic --trustedCurators 123 124

## Mapping Objects from CIViC to GraphKB

In general CIViC (v1) and GraphKB have a lot in common so this mapping can be fairly straightforward. In CIViC Evidence Items are similar to GraphKB statements. However, there are a couple of key differences
In general CIViC (v2.2) and GraphKB have a lot in common so this mapping can be fairly straightforward. In CIViC Evidence Items are similar to GraphKB statements. However, there are a couple of key differences

- In CIViC a list of drugs can be given as "substitutes", in GraphKB these are separate statements
- In CIViC, generally, there is a 1 to 1 relationship with variants and evidence items, in GraphKB any number of variants can be associated with a statement
- In CIViC a list of therapies (formely drugs) can be given as "substitutes", in GraphKB these are separate statements
- In CIViC, while evidence items are assigned a unique molecular profile, each profile can be associated with any number of variants using conditional expression with AND/OR/NOT operators. In GraphKB, statements are associated with any number of variants as implicit necessary conditions (AND operator). Alternative conditions (OR operator) are supported by creating separate statements like with therapy substitutes. Negative conditions (NOT operator) are yet to be supported
- GraphKB has a separate field for "appliesTo", this is the target of the statement
- Each Evidence Item in CIViC is associated with 1 PubMed article. In GraphKB a statement may have 1-n associated articles.

Expand All @@ -37,33 +37,44 @@ A mapping between CIViC and GraphKB for Evidence Item vs Statement fields is giv
| ------------- | --------------------- |
| conditions | disease |
| conditions | variant |
| conditions | drug |
| conditions | therapy |
| relevance | evidence type |
| relevance | clinical significance |
| relevance | evidence direction |
| relevance | significance |
| evidence | source |

The current implementation of the relevance mapping from CIViC to GraphKB is summarized below

| CIViC Evidence Type | CIViC Evidence Direction | CIViC Clinical Significance | GraphKB Relevance |
| CIViC Evidence Type | CIViC Evidence Direction | CIViC Significance | GraphKB Relevance |
| ------------------- | ------------------------ | --------------------------- | ---------------------- |
| Diagnostic | Supports | Negative | opposes diagnosis |
| Diagnostic | Supports | Positive | favours diagnosis |
| Functional | Supports | Dominant Negative | dominant negative |
| Functional | Does Not Support | Dominant Negative | no dominant negative |
| Functional | Supports | Gain of Function | gain of function |
| Functional | Does Not Support | Gain of Function | no gain of function |
| Functional | Supports | Loss of Function | loss of function |
| Functional | Supports | Neomorphic | neomorphic |
| Predictive | Does Not Support | Sensitivity | no response |
| Predictive | Does Not Support | Sensitivity/Response | no response |
| Functional | Does Not Support | Neomorphic | no neomorphic |
| Functional | Supports | Unaltered function | Unaltered function |
| Oncogenic | Supports | Oncogenicity | likely oncogenic |
| Oncogenic | Does Not Support | Oncogenicity | likely benign |
| Predictive | Supports | Adverse Response | adverse response |
| Predictive | Supports | Reduced Sensitivity | reduced Sensitivity |
| Predictive | Supports | Resistance | resistance |
| Predictive | Does Not Support | Resistance | no resistance |
| Predictive | Supports | Sensitivity | sensitivity |
| Predictive | Supports | Sensitivity/Response | sensitivity |
| Predisposing | Supports | Likely Pathogenic | likely pathogenic |
| Predisposing | Supports | Pathogenic | pathogenic |
| Predisposing | Supports | Uncertain Significance | likely predisposing |
| Predictive | Does Not Support | Sensitivity/Response | no response |
| Predisposing | Supports | Predisposition | likely predisposing |
| Predisposing | Supports | Protectiveness | likely protective |
| Prognostic | Supports | Better Outcome | favourable prognosis |
| Prognostic | Supports | Negative | unfavourable prognosis |
| Prognostic | Supports | Poor Outcome | unfavourable prognosis |
| Prognostic | Supports | Positive | favourable prognosis |

Deprecated CIViC terms still supported for relevance mapping are summarized below

| CIViC Evidence Type | CIViC Evidence Direction | CIViC Significance | GraphKB Relevance |
| ------------------- | ------------------------ | --------------------------- | ---------------------- |
| Predisposing | Supports | Likely Pathogenic | likely pathogenic |
| Predisposing | Supports | Pathogenic | pathogenic |
| Predisposing | Supports | Positive | Predisposing |
| Predisposing | Supports | Uncertain Significance | likely predisposing |
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