Evidence missing from JSON full data download

Data Access
1

The evidence for ENSG00000000003/MONDO_0004992 indicates europepmc and expression_atlas datasourceIds, but only the europepmc evidence is present in the 23.09 and 24.03 JSON downloads (7 lines total).

I’m using the data available at ftp.ebi.ac.uk/pub/databases/opentargets/platform/24.03/output/etl/json/evidence.

2

Hi Tim,

I might misunderstand the questions, but when I fetch data from the linked URL (https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/24.03/output/etl/json/evidence/sourceId\=expression_atlas/), the resulting dataset has 200 JSON partitions with 230,182 evidence strings.

P="https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/24.03/output/etl/json/evidence/sourceId\=expression_atlas/"

wget --recursive --no-parent -e robots=off  --cut-dirs=8  $P

cat ftp.ebi.ac.uk/evidence/sourceId=expression_atlas/*json | wc -l  #  230182

Let me know if there’s anything I have missed.

3

The expression_atlas data is missing from specific disease/target pairs. Sorry the specific example got obscured in the link.

The evidence link for ENSG00000000003 => MONDO_0004992 displays expression_atlas data which is missing from the download.

There are other pairs which are missing the expression_atlas data, but I don’t have a list handy ATM.

4

Ah, OK, this UI vs data question also boils down to the discrepancy between direct and indirect evidence. Direct evidence is when the source explicitly tells target x is linked to breast cancer. However, we can take advantage of the disease ontology and we can infer that target x is also linked to cancer (as being an ancestor of breast cancer), this is what we called indirect evidence.

By default the evidence widgets show indirect evidence. Please go the cited platform page, find the expression_atlas widget, click on API Query button in the top-right corner. This will show you the actual graphql query that fetches the data for the widget. You’ll see the enableIndirect: true option. Switch it to false and you’ll get only direct evidence which will be consistent with the downloadable data.

This is a recurring issue that causes confusion (see here, here and here), we are currently working on a suitable resolution to ensure the association page and the content of the widget is consistent.

5

Thank you, Daniel. That makes sense.