Study page FE scoping

[buniello]

Please note - details below are going to be discussed in person next week. See here for current Open Targets Genetics study page.

• [ ] Scenario n1 - GWAS Catalog and FinnGen data (see example datasets below)

For studyType gwas :

• Page header: studyId (fixed study)

• Small links below header: Trait: [link] (+Background trait if present in data) [link] | Source: [link] Example:

  1. Trait link: Trait: traitFromSource hyperlinked to https://platform.opentargets.org/disease/traitFromSourceMappedIds & for projectId GCST -- if backgroundTraitFromSourceMappedIds is not null show Background trait: backgroundTraitFromSource hyperlinked to https://platform.opentargets.org/disease/backgroundTraitFromSourceMappedIds

2. Source link:
   • If projectId is GCST show Source: GWAS Catalog hyperlinked with https://www.ebi.ac.uk/gwas/studies/studyId
   • If projectId is FINNGEN_R10 show Source: FinnGenR10 hyperlinked to [https://r10.finngen.fi/pheno/studyID]

• Page section: Study Summary

• If projectId is GCST Author: publicationFirstAuthor Publication date: publicationYear Journal: publicationJournal PubMed: pubmedId hyperlinked to https://europepmc.org/article/med/pubmedId Has summary stats: yes if summarystatsLocation is not null & no if summarystatsLocation is null Summary stats location: summarystatsLocation N study: nSamples N discovery: initialSampleSize N replication: replicationSamples N cases: nCases N controls: nControls Cohorts: cohorts - TOOLTIP: LD structure: ldPopulationStructure QC: qualityControls Study flags: analysisFlags

• If projectId is FINNGEN_R10 Author: FINNGEN_R10 Publication date: 2023 Journal: NA PubMed: NA Has summary stats: yes Summary stats location: summarystatsLocation N study: nSamples N discovery: discoverySamples Tooltip: initialSampleSize N replication: NA N cases: nCases N controls: nControls Cohorts: FinnGen - TOOLTIP: LD structure: ldPopulationStructure QC: NA Study flags: NA

GWAS Catalog study:

-RECORD 0---------------------------------------------------------------------------------------------------------------------------------
 studyId                            | GCST000124
 projectId                          | GCST
 studyType                          | gwas
 traitFromSource                    | Alzheimer's disease
 geneId                             | null
 biosampleFromSourceId              | null
 nSamples                           | 1489
 summarystatsLocation               | null
 hasSumstats                        | false
 cohorts                            | [null]
 initialSampleSize                  | 753 European ancestry cases, 736 European ancestry controls
 traitFromSourceMappedIds           | [MONDO_0004975]
 publicationJournal                 | Arch Neurol
 publicationDate                    | 2007-11-12
 ldPopulationStructure              | [{nfe, 1.0}]
 backgroundTraitFromSourceMappedIds | null
 qualityControls                    | null
 replicationSamples                 | [{European, 667}]
 nControls                          | 736
 pubmedId                           | 17998437
 publicationFirstAuthor             | Li H
 publicationTitle                   | Candidate single-nucleotide polymorphisms from a genomewide association study of Alzheimer disease.
 discoverySamples                   | [{European, 1489}]
 nCases                             | 753
 analysisFlags                      | null

A finngen study:

-RECORD 0--------------------------------------------------------------------------------------------
 studyId               |AB1_ACTINOMYCOSIS
 traitFromSource       | Actinomycosis
 nCases                | 101
 nControls             | 363227
 nSamples              | 363328
 projectId             | FINNGEN_R10
 studyType             | gwas
 hasSumstats           | true
 initialSampleSize     | 377,277 (210,870 females and 166,407 males)
 discoverySamples      | [{377277, Finnish}]
 cohorts               | [FinnGen]
 summarystatsLocation  | gs://finngen-public-data-r10/summary_stats/finngen_R10_AB1_ACTINOMYCOSIS.gz
 ldPopulationStructure | [{fin, 1.0}]

[buniello]

• [ ] Scenario n2 - QTLs

For studyType eqtl:

• Page header: projectId

• Small links below header: Affected gene [link]in cell type [link] \ Source [link]

Affected gene:traitFromSource hyperlinked to https://platform.opentargets.org/target/geneId in cell type: biosampleFromSourceId (we need a biosampleFromSourcename but I think this object will be resolved later). Source: eQTL Catalog hyperlinked to `https://www.ebi.ac.uk/eqtl/Studies/

• Page section: Study Summary
• If datatype is eQTL Author: publicationFirstAuthor Publication date: publicationDate Journal: publicationJournal PubMed: pubmedId Has summary stats: yes Summary stats location: summarystatsLocation N study: nSamples N discovery: NA N replication: NA N cases: NA N controls: NA Cohorts: NA QC: NA Study flags: NA

sceQTL study:

-RECORD 0--------------------------------------------------------------------------------------------------------
 studyId                            | Cytoimmgen_TCM_STIM_16H_ENSG00000151640
 projectId                          | Cytoimmgen
 studyType                          | eqtl
 traitFromSource                    | ENSG00000151640
 geneId                             | ENSG00000151640
 biosampleFromSourceId              | CL_0000624
 nSamples                           | 100
 summarystatsLocation               | https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/QTS000041/QTD000726
 hasSumstats                        | true
 cohorts                            | null
 initialSampleSize                  | null
 traitFromSourceMappedIds           | null
 publicationJournal                 | null
 publicationDate                    | null
 ldPopulationStructure              | null
 backgroundTraitFromSourceMappedIds | null
 qualityControls                    | null
 replicationSamples                 | null
 nControls                          | null
 pubmedId                           | null
 publicationFirstAuthor             | null
 publicationTitle                   | null
 discoverySamples                   | null
 nCases                             | null
 analysisFlags                      | null