Create new PheWAS Catalog evidence table in rewrite version

andrewhercules commented 3 years ago

On the evidence page in the rewrite, can we please create a new data table that displays the PheWAS Catalog evidence data?

Example GraphQL API query NOD2 in respiratory system disease

Data table

Data table column	Disease/phenotype	Reported disease/phenotype [Phecode]	Variant	Functional consequence	P-value	Cases	Odds ratio
GraphQL API field	`evidences.rows[x].disease.name`	`evidences.rows[x].diseaseFromSource`	`evidences.rows[x].variantRsId`	`evidences.rows[x].variantFunctionalConsequenceId`	`evidences.rows[x].resourceScore`	`evidences.rows[x].studyCases`	`evidences.rows[x].oddsRatio`
Sample data	Respiratory system disease	Chronic pharyngitis and nasopharyngitis	rs9302752	sequence variant	0.03152	844	0.866

Within the data table, can we please do the following?

Link the value in the "Disease/phenotype" column to the relevant profile page in the Platform
Link the value in the "Variant" column to Ensembl using the following construct - http://www.ensembl.org/Homo_sapiens/Variation/Explore?v= + evidences.rows[x].variantRsId (e.g. rs5743289)
Round the value in the "P-value" and "Odds ratio" columns to 5 decimal points

As a placeholder, in the "Functional consequence" column, we can show the SO code.

QC checks

d0choa commented 3 years ago

It's a known issue that all functional consequences in this datasource have the same value. Don't worry about it. We will fix it at source.

d0choa commented 3 years ago

It's an open question if we want to keep the rsId links consistent with Genetics Portal. Currently pointing to dbSNP in the rewrite. Thoughts?

AsierGonzalez commented 3 years ago

Personally, I find dbSNP more informative but I don't know if we want to give preference to EBI resources.

andrewhercules commented 3 years ago

Can we please make some minor adjustments to the data table?

Table functionality

[x] Implement "Rows per page" feature to allow users to set number of rows visible in table
[x] Allow user to sort by all numeric columns - "P-value", "Cases", and "Odds ratio"
[x] By default, sort by p-value (ascending)

Table columns

General formatting

[x] Fix the formatting of the values in the "Odds ratio column" as extra zeros are added (e.g. table should show 1.569 instead of 1.56900)

External links

[x] Update the links in the "Variant" column to use the identifiers.org service to direct users to dbSNP using the following construct - https://identifiers.org/ncbi/DBSNP: + evidences.rows[x].variantRsId (e.g. rs2076756) *note: this is similar to the links constructed for RSIDs in the Open Targets Genetics Portal evidence data table

Data table number formatting

[x] Ensure tabular, spaced numbers are used
[x] Add comma for large integers (e.g. 336,526 vs 336526)
[x] Please review the "Features" section on the Inter font website - https://rsms.me/inter/ - to ensure the data table component is using all available number formatting features

mirandaio commented 3 years ago

@andrewhercules adjustments have been merged. Feel free to check again and close if done.

andrewhercules commented 3 years ago

With the latest iteration of the GraphQL API, can we please make one small adjustment to the PheWAS evidence table?

[x] In the "Variant" column, update the name of the column to "Variant RSID (ID)" and always show the variantRsId value and if available, show the variantId value in brackets with a link to the variant page in the Open Targets Genetics Portal. This would be similar to line 57 in the Body.js file for the Open Targets Genetics Portal evidence table except reversed and displayed in the following way:

Note that sometimes the variantId value is null

d0choa commented 3 years ago

Changes:

[x] Move reported disease/phenotype as tooltip in disease column. The tooltip content would be “Reported disease or phenotype:\n{diseaseFromSource}”
[x] Same formatting for variants as in genetics portal regarding font sizes
[x] Format p-value in header as in genetics portal
[x] make sure numbers use the proper font formatting (as in genetics portal widget)

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