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Repository to collect user requests and bug reports for the GWAS Catalog
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Missing mapped traits from study table #82

Open DSuveges opened 11 months ago

DSuveges commented 11 months ago

Hi Guys, I have noticed that the downloadable study table (ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2023/11/09/gwas-catalog-download-studies-v1.0.3.1.txt) has number of studies where the MAPPED_TRAIT and the MAPPED_TRAIT_URI fields are empty. Here is the list:

+------------+------------------+-----------------------------------------------------------------+-----------+--------------+
|studyId     |addedToCatalogDate|traitFromSource                                                  |mappedTrait|mappedTraitIds|
+------------+------------------+-----------------------------------------------------------------+-----------+--------------+
|GCST000993  |2013-04-30        |Vascular dementia                                                |null       |null          |
|GCST90058029|2022-10-25        |Anti-N-methyl-D-aspartate receptor encephalitis                  |null       |null          |
|GCST000412  |2009-06-16        |Male infertility                                                 |null       |null          |
|GCST90269775|2023-06-26        |ICD10 J35: Chronic diseases of tonsils and adenoids              |null       |null          |
|GCST90269792|2023-06-26        |Chronic diseases of tonsils or adenoids (MTAG)                   |null       |null          |
|GCST90274931|2023-10-11        |Plasma oxylipin 13-hydroxyoctadecadienoic acid levels            |null       |null          |
|GCST90274935|2023-10-11        |Plasma oxylipin 11-hydroxy-arachidonic acid levels               |null       |null          |
|GCST90274933|2023-10-11        |Plasma oxylipin 9,10-dihydroxyoctadec-12-enoic acid levels       |null       |null          |
|GCST90274936|2023-10-11        |Plasma oxylipin 5-hydroxy-6,8,11,14-eicosatetraenoic acid levels |null       |null          |
|GCST90274941|2023-10-11        |Plasma oxylipin levels (PC1)                                     |null       |null          |
|GCST90274930|2023-10-11        |Plasma oxylipin 12,13-dihydroxyoctadec-9-enoic acid levels       |null       |null          |
|GCST90274934|2023-10-11        |Plasma oxylipin 9,10-dihydroxyoctadeca-12,15-dienoic acid levels |null       |null          |
|GCST90274932|2023-10-11        |Plasma oxylipin 9-hydroxylinoleic acid levels                    |null       |null          |
|GCST90274938|2023-10-11        |Plasma oxylipin 11,12-dihydroxyicosa-5,8,14-trienoic acid levels |null       |null          |
|GCST90274939|2023-10-11        |Plasma oxylipin 14,15-dihydroxyeicosa-5,8,11-trienoic acid levels|null       |null          |
|GCST90274937|2023-10-11        |Plasma oxylipin 12-hydroxy-5,8,10,14-eicosatetraenoic acid levels|null       |null          |
|GCST90274940|2023-10-11        |Plasma oxylipin levels (PC2)                                     |null       |null          |
|GCST001328  |2011-12-20        |Vascular dementia                                                |null       |null          |
|GCST90239716|2022-11-22        |Spermatogenic failure                                            |null       |null          |
|GCST90239719|2022-11-22        |Hypospermatogenesis                                              |null       |null          |
|GCST90239720|2022-11-22        |Male infertility (maturation arrest)                             |null       |null          |
|GCST90239722|2022-11-22        |Unsuccessful sperm retrieval in biopsy                           |null       |null          |
|GCST90128945|2022-07-18        |X-11421 levels                                                   |null       |null          |
|GCST90128944|2022-07-18        |X-11255 levels                                                   |null       |null          |
|GCST90128899|2022-07-18        |N-acetylornithine levels                                         |null       |null          |
|GCST90128943|2022-07-18        |X-11244 levels                                                   |null       |null          |
+------------+------------------+-----------------------------------------------------------------+-----------+--------------+

It's very puzzling given these studies have mapped traits on the UI. Eg.GCST90239722 has no EFO, however the UI indicates this study is assigned to male infertility (MONDO_0005372). If I take a look at this trait in the source file from ftp:

curl -s ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2023/11/09/gwas-catalog-download-studies-v1.0.3.1.txt | grep MONDO_0005372

it returns only one study: GCST90239775, where this trait is a background trait! Can it be a shared cause?