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clingen-data-model / data-exchange-shared-json

JSON schema utilized to share data from the curation interfaces into the Data Exchange. CONTAINS GENE EXPRESS JSON DATA
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Disease names in gene-disease pairs #21

Closed ronakypatel closed 5 years ago

ronakypatel commented 7 years ago

In the AWG curated data, there is no place where name of diseases are captured for each OMIM. We do store OMIM identifiers but not the names associated with each of them. One can easily get the names from the identifiers, though.

Say for example: the gene-disease pairs given here (https://www.clinicalgenome.org/working-groups/actionability/projects-initiatives/actionability-evidence-based-summaries/) for ARVD include:

Arrhythmogenic Right Ventricular Dysplasia,Familial, 9; ARVD9 Arrhythmogenic Right Ventricular Dysplasia, Familial, 8; ARVD8 Arrhythmogenic Right Ventricular Dysplasia,Familial, 11; ARVD11 Arrhythmogenic Right Ventricular Dysplasia, Familial, 5; ARVD5 Arrhythmogenic Right Ventricular Dysplasia, Familial, 10; ARVD10

In the AWG provided summaries (https://www.clinicalgenome.org/site/assets/files/6360/binning_arvd_05252016.pdf), there is no mention of any of these subtypes (although OMIMs are there) directly, neither it is in the curation interface.

In the curation interface, the following information is there:

Document: Arrhythmogenic Right Ventricular Dysplasia

Has genes: PKP2, DSP, DSC2, TMEM43, DSG2

With these pairs: DSC2⇔610476 DSG2⇔610193 DSP⇔607450 PKP2⇔609040 TMEM43⇔604400

Providing just OMIMs (and not actual name) should hopefully be fine?

sgoehringer commented 7 years ago

We don't need the Disease name and we can remove that... the OMIM will be fine.

sgoehringer commented 7 years ago

Since we are on this topic... I wanted to inquire about one more item. Does the interface associate DSC2⇔610476 with a specific intervention? The following would be the example

DSC2⇔610476 Example Outcome 1 / Example Intervention A = Score ABC

DSG2⇔610193 Example Outcome 2 / Example Intervention B = Score XYZ

Both of the above would be associated to a single report like the one you referenced earlier.

ronakypatel commented 7 years ago

No.

However, the gene might be. But in that case, the outcome will be named as

Gene1 - Outcome1 / Intervention 1 Gene2 - Outcome1 / Intervention 1

sgoehringer commented 7 years ago

Okay, but if I understand things correctly... if this curation was done for "Gene1 & Gene2" and "OMIM1 & OMIM2" it isn't possible (or maybe it isn't necessary) to associate interventions with specific pairs? I think this means the following would occur on a single curation.

Gene1 - "Outcome1 / Intervention 1" is connected to OMIM1 & OMIM2 Gene2 - "Outcome1 / Intervention 1" is connected to OMIM1 & OMIM2

The reason I am asking is what if "Gene2 - Outcome1 / Intervention 1" shouldn't be associated to OMIM2 and should only be related to OMIM1? Maybe this isn't how things are curated though and may not be an issue.

sgoehringer commented 5 years ago

Cleanup - Closing old issue.