Improve structure and accessibility of the PPP project specific documentation

[buniello]

As a user, I would like to easily access the PPP project specific documentation from the OTAR CRISPR, ENCORE and Validation Lab widgets. At the moment, the widget headers all link to the Intranet Home Page: EXAMPLE from the Encore Widget: Interim data from dual-knockout screens generated by the OTAR2-062 ENCORE project, associating MLH1 and Open Targets ENCORE. Source: Open Targets

Background

We received the feedback below from GSK:

We received comments from folk who have tried to look at a couple of genes on the OT Platform that did have some annotation regarding readouts from OTAR-related screens (specifically OTAR2054).  It was really challenging to understand the output that was shared given that they were not a member of the project team.  Providing some information about the experimental context, terms, and metrics utilized such that the data can be meaningfully interpreted by individuals not associated with a given project. 

Tasks

• [x] Review the structure of the PPP project specific documentation on the Intranet (currently project specific documentation are nested in pdf files. Example for OTAR033 @prashantuniyal02 @sarahyoung3 (already discussed with Prashant)

• [ ] Replace the Source "Open Targets" link in the widget headers with the new PPP specific documentation page, containing clear links to the project specific documentation (FE)

OPTIONAL: review the schema in widgets to assess whether we could improve interpretability by adding more info/new column

[buniello]

@prashantuniyal02 can you please remind us whether the project specific documentation links are now ready for us to add to the widgets? If so, the first box in tasks should be ticked

[prashantuniyal02]

Hi @buniello and @chinmehta, here is the document containing the links.

[buniello]

Thanks for the placeholder links @prashantuniyal02.

@chinmehta, as we briefly discussed already, the unique project links (from doc above) have to be replaced at the top of the OTAR projects, ENCORE and Validation Lab PPP widgets. Please do let me know if you have any questions!

Example of Widget API query

``` query CrisprQuery($ensemblId: String!, $efoId: String!, $size: Int!) { disease(efoId: $efoId) { id evidences( ensemblIds: [$ensemblId] enableIndirect: true datasourceIds: ["ot_crispr"] size: $size ) { rows { disease { id name __typename } projectId contrast studyOverview cellType cellLineBackground crisprScreenLibrary statisticalTestTail resourceScore log2FoldChangeValue diseaseCellLines { name __typename } releaseVersion __typename } __typename } __typename } } { "ensemblId": "ENSG00000168395", "efoId": "MONDO_0005180", "size": 1 } ```

API response with **projectId** field to identify unique links to replace in the widget header

``` { "data": { "disease": { "id": "MONDO_0005180", "evidences": { "rows": [ { "disease": { "id": "MONDO_0005180", "name": "Parkinson disease", "__typename": "Disease" }, "projectId": "OTAR035", "contrast": "Enrichment of gRNAs (KO) in the survival of dopamine neurons against oxidative stress (rotenone)", "studyOverview": null, "cellType": "human iPSC-derived dopaminergic neuron", "cellLineBackground": "KOLF2-C1", "crisprScreenLibrary": "Kosuke v1.1 (Behan et al., 2018)", "statisticalTestTail": "upper tail", "resourceScore": 0.0084696, "log2FoldChangeValue": 0.53881, "diseaseCellLines": null, "releaseVersion": "OTAR035-44256", "__typename": "Evidence" } ], "__typename": "Evidences" }, "__typename": "Disease" } } } ```

Please note: links have to be set up with this text structure: source Open Targets project xxxx. This will help in cases where we will have multiple projects data sourcing the same widget. For the Validation Lab, we can leave the text link as it is now: Open Targets

[prashantuniyal02]

@chinmehta also update the project links in the widget present in the disease profile page.

[prashantuniyal02]

works correctly in the latest PPP dev