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Update Actionabilty APIs authored by Neethu Shah's avatar Neethu Shah
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Actionabilty-APIs.md
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...@@ -134,7 +134,7 @@ Summary of actionability APIs: ...@@ -134,7 +134,7 @@ Summary of actionability APIs:
* <span dir="">Status-overall = Released only; Exclude records with Status-overall = Retracted</span> * <span dir="">Status-overall = Released only; Exclude records with Status-overall = Retracted</span>
* <span dir="">Consensus Assertion = Definitive, Strong, Moderate, Limited, N/A – Insufficient evidence: early rule-out, or N/A – Insufficient evidence: expert review</span> * <span dir="">Consensus Assertion = Definitive, Strong, Moderate, Limited, N/A – Insufficient evidence: early rule-out, or N/A – Insufficient evidence: expert review</span>
* <span dir="">If the same gene-disease pair is listed in adults and peds reports, these should be counted as two separate gene-disease pairs</span> * <span dir="">If the same gene-disease pair is listed in adults and peds reports, these should be counted as two separate gene-disease pairs</span>
* <span dir=""> If the same gene-disease pair is listed records with different doc IDs, these should be counted separately</span> * <span dir="">If the same gene-disease pair is listed records with different doc IDs, these should be counted separately</span>
* <span dir="">Removing duplicates should be unnecessary</span> * <span dir="">Removing duplicates should be unnecessary</span>
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...@@ -158,11 +158,158 @@ Summary of actionability APIs: ...@@ -158,11 +158,158 @@ Summary of actionability APIs:
* <span dir="">Status-overall = Released only; Exclude records with Status-overall = Retracted</span> * <span dir="">Status-overall = Released only; Exclude records with Status-overall = Retracted</span>
* <span dir="">Consensus Assertion = Assertion Pending</span> * <span dir="">Consensus Assertion = Assertion Pending</span>
* <span dir=""> If the same gene-disease pair is listed in adults and peds reports, these should be counted as two separate gene-disease pairs</span> * <span dir="">If the same gene-disease pair is listed in adults and peds reports, these should be counted as two separate gene-disease pairs</span>
* <span dir="">If the same gene-disease pair is listed records with different doc IDs, these should be counted separately</span> * <span dir="">If the same gene-disease pair is listed records with different doc IDs, these should be counted separately</span>
* <span dir="">Removing duplicates should be unnecessary</span> * <span dir="">Removing duplicates should be unnecessary</span>
</td> </td>
</tr> </tr>
<tr>
<td>
<span dir="">Definitive Actionability</span>
</td>
<td>
**_CONTEXT specific_**
* [<span dir="">https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Definitive%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Definitive%20Actionability)
* [<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Definitive%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Definitive%20Actionability)
</td>
<td>
<span dir="">Same as “Total Actionability Assertions (by gene)” only filtered on Consensus Assertion = Definitive</span>
</td>
</tr>
<tr>
<td>
<span dir="">Strong Actionability</span>
</td>
<td>
**_CONTEXT specific_**
* [<span dir="">https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Strong%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Strong%20Actionability)
* [<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Strong%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Strong%20Actionability)
</td>
<td>Same as “Total Actionability Assertions (by gene)” only filtered on Consensus Assertion = Strong</td>
</tr>
<tr>
<td>
<span dir="">Moderate Actionability</span>
</td>
<td>
**CONTEXT specific**
* [<span dir="">https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Moderate%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Moderate%20Actionability)
* [<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Strong%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Strong%20Actionability)
</td>
<td>
Same as “Total Actionability Assertions (by gene)” only filtered on Consensus Assertion = Moderate
<span dir=""> </span>
</td>
</tr>
<tr>
<td>
<span dir="">Limited Actionability</span>
</td>
<td>
**_CONTEXT specific_**
* [<span dir="">https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Limited%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=Limited%20Actionability)
* [<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Limited%20Actionability</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=Limited%20Actionability)
</td>
<td>
<span dir="">Same as “Total Actionability Assertions (by gene)” only filtered on Consensus Assertion = Limited</span>
<span dir=""> </span>
</td>
</tr>
<tr>
<td>
<span dir="">N/A – Insufficient evidence: expert review</span>
</td>
<td>
**_CONTEXT specific_**
* [<span dir="">https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=N/A%20-%20Insufficient%20evidence:%20expert%20review</span>](https://actionability.clinicalgenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=N/A%20-%20Insufficient%20evidence:%20expert%20review)
* [<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=N/A%20-%20Insufficient%20evidence:%20expert%20review</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=N/A%20-%20Insufficient%20evidence:%20expert%20review)
</td>
<td>
Same as “Total Actionability Assertions (by gene)” only filtered on Consensus Assertion = N/A Insufficient evidence: expert review
</td>
</tr>
<tr>
<td>
<span dir="">N/A Insufficient evidence: early rule-out</span>
</td>
<td>
**_CONTEXT specific_**
[<span dir="">https://actionability.cliniclagenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=N/A</span>](https://actionability.cliniclagenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=N/A)[<span dir=""> - Insufficient evidence: early rule-out</span>](https://actionability.cliniclagenome.org/ac/Adult/ui/summ/assertion?col=consensusAssertion&search=N/A%20-%20Insufficient%20evidence:%20early%20rule-out)
[<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=N/A%20-%20Insufficient%20evidence:%20early%20rule-out</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ/assertion?col=consensusAssertion&search=N/A%20-%20Insufficient%20evidence:%20early%20rule-out)
</td>
<td>Same as “Total Actionability Assertions (by gene)” only filtered on Consensus Assertion = N/A Insufficient evidence: early rule-out</td>
</tr>
<tr>
<td>
<span dir="">Score == 12</span>-6
</td>
<td>
**/ac/{context}/ui/summ?col=overal$search={score}**
* [<span dir="">https://actionability.clinicalgenome.org/ac/Adult/ui/summ?col=overall&search=12 </span>](https://actionability.clinicalgenome.org/ac/Adult/ui/summ?col=overall&search=12)
* [<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ?col=overall&search=12</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ?col=overall&search=12)<span dir=""> </span>
</td>
<td>Search by overall score </td>
</tr>
<tr>
<td>
<span dir="">Score <=5 </span>
</td>
<td>
**_CONTEXT specific_**
* <https://actionability.clinicalgenome.org/ac/Adult/ui/summ?col=overall&search=5&matchOp=%3C=>
* <https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ?col=overall&search=5&matchOp=%3C=>
</td>
<td>Search by less than or equal to an overall score</td>
</tr>
<tr>
<td>
<span dir="">Outcome Intervention Pairs </span>
</td>
<td>
**_CONTEXT specific_**
**/ac/{context}/ui/summ?searchType=oiScored**
[<span dir="">https://actionability.clinicalgenome.org/ac/Adult/ui/summ?searchType=oiScored</span>](https://actionability.clinicalgenome.org/ac/Adult/ui/summ?searchType=oiScored)
[<span dir="">https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ?searchType=oiScored</span>](https://actionability.clinicalgenome.org/ac/Pediatric/ui/summ?searchType=oiScored)
</td>
<td>Outcome intervention pairs that are scored, specific to a context and specific to a scoring group(a set of gene-disease pairs)</td>
</tr>
</table> </table>
#### Variant Condition Framework Test Data #### Variant Condition Framework Test Data
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